CANADIAN AQUACULTURE R&D REVIEW 2017

INSIDE Effects of Cage Aquaculture on Freshwater Benthic Communities Impact of Mussel Culture on Infauna and Sediment Biogeochemistry Marine Reservoirs of Infectious Agents Associated with Proliferative Gill Disorders in Farmed Salmon Epidemiological Analysis and Modeling of Aquatic Pathogens Susceptibility of Sockeye Salmon to Viral Hemorrhagic Septicemia The Effect of Dietary Camelina Oil on Health of Salmon The Effects of Smolt Size on the Intensity of Kudoa thyrsites Infections in Atlantic Salmon

AQUACULTURE ASSOCIATION OF CANADA SPECIAL PUBLICATION 25 Canadian Aquaculture R&D Review 2017 AAC Special Publication #25 ISBN: 978-0-9881415-7-5 © 2017 Aquaculture Association of Canada Cover Photo (Front): Atlantic Salmon farm in Doctor's Cove, New Brunswick (Photo: Kobb Media) Photo Inside Cover (Front): La Butte Ronde on the island of Havre-aux-Maisons, Magdalen Islands (Québec), overlooking baie de Plaisance (Photo: Dan McPhee – DFO) Cover Photo (Back): Atlantic Salmon farm in Doctor's Cove, New Brunswick (Photo: Kobb Media) Photo Inside Cover (Back): Shoreline on the island of Havre-aux-Maisons in the Magdalen Islands Québec (Photo: Dan McPhee – DFO) The Canadian Aquaculture R&D Review 2017 has been published with support provided by Fisheries and Oceans Canada's Aquaculture Collaborative Research and Development Program (ACRDP) and the Aquaculture Association of Canada (AAC). Submitted materials may have been edited for length and writing style. Projects not included in this edition should be submitted before the deadline to be set for the next edition. Editors: Dan McPhee, Johannie Duhaime, Alex Tuen, and G. Jay Parsons Cited as: D McPhee, J Duhaime, A Tuen, and GJ Parsons (eds). Canadian Aquaculture R&D Review 2017. Aquaculture Association of Canada Special Publication 25 (2017) TABLE OF CONTENTS

Introduction 2

Finfish: Freshwater 3

Finfish: Salmon 13

Sea Lice 25

Fish Health 34

Environmental Interactions 53

CIMTAN 79

Shellfish: Mussels 90

Shellfish: Oysters 100

Shellfish: Other 104

Miscellaneous 108

Organizations 122

Glossary 134

Index of Project Leads 136 INTRODUCTION

Welcome to the seventh edition of the biennial Canadian Aquaculture R&D Review. The review is an ongoing compendium of the aquaculture research and development projects that have been underway over the past two years from all across Canada, whether they are undertaken by researchers from academia, government labs, or other research organisations. The review contains over 210 project descriptions detailing an impressive array of topics, disciplines, species, and geography. Projects include marine and freshwater species with topics ranging from finfish and shellfish health, seaweeds, production, husbandry technology, nutrition, integrated multi-trophic aquaculture, and environmental interactions to name a few. This is the fourth issue of the review that has been produced by Fisheries and Oceans Canada (DFO) in partnership with the Aquaculture Association of Canada (AAC). This partnership is highly relevant and mutually beneficial to our respective roles in the area of knowledge translation and mobilisation at both the AAC and DFO. This collaboration has allowed us to produce this 2017 edition as an AAC Special Publication, which is an accessible, electronic citation. Digital versions of this document are also available on both the DFO and AAC websites. Aquaculture continues to be an important and growing sector of the seafood industry in Canada as well as globally. As aquaculture continues to grow, the role of science in supporting the sustainable management, regulation, and responsible development of this sector is more crucial than ever. This is coupled with the growing need for healthy and secure seafood products while ensuring that it occurs in an environmentally responsible manner. The AAC wants to profile advances in aquaculture research in Canada and provide this information to its members for an expanded dialogue on present and future challenges and opportunities for the industry. As such, this publication falls within the AAC’s mandate of disseminating knowledge and further education and we hope it will be of interest to a wide audience. Likewise, DFO has a mandate to enable the sustainable development of Canada’s aquatic resources, including aquaculture, and to provide access to information on its scientific activities underway within the department and elsewhere in Canada. Publication of ongoing aquaculture research in the Canadian Aquaculture R&D Review contributes towards achieving our shared mandates and to reach out to the science community, interested stakeholders, and the public. Additionally, the publication serves to increase the understanding and breadth of scientific activities underway and to encouraging development of collaborations, synergies, and coordination of future activities. Communication and analysis of scientific knowledge is also increasingly pertinent in ensuring a robust evidence-based approach to decision making and regulation of the aquaculture industry, which contributes to improved social acceptability and confidence. We would like to take the opportunity to recognize and thank several people who contributed significantly to the production of this Review. Dan McPhee (DFO) undertook the overall coordination of this project and was instrumental in seeing this project through to completion from beginning to end. Johannie Duhaime and Alex Tuen were also actively involved in various aspects of this project. We would also like to thank the AAC office staff (Catriona McLanaghan) and Publications Committee for their support.

G. Jay Parsons, PhD Tillmann Benfey, PhD Ecosystems and Oceans Science Sector President Fisheries and Oceans Canada Aquaculture Association of Canada CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: FRESHWATER 3 FINFISH: FRESHWATER

Ontario’s Contributions to a Bi-National Initiative Improving the Growth, Health, and Survival of Evaluation of Four Commercial Starter Feeds for to Restore Bloater (Coregonus hoyi), an Extirpated Tilapia in a Greenhouse-Enclosed Intensive Rainbow Trout (Oncorhyncus mykiss) Held Under Species, to Lake Ontario Recirculating Aquaculture System Typical Commercial Hatchery Conditions Development of Walleye (Sander vitreus) Intensive The Development of Fast Growing, Late Maturing, The Effects of Light Emitting Diodes on the Culture Techniques to Enable Increased and Salinity Tolerant Strains of Arctic Charr Growth and Feeding Behaviour of Rainbow Production to Meet Demands Trout (Oncorhyncus mykiss) Change in Rainbow Trout Phosphorus Proprietary Infection Model for Saprolegnia Absorption: Physiological Adaptations to Modulation of the Metabolism and Digestive Research Via in Vitro and in Vivo Systems a Phosphorus Deficiency Capacity of the Arctic Charr (Salvelinus alpinus) Through Dietary Restriction Reducing the Problem of Early Sexual Aquastats: Ontario Aquaculture Statistics Program Maturation in Arctic Charr Overview on the Improvement of the Fraser Strain Development of Predictive Modeling Tools to of Arctic Charr (Salvelinus alpinus) at the Coastal Assist with Freshwater Aquaculture Site Decisions Zones Research Institute Impacts of Stocking Density on the Welfare Evaluating Four Commercially Available and Production Performance of Arctic Charr Rainbow Trout Diets on the Growth and Feed (Salvelinus alpinus) Conversion of Ontario Domestic Rainbow Trout (Oncorhynchus mykiss) 4 FINFISH: FRESHWATER CANADIAN AQUACULTURE R&D REVIEW 2017

Ontario’s Contributions to a Bi-National Initiative to Restore Bloater (Coregonus hoyi), an Extirpated Species, to Lake Ontario

istorically, Lake Ontario was home to variety of diet and temperature trials four species of Deepwater Ciscoes conducted over the next four years resulted H(Coregonus spp.), a group of species in significant improvements in performance. related to Lake Whitefish. Collectively, these Six year classes of brood stock have now species formed the cornerstone of the deep been established. While both sexes have water prey-fish community. Unfortunately, all shown signs of maturation, the timing and four species were extirpated from the lake in degree of maturation has been variable. the last century. Hormone induction and cryopreservation In 2010, the Ontario Ministry of Natural studies are now underway in collaboration Resources and Forestry (MNRF) and the with the University of Windsor. This research Bloater (Coregonus hoyi) yearling. New York State Department of Environmental aims to restore a self-sustaining Bloater Photo: MNRF Conservation developed a draft plan to population within 25 years. restore Deepwater Ciscoes to Lake Ontario which, if successful, would increase the DATE: JAN. 2011–JAN. 2020 availability of prey to native predators like FUNDED BY: Ontario Ministry of Natural Resources Lake Trout and Atlantic Salmon. Initial efforts and Forestry (MNRF) were to focus on Bloater (C. hoyi). In winter 2011 and 2012, MNRF received CO-FUNDED BY: Canada-Ontario Agreement; Great Lake Fish and Wildlife Restoration Act its first fertilized gametes collected from wild populations in Lake Michigan. Given the PROJECT LEAD: Kevin Loftus (MNRF) challenge of collecting gametes at this time PROJECT TEAM: Tim Drew, Ryan Zheng, of year, a decision was made to set aside Jennifer Smith, Jake Ruegg, Matt Brailey, some surviving fish from each year class to Brian Rosborough, Chris Wilson (MNRF) begin developing brood stocks. Initial culture COLLABORATORS: NYSDEC; USFWS; USGS; Great efforts were aimed simply at learning how Lakes Fishery Commission; U Guelph; U Windsor to keep the fish alive. Our Lake Whitefish CONTACT: [email protected] culture protocol was used as a starting point. While initial survival rates were very low, a Female Bloater (Coregonus hoyi) brood fish. Photo: U Windsor

Development of Walleye (Sander vitreus) Intensive Culture Techniques to Enable Increased Production to Meet Demands

his research aims to increase the life stages to enhance fishing opportunities effects of tank size on growth and survival. ability to produce Walleye for stocking and to restore degraded populations. To date, there has been significant progress. Tinto public waters to support provincial Unfortunately, the MNRF is not able to meet We are now able to achieve survival rates in fisheries management objectives and to the current demand for Walleye by stocking our flow through system comparable to those improve the ability to produce Walleye using traditional extensive (i.e., pond) culture achieved by our U.S. colleagues, and similar fingerlings to support the commercial methods. To address this gap, the MNRF is performance is within sight in our RAS aquaculture industry. developing expertise in the intensive (i.e., system. Success depends upon careful Walleye (Sander vitreus) is one of the most indoor) culture of Walleye. They are building control of key parameters including turbidity, sought after recreational species in Ontario upon techniques pioneered in flow through temperature, light, diet, and feeding regime. but some populations are in decline. The systems by Summerfelt and colleagues in Ontario Ministry of Natural Resources and the 1990s and advanced by others in Iowa, DATE: APR. 2013–OCT. 2018 Forestry (MNRF) stocks Walleye at different Wisconsin and elsewhere. The ability FUNDED BY: Canada-Ontario Agreement to reliably grow Walleye intensively from hatch to the autumn fingerling stage would CO-FUNDED BY: Ontario Ministry of Natural increase the options available to MNRF Resources and Forestry (MNRF) to meet stocking targets and would also PROJECT LEAD: Kevin Loftus (MNRF) provide benefits to the commercial PROJECT TEAM: Ryan Zheng, Jennifer Smith, aquaculture sector. Tim Drew, Paul Methner, Kyle Reynolds, Two MNRF Fish Culture Stations (FCSs) Steffi Krause, Chris Wilson (MNRF) are involved in this effort: Blue Jay Creek COLLABORATORS: Alan Johnson (DNR); FCS with a Recirculating Aquaculture System Greg Fischer (U Wisconsin at Stevens Point) (RAS); and White Lake FCS with a flow through system. Rearing trials have focused CONTACT: [email protected] on finding a readily available, high quality, early rearing diet, and on investigating the Walleye rearing room at the Blue Jay Creek Fish Culture Station. Photo: MNRF CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: FRESHWATER 5

Proprietary Infection Model for Saprolegnia Research Via in Vitro and in Vivo Systems

nfections by the Oomycete “water mould” 1) new therapeutant development and DATE: FEB. 2016–ONGOING (Saprolegnia sp.) are problematic at most testing; 2) regulatory approval data FUNDED BY: New Brunswick Innovation Ifreshwater fish hatcheries of the world. collection; 3) genomic profiling; 4) taxonomic Foundation (NBIF) At some hatcheries, egg losses associated assessment; and 5) investigative biology. In CO-FUNDED BY: National Research Council– with Saprolegnia can vary between 10-50%. 2016, HMSC used the infection model with Industrial Research Assistance Program (NRC–IRAP); Infections on eggs can be manually removed clients with great success to test efficacy, Atlantic Canada Opportunities Agency (ACOA) via “egg picking”; however, it is quite laborious, develop suggested use labels, re-infection PROJECT LEAD: Duane Barker (HMSC) can only be performed on eyed-eggs, and is rates following treatment, etc. One of the not 100% efficient. The most commonly used greatest advantages of the model is control PROJECT TEAM: Anne McCarthy, approved therapeutant at hatcheries is formalin over the infection process. Esther Keddie (HMSC) (Parasite-S™), but there are concerns about its This model will be quite useful for research CONTACT: [email protected] safety for the fish and the user. Consequently, aimed at development of novel, alternative, WEBSITE: http://www.huntsmanmarine.ca/ there is an urgent need to develop an and safe treatments against Saprolegnia alternative, safe treatment. infections at hatcheries. The Huntsman Marine Science Centre (HMSC) has developed a proprietary Saprolegnia infection model that can be used for in vitro or in vivo research. The model begins with Saprolegnia culture isolation and purification and has the option of infection via zoospores or hyphae. Moreover, the infection model allows control over rate of infection with specific control points on timing and temperature and has the added benefit of being maintained through in vitro or in vivo systems. Infections can be created and maintained on any life-stage of freshwater (a) Pure culture infection of Saprolegnia on SDA media. (b) SDA media plate of Saprolegnia-exposed eggs fish. The model has many applications: corresponding to scores of 0 (uninfected), 1 (infected), and 2 (heavy infection). (c) Saprolegnia-infected eggs in 24 micro-well, tissue culture plates for therapeutant testing. Photo: Duane Barker, Anne McCarthy (HMSC)

Reducing the Problem of Early Sexual Maturation in Arctic Charr

decision to commence sexual maturation, but achieved by combining LL with reducing how they interact is unclear. Fraser River Arctic somatic growth in winter, by either food Charr is a good “model salmonid” for study as deprivation or rearing at 5°C rather than both sexes suffer a high rate (>70%) of early 10°C. Compensatory growth following the sexual maturation in culture (10°C groundwater), return to full ration in April indicates winter a trait that has limited its commercialization in growth suppression is practical. We propose Canada. Preventing sexual maturation would that a two-step gating mechanism controls the greatly increase commercial viability of farming growth-independent and growth-dependent diploid Arctic Charr. factors dictating the physiological decision Reducing the incidence of maturity to less to mature. than 20% has been consistently achieved in three year classes by rearing fish under 24 h DATE: SEP. 2013–MAR. 2018 Top: Marketable silvery immature fish; bottom: light (LL) from October to February. The timing unmarketable highly coloured mature fish. FUNDED BY: Atlantic Canada Opportunities Photo: Paul MacIsaac (Dalhousie U) of both the start-date and end-date of LL Agency–Atlantic Innovation Fund (ACOA–AIF) has been shown to be critically important. Reduction of the maturation rate was PROJECT LEAD: Jim Duston (Dalhousie U) arly sexual maturation among diploid independent of somatic growth. This leads us PROJECT TEAM: Qi Liu (Dalhousie U) Arctic Charr and other farmed salmonids to question the conventional model that the COLLABORATORS: Tony Manning (NB–Research Eremains a serious problem, reducing physiological trigger to mature is dependent and Productivity Council); Rodrigue Yossa (Coastal meat quality and revenue. Photoperiod, on defined threshold levels of growth and/or Zones Research Institute) temperature, and food availability exert a body size. Nevertheless, further reductions in CONTACT: [email protected] strong influence on somatic growth and the the maturity rate, to 0% in some cases, were 6 FINFISH: FRESHWATER CANADIAN AQUACULTURE R&D REVIEW 2017

Development of Predictive Modeling Tools to Assist with Freshwater Aquaculture Site Decisions

overnmental agencies charged with the DATE: MAY 2012–MAR. 2016 responsibility of licensing and regulating FUNDED BY: DFO–Aquaculture Collaborative Gthe aquaculture industry are in need of Research and Development Program (DFO–ACRDP) objective tools to assist in their decision-making CO-FUNDED BY: Wild West Steelhead processes. The development of such tools would also benefit industry, as currently, the PROJECT LEAD: Cheryl Podemski (DFO) primary factor limiting the expansion of the COLLABORATORS: Rory Ylioja (Wild West Steelhead) freshwater industry is access to new sites. CONTACT: [email protected] The lack of tools to estimate ecological consequences of new sites has resulted in a WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ very precautionary atmosphere, a complex and acrdp-pcrda/projects-projets/CA-08-02-003-eng.html expensive application process, and ultimately, limited development of the industry. The primary environmental concerns with cage aquaculture are related to benthic impacts and exceedance of the assimilative capacity of an ecosystem for nutrient inputs. Cage aquaculture has the potential to have far-ranging impacts on the lake ecosystem. Increased nutrient inputs can affect overall ecosystem productivity and excessive nutrient inputs can lead to eutrophication, which may include such undesirable consequences as the development of nuisance algal blooms, oxygen deficiency, and loss of biodiversity. The deposition of solid wastes under farms contributes to increased sediment oxygen demand, as well as the potential to significantly alter the quality of benthic habitat and the Collecting sediment trap samples for suspended Collecting sediment cores for benthic invertebrate composition of benthic communities beneath particle analyses. Photo: Kristy Hugill (DFO) and chemistry analyses. Photo: Megan Otu (DFO) and surrounding farms.

Impacts of Stocking Density on the Welfare and Production Performance of Arctic Charr (Salvelinus alpinus)

his project aims to observe the effects The goal of this project is to improve the of stocking density on Arctic Charr welfare of farm-reared fishes (specifically that Twith respect to welfare. Currently, of Arctic Charr). Improving the welfare of aquaculturally-reared salmonids are primarily farmed fishes may subsequently result in stocked at high densities in order to increased growth rates/improved production stimulate schooling, reduce potential performance, thus increasing the quality of conspecific aggressive behaviour, and marketable product as well as quantity of ultimately increase the production quantity farm sales. of market quality product. However, with such high stocking densities, stress, and Arctic Charr reared at 20 kg per cubic meter. DATE: NOV. 2016–DEC. 2017 Photo: Michael Burke (U Guelph) other factors, which can be attributed to FUNDED BY: Ontario Ministry of Agriculture, Food high stocking densities, may result in and Rural Affairs (OMAFRA) increased instances of infection and other detriments to production performance. PROJECT LEADER: Richard Moccia (U Guelph) To date, little research has been done PROJECT TEAM: Andrew Sevier (U Guelph) examining the effects of stocking density COLLABORATORS: Alma Aquaculture Research on the welfare of farmed fishes. As such, Station (U Guelph) this project will analyze genetic, biochemical/ [email protected] proteomic, and physiological parameters CONTACT: pertaining to welfare among 5 treatment WEBSITE: www.aps.uoguelph.ca/aquacentre/ densities: 20, 40, 80, 120 and 160 kg•m-3 (low to excessive, respectively). Arctic Charr reared at 160 kg per cubic meter. Photo: Michael Burke (U Guelph) CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: FRESHWATER 7

Improving the Growth, Health, and Survival of Tilapia in a Greenhouse-Enclosed Intensive Recirculating Aquaculture System

arm-water tilapia (Oreochromis niloticus) is becoming an important Wcommercial freshwater fish in North America. Viva Aquaculture and Seafood Distribution Ltd. (Viva) in collaboration with The University of British Columbia (UBC) has engaged in sustainable tilapia aquaculture production to supply the strong market demand in British Columbia. To overcome technological uncertainties which cannot be removed using standard practice, the general project objective is to produce healthy tilapia in sustainable, environment-friendly, and in a less expensive way within a land-based facility without affecting the Aquaponics system for intensive tilapia culture. Photo: Jesse Ronquillo (UBC) surrounding environment by generating “zero waste”. Based on biological principles, the research team has developed a sustainable land-based tilapia aquaculture system in a Canadian climate. Beneficial nitrifying bacteria were used to convert toxic nitrogenous wastes into non-harmful compounds, which are absorbed by selected aquatic vascular plants and microalgae. Innovative bio-engineering design to recirculate clean water and conserve heat to maintain suitable condition for tilapia culture was employed. A “zero waste” system is being developed to make fish production more sustainable, profitable, and environment-friendly. Our research has yielded initial results that show encouraging outcomes during the first year of project implementation. It is expected that employing these new innovations will lead to lower production cost, increased economic benefits, and improved fish quality; all of Aquaponics system for intensive tilapia culture. Photo: Jesse Ronquillo (UBC) which will lead to an environmentally sustainable production of live tilapia. Culturing tilapia in a land-based, enclosed intensive recirculating system using innovative bioengineering design, beneficial microbes, algae, and vascular aquatic plants will lessen environmental impact, lower production cost, provide economic opportunities, and produce a healthy and diversified source of seafood for Canadian consumers.

DATE: FEB. 2015–DEC. 2018

FUNDED BY: Viva Aquaculture and Seafood Distribution Ltd. (“Viva”)

CO-FUNDED BY: Hero Invincible Bio Aqua Farm

PROJECT LEAD: Jesse Ronquillo (UBC; Viva)

PROJECT TEAM: Chang Lin Ye, Kai Chen (Viva)

COLLABORATORS: David Kitts (UBC)

CONTACT: [email protected]

WEBSITE: www.vivaseafood.com

Aquaponics system for intensive tilapia culture. Video: Jesse Ronquillo (UBC) 8 FINFISH: FRESHWATER CANADIAN AQUACULTURE R&D REVIEW 2017

The Development of Fast Growing, Late Maturing, and Salinity Tolerant Strains of Arctic Charr

he genetic improvement of Canadian The combination of detailed genotype strains of Arctic Charr to reduce the and phenotype data will enable the Tundesirable characteristics of poor identification of regions of the Arctic Charr growth, early maturation, and inability to genome associated with traits of economic tolerate seawater (and stress in general) interest. This information can facilitate would greatly facilitate development of the marker assisted selection of Canadian industry. Our goal is to integrate genomic aquaculture Arctic Charr, increasing the methodologies into selective breeding industry’s productivity and worldwide programs to develop better performing competitiveness. strains in a lower number of generations than by conventional breeding methods DATE: MAR. 2012–DEC. 2018 alone. We will first develop genomic FUNDED BY: Atlantic Canada Innovation Fund resources for Arctic Charr: 1) discover (ACOA) genetic markers [single nucleotide polymorphisms (SNPs)] from the Fraser, CO-FUNDED BY: Natural Sciences and Engineering Research Council (NSERC)–Discovery Program Nauyuk, and Tree River strains; 2) find out where the SNPs are located relative to each PROJECT LEAD: Moira Ferguson (U Guelph) other in the genome through genetic linkage PROJECT TEAM: Cameron Nugent, Anne Easton, mapping; and 3) develop a high resolution Roy Danzmann (U Guelph) genotyping tool (array). We will then use COLLABORATORS: Michael Burke (Alma those resources to find SNPs that are Aquaculture Research Station); Claude Pelletier located in or near genes that control the (CZRI); Ben Koop (UVic); William Davidson (SFU) economically important traits under study. Cameron Nugent and Oliver Franklin collecting Fraser CONTACT: [email protected] strain Arctic Charr for measurement. Adult fish with these SNPs could then be Photo: Anne Easton (U Guelph) bred to produce better quality offspring to serve as parents for the next generation. Rearing trials with families from the Fraser and Nauyuk strains have been conducted at the Coastal Zones Research Institute (New Brunswick) and the Alma Aquaculture Research Station (Ontario). We have tracked the phenotypic performance of individuals (growth, age of maturation, and salinity tolerance) and will genotype each of those fish for up to 90 thousand SNPs. Tracking the inheritance of these markers will also allow us to expand our current SNP based linkage map of the Arctic Charr genome. A sexually mature three year old female Arctic Charr. Photo: Anne Easton (U Guelph)

Change in Rainbow Trout Phosphorus Absorption: Physiological Adaptations to a Phosphorus Deficiency

relatively low (< 0.1 ppm of P in the water) absorb P specifically through the gills via the concentration of this element in the natural McKim and Goeden holding device (1982); environment of freshwater fish. However, and 5) confirm P absorption by monitoring preliminary observations in a recirculated P concentrations in the blood (aortic cannula) system, in which P concentrations were about and urine (urinary catheter). 1 ppm, found that physiological mechanisms This project will contribute to significantly appear to enable trout to absorb ambient P. advancing knowledge on phenotypic plasticity Phosphorus deficient Rainbow Trout therefore in fish and on the impact of nutritional appears to develop the ability to absorb deficiency, and will help to identify new external P to maintain homeostasis by homeostasis strategies. introducing sodium phosphate (NaPi) cotransporters into gill tissue. Phosphorus-deficient Rainbow Trout in holding to DATE: JAN. 2013–MAR. 2018 To test these hypothesis, we propose to: measure specific absorption through the gills. FUNDED BY: Natural Sciences and Engineering Photo: Émilie Proulx (U Laval) 1) produce P-deficient fish through a prolonged Research Council of Canada (NSERC) dietary deficiency in phosphorus; 2) monitor the change in P status in scales and carcasses and PROJECT LEAD: Grant Vandenberg (U Laval) he proposed project challenges the the overexpression of sodium phosphate (NaPi) PROJECT TEAM: Waly Ndiay, hypothesis that the only source of cotransporters in the tissue of trout (gills, pyloric Marie-Hélène Deschamps, Émilie Proulx (U Laval) Tphosphorus (P) available to freshwater caecum, proximal and distal intestine); 3) confirm CONTACT: [email protected] fish is their food. The assumption is that they are the capacity of deficient trout to absorb ambient WEBSITE: http://www.vrrc.ulaval.ca/fileadmin/ incapable of absorbing significant quantities of P through phosphorus absorption tests in tanks; ulaval_ca/Images/recherche/bd/chercheur/ P from their environment is supported by the 4) demonstrate the ability of deficient trout to fiche/424160.html CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: FRESHWATER 9

Aquastats: Ontario Aquaculture Statistics Program Overview on the Improvement of the Fraser Strain of Arctic Charr (Salvelinus alpinus) at the Coastal Zones Research Institute

Arctic Charr (Salvelinus alpinus) mature broodstock. Photo: CZRI he growers and scientists of the Atlantic region have identified the Tmajor challenges faced by the Arctic Charr (Salvelinus alpinus) aquaculture industry: early maturation, poor egg quality and supply, and inconsistency of fillet Ontario trout production 1988-2015. pigmentation. To solve these issues, the Coastal Zones Research Institute (CZRI) implemented a breeding program n 2015, we estimate that Ontario fish Indirect employment is conservatively whose objectives are: 1) to develop a farms produced 4,510 tonnes of Rainbow estimated at 150 person-years. fast-growing Arctic Charr that is commercially Trout, primarily for human consumption. The total annual contribution that I profitable in Canada and abroad; and Lake-based cage production of Rainbow aquaculture makes to the Ontario economy 2) to develop and provide certified high Trout in the North Channel & Eastern is estimated to be $80 million, with additional quality eggs to the industry. In collaboration Georgian Bay area accounted for 92% of the economic value realised via the recreational with its industrial and scientific partners, total production. Our records suggest that and aquaria trade. CZRI has rigorously performed selected approximately 66 facilities culture one or This project maintains a 27-year data breeding in order to improve the growth more of tilapia, Arctic Charr, Brook Trout, collection series on Ontario aquaculture. potential of each generation of the Fraser bass, Walleye, and other species, with an strain of Arctic Charr, while minimizing estimated total production of 380 tonnes DATE: JAN. 2016–MAY 2016 inbreeding and reducing the occurrence of in 2015. FUNDED BY: Ontario Ministry of Natural Resources early maturation. A seventh generation with The total farm-gate value of the 4,510 tonnes and Forestry (MNRF) 41 families was obtained in the autumn of of Rainbow Trout produced is estimated to 2015 and 2016, with a weight gain potential be $23.2 million, with an average price of CO-FUNDED BY: Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA) which has increased by 121% compared with $5.13/kg. The sale of tilapia, Arctic Charr, the first generation. Overall, the team at CZRI Brook Trout, bass, and other fish species is PROJECT LEAD: Richard Moccia (U Guelph) overcame important challenges over the estimated to be an additional $2.2 million. PROJECT TEAM: David Bevan (U Guelph) last decade and is progressing toward the More than 80 facilities are involved with pond COLLABORATORS: Sarah Desjardins, Mary Duda production of one of the most promising stocking, typically Rainbow Trout, Brook Trout, (Ontario Ministry of Natural Resources and Forestry) strains of Arctic Charr for aquaculture. and bass, conservatively estimated to be The overall objective is to provide a $1.5 million annually. CONTACT: [email protected] commercial and competitive Arctic Charr The Ontario aquaculture industry WEBSITE: www.aps.uoguelph.ca/aquacentre/ to the Canadian industry and abroad. is estimated to have generated a total of 195 person-years of direct, on-farm employment (137 person-years of full-time and DATE: APR. 2013–MAR. 2019 58 person years of part-time employment). FUNDED BY: Department of Agriculture, Aquaculture and Fisheries of New Brunswick (DAAF)

CO-FUNDED BY: Atlantic Canada Opportunities Agency (ACOA); Coastal Zones Research Institute (CZRI)

PROJECT LEAD: Claude Pelletier (U Moncton)

PROJECT TEAM: Caroline Roussel, Claude Landry, Luc Desjardins, Maurice Boudreau, Rodrigue Yossa (CZRI); Michel Desjardins (DAAF)

COLLABORATORS: Christophe Herbinger, Philippe Fullsack (Dalhousie U)

CONTACT: [email protected]

WEBSITE: http://www.irzc.umcs.ca/flash_content/ anglais/nousjoindre.html 10 FINFISH: FRESHWATER CANADIAN AQUACULTURE R&D REVIEW 2017

Evaluating Four Commercially Available Rainbow Trout Diets on the Growth and Feed Conversion of Ontario Domestic Rainbow Trout (Oncorhynchus mykiss)

n aquaculture, feed can account for farm to farm and year to year, data collected approximately 40-60% of a Rainbow Trout by farmers are generally considered Ifarm’s operating costs depending upon ineffective in determining which brand the type and size of the farm and the feeding of feed to use. husbandry practices followed. Since the The purpose of this study is to grow introduction of high-pressure moist extrusion Rainbow Trout (Oncorhynchus mykiss) from technologies in the 1980s, modern dry and 450 g to market size of 1,200 g using four durable high-energy salmon and trout diets different commercially available grower feeds. have been available to Ontario Rainbow This trial will indicate which feeds result in Trout farmers. Choice of manufacturer is superior growth rates and feed conversion dictated by the cost, availability, and so that the aquaculturalist can make an performance of the fish. While unit cost and informed decision in selecting a feed availability of the feed are easily determined manufacturer and/or brand of feed. A by the farmer, the performance of the fish fed significant reduction in feed costs can be any particular brand of feed is more difficult achieved if fish growth, feed conversion, to ascertain. Feed evaluations are usually and cost/unit feed can be reliably evaluated. offered by the manufacturer or by fish farmers. There are obvious problems with DATE: MAR. 2016–AUG. 2016 either of these sources. Manufacturers FUNDED BY: Aqua-Cage Fisheries Inc. promote their feed with a bias and seldom provide the relevant data to support their CO-FUNDED BY: Ontario Ministry of Agriculture, claims. Evaluations of fish feeds from fish Food and Rural Affairs (OMAFRA) farmers tend to be largely anecdotal. PROJECT LEAD: Richard Moccia (U Guelph) Furthermore, the effects of environmental PROJECT TEAM: Alma Aquaculture Research conditions (water temperature, dissolved Station (U Guelph) oxygen, fish densities, etc.), fish genetics, Martin Mills Inc.; Skretting and culture methodologies can have greater COLLABORATORS: Canada; Aqua-Cage Fisheries Ltd. influences on the growth and mortality of CONTACT: [email protected] Sampling Rainbow Trout for growth trial. fish than does nutrition. As these effects are Photo: David Bevan (U Guelph) seldom accounted for and vary greatly from WEBSITE: www.aps.uoguelph.ca/aquacentre/

Evaluation of Four Commercial Starter Feeds for Rainbow Trout (Oncorhyncus mykiss) Held Under Typical Commercial Hatchery Conditions

he rapid proliferation of aquaculture feeds purchased from four different feed over the past two decades has seen manufacturers. The objective was to Tthe growth of fish feed manufacturers determine which feeds best promoted on the global, national, and local levels. growth and survivability. Choice of feed manufacturer is dictated by There were no significant differences the cost, availability, and performance of the in either growth or mortalities when using fish. While unit cost and availability is easily starter feeds purchased from four different determined by the aquaculturalist, the feed manufacturers. This suggests that the performance of the fish fed any particular nutritional and energy requirements for brand of feed is more difficult to ascertain. Rainbow Trout starter feeds were meet, Feed evaluations are usually presented by or exceeded, by all four manufacturers. the manufacturer or by fish farmers. There are obvious problems with either of these DATE: DEC. 2014–JUL. 2015 sources. Manufacturers promote their feed FUNDED BY: Ontario Ministry of Agriculture, with a bias and seldom provide data that Food and Rural Affairs (OMAFRA) supports their claims. Evaluations of fish Starter feeds for rainbow trout. Photo: David Bevan PROJECT LEAD: Richard Moccia (U Guelph) feeds from fish farmers tend to be largely (U Guelph) anecdotal. Furthermore, the effects PROJECT TEAM: Michael Burke (U Guelph) of environmental conditions (water COLLABORATORS: Alma Aquaculture Research temperature, dissolved oxygen, fish to farm and year to year, data collected by Station (U Guelph) densities, etc.), fish genetics, and culture farmers are generally considered ineffective [email protected] methodologies can have greater influences in determining which brand of feed to use. CONTACT: on the growth and mortality of fish than The purpose of this study was to grow WEBSITE: www.aps.uoguelph.ca/aquacentre/ does nutrition. As these effects are seldom Rainbow Trout (Oncorhynchus mykiss) accounted for and vary greatly from farm fry from first feeding to 35 g using starter CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: FRESHWATER 11

The Effects of Light Emitting Diodes on the Growth and Feeding Behaviour of Rainbow Trout (Oncorhyncus mykiss)

here is considerable economic pressure for hatcheries to switch from Tincandescent lighting to light emitting diodes, as these bulbs last longer and greatly reduce operating expenses. Current LEDs being marketed to the aquaculture industry produce a significantly different light spectrum than incandescent, with more short wavelength (blue-shifted) light and less long wavelength (red and infrared shifted) light. In an aquaculture setting, Rainbow Trout are visual feeders, relying entirely on seeing the pellets to feed efficiently. Little is known on how the shift from incandescent to LEDs will affect feeding behaviour and growth of these commercially important salmonids. Feeding behaviour and growth rates will ultimately affect the bottom line of any hatchery or aquaculture facility; therefore, optimizing these under new lighting Spectrum emitted by traditional incandescent bulbs. Displays various intensity levels at different locations conditions is key. within AARS photoperiod lab. Three decades of aquaculture research has been carried out at the Alma Aquaculture Research Station (AARS), a large portion of which has been done indoors using incandescent lighting. As the AARS is preparing to switch to LEDs to reduce energy costs, it is important to determine how these new lights will affect Rainbow Trout growth, and how this will change how previous studies are interpreted.

DATE: AUG. 2016–DEC. 2016

FUNDED BY: Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA)

PROJECT LEAD: Richard Moccia (U Guelph)

PROJECT TEAM: Wes Chase (U Guelph)

COLLABORATORS: Alma Aquaculture Research Station (U Guelph)

CONTACT: [email protected]

WEBSITE: www.aps.uoguelph.ca/aquacentre/

Spectrum emitted by the AquaShift MLA-BL bulbs. Displays various intensity levels at different locations within AARS photoperiod lab. 12 FINFISH: FRESHWATER CANADIAN AQUACULTURE R&D REVIEW 2017

Modulation of the Metabolism and Digestive Capacity of the Arctic Charr (Salvelinus alpinus) Through Dietary Restriction

his project seeks to improve zootechnics for the development of a competitive TArctic Charr culture industry. Reducing or alternating the frequency of feeding can induce a mechanism that fish use to counter the effects of dietary restriction: compensatory growth. Salmonids can actually increase their conversion efficacy and remarkably, regain their body mass following a dietary restriction. To assess the effects of various feeding methods on the productivity of commercial Arctic Charr culture, the physiological parameters that dictate growth performances, such as digestive capacity, will be examined. Dietary restriction modulates the fish’s physiology in various ways based on the severity of restriction and feeding frequency. The goal of the project is to identify the most effective and sustainable feeding sequence that will ensure optimal physiological health and growth capacity. To achieve this, we will monitor digestive capacity after restriction and refeeding, and measure the digestibility parameters (e.g., trypsin activity and certain energy metabolism enzymes in the pyloric ceca). Mirelle Caouette Houle, UQAR aquaculture tank room/ISMER, Pointe-au-Père (Rimouski). Reducing the amount of food to reach Photo: Vincent Roy (UQAR) a given growth level and optimizing food conversion helps reducing costs and reduce organic waste (e.g., phosphorus) in the environment. The current challenge is to increase the competitiveness of the aquaculture industry while maintaining good growth performances. Dietary restriction and refeeding trials have been conducted in partnership with Aquaculture Gaspésie Inc. The goal of this project is to optimize zootechnics of the Arctic Charr, which is a strategic species in Canada for the development of consumer products.

DATE: SEP. 2014–APR. 2017 Feeding sequences. FUNDED BY: Atlantic Canada Opportunities Agency (ACOA)

CO-FUNDED BY: Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec (MAPAQ)

PROJECT LEADS: Nathalie Le François (Biodome de Montréal); Pierre Blier (UQAR)

PROJECT TEAM: Mirelle Caouette Houle, Arianne Savoie (UQAR)

COLLABORATORS: Francis Dupuis (Aquaculture Gaspésie Inc.); Moïse Cantin, Catherine Roy (Pisciculture des Monts De Bellechasse)

CONTACT: [email protected] CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 13 FINFISH: SALMON

Harvest Quality Trait Evaluation to Inform Atlantic Identification of Genetic Markers Associated Determination of the Potential Spatial Overlap Salmon Broodstock Selection with Growth Performance in a Soybean Meal and Interaction Between Commercial Fisheries Based Diet for Salmon (American Lobster, Snow Crab) and Finfish Enhancing Production in Coho: Culture, Aquaculture Activities in Connaigre Bay, Community, Catch High Density SNP Linkage Map for North Newfoundland American Atlantic Salmon (Salmo salar) Domestication Compromises Athleticism and Family Variation and Heritability of Male and Respiratory Plasticity in Response to Aerobic Using a Genomics Approach to Identify Atlantic Female Atlantic Salmon Fitness Traits Exercise Training in Atlantic Salmon (Salmo salar) Salmon Aquaculture Escapees and Hybrids Hybridization of Farmed Escaped and Wild What is a Farmed Salmon? Understanding the Life Use of Hydro-Acoustic Methods to Assess the Atlantic Salmon: So What? An Empirical and Model of a Seafood Commodity from Ocean to Table Migration Timing and Distribution of Juvenile Salmon Based Exploration of the Consequences for Wild in Discovery Islands and Johnstone Strait Growth Performance of Aquadvantage® Salmon Populations throughout the North Atlantic Using Two Different Diets The Historical and Social Dimensions of Salmon Quantifying Direct Genetic Impacts of Escaped Aquaculture Science Detecting Hybridization among Wild and Farmed Salmon on Wild Salmon in Atlantic Canada Farmed Escaped Atlantic Salmon in Southern Migration Timing and Distribution of Juvenile Probability of Detecting Escaped Aquaculture Newfoundland: Field Collections Salmon in Discovery Islands and Johnstone Strait Salmon is Related to Distance Between Genetic and Genomic Impacts of Escaped Farmed Spatial and Temporal Distribution and Survival Production Areas and Rivers Salmon in Atlantic Canada: Evaluating the Use of of Farmed Atlantic Salmon after Experimental Heritability of Blood Parameters as Health Indices Archived Atlantic Salmon Scales as a Source of Release from Sea Cage Locations for an Atlantic Salmon (Salmo salar) Pre-Impact DNA Studying Effects of Atlantic Salmon Selective Breeding Program Fundy Salmon Recovery: Recovering Endangered Broodstock Age and Egg Size on Later Atlantic Salmon through Innovation and Performance of Progeny Collaboration with Atlantic Canada’s Thermal and pH Tolerance of Farmed, Wild, and Aquaculture Industry First Generation Farmed-Wild Hybrid Salmon Reduction of Ammonia and Solids from Chinook Salmon Culture Facilities 14 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

Harvest Quality Trait Evaluation Enhancing Production in Coho: Culture, Community, Catch to Inform Atlantic Salmon oho Salmon, one of the most highly implementation of EPIC4 scientific knowledge Broodstock Selection valued species in British Columbia about Coho Salmon to help revive and sustain arvest quality traits are those that are C(BC), began suffering declines in the wild Coho fisheries. The work on this most important to the consumer. 1989 due to lower returns and high harvest project could lead to more economically Associated traits that are under genetic rates to the point where the commercial viable Coho Salmon fisheries serving both H fishery for Coho Salmon was essentially domestic and export markets. Our results control may be incorporated into selection indices within a breeding program. Nearly all closed in 1997. Reopening the Coho Salmon should also be transferable to other species of the harvest quality traits are not appropriate fishery using recovered and enhanced of Pacific Salmon as well as salmonids from for or cannot be evaluated on the breeding populations would bring economic and other regions of Canada. population itself. Instead, these traits are social benefits to BC. assessed on a commercial comparison group The Enhancing Production In Coho: DATE: OCT. 2015–SEP. 2019 Culture, Community, Catch (EPIC4) project of breeding nucleus siblings that are raised FUNDED BY: Genome Canada; Genome British aims to develop and use new genomics tools and harvested using accepted commercial Columbia practices. Harvest evaluations present the to address challenges facing safe, secure, and sustainable production of Coho Salmon. CO-FUNDED BY: Genome Quebec; DFO; greatest opportunity to assess multiple University of Victoria (UVic); Aquainnovo S.A.; The interdisciplinary team has sequenced the important traits within a single sampling effort Ressources Aquatiques Québec (RAQ); Institut de for potential inclusion in a selective breeding Coho Salmon genome and the first results Biologie Intégrative et des Systemes (IBIS); Thermo program. Over 30 harvest quality traits are have resolved clear patterns of regional Fisher Scientific Inc. populations structuring, both within BC and presently evaluated within the Atlantic Salmon PROJECT LEADS: William Davidson (SFU); broodstock program at the Huntsman Marine at the scale of the entire distribution range. Louis Bernatchez (U Laval) Science Centre. Representative traits with Genotyping of the hatchery broodstocks sampled in 2014 and 2015 showed strong PROJECT TEAM: Ben Koop, Rosemary Ommer associated heritability, h2, for one year class (UVic); Roberto Neira, Jose Yanez (Universidad de regional population structuring and allowed include: fillet weight (0.48 ± 0.08); fillet Chile); Terry Beacham, Robert Devlin, Ruth Withler brightness (0.39 ± 0.08); fillet redness high levels of accuracy in assigning salmon (DFO); Grant Murray (VIU, Duke U); Kerry Naish (0.52 ± 0.09); fillet yellowness (0.55 ± 0.09); to specific hatcheries or geographic regions. (U Washington); Rashid Sumaila, Ralph Matthews (UBC); Steven Jones (SFU) flesh moisture (0.62 ± 0.17); flesh fat content In addition, first results on the heritability and (0.60 ± 0.17); and flesh protein (0.36 ± 0.16). genetic correlation shed light on the genetic COLLABORATORS: David Willis (DFO); Brian Additional traits assessed at this time include basis of flesh colour and the response of this Riddel (PSF); Jean Paul Lhorente (Aquainnovo S.A.) trait to artificial selection for harvest weight the omega fatty acids, other measurements CONTACT: [email protected] of colour, maturation status, body/fillet shape, over the time course of eight generations. WEBSITE: http://www.epic-4.org presence/absence of various deformities or The team is also working with stakeholders, abnormalities (e.g., pigmentation variation), and including First Nations, regarding the differential mortality/survival within commercial production environments. Each year class of the Atlantic Salmon broodstock program has an associated harvest evaluation completed that will continually build our dataset to improve selection efforts.

DATE: MAY 2015–APR. 2020

FUNDED BY: Atlantic Canada Opportunities Agency–Atlantic Innovation Fund (ACOA–AIF)

CO-FUNDED BY: New Brunswick Innovation Foundation; Northern Harvest Sea Farms Ltd.; Huntsman Marine Science Centre (HMSC)

PROJECT LEAD: Amber Garber (Huntsman Marine Science Centre)

PROJECT TEAM: Chris Bridger, Susan Hodkinson, Philip Wiper, Brooke Barrett, Jamie Carpenter, Anne McCarthy, Esther Keddie, Erica Harvey, Chantal Audet (HMSC)

COLLABORATORS: Aaron Craig (Northern Harvest Sea Farms Ltd.); Bruce Swift, Salvador Gezan (TRIGEN Fish Improvement) EPIC4's integrated approach toward sustainable fisheries & aquaculture CONTACT: [email protected]

WEBSITE: http://www.huntsmanmarine.ca/ CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 15

Domestication Compromises Athleticism and Respiratory Plasticity in Response to Aerobic Exercise Training in Atlantic Salmon (Salmo salar)

DATE: JAN. 2013–DEC. 2016

FUNDED BY: The Research Council of Norway; The Fishery and Aquaculture Industry Research Fund

CO-FUNDED BY: Canada Research Chairs Program (CRCP); Kone Foundation–Elizabeth R. Howland Fellowship

PROJECT LEADS: Sven Martin Jørgensen (Nofima AS); Anthony P. Farrell (UBC)

PROJECT TEAM: Yangfan Zhang (UBC); Gerrit Timmerhaus (Nofima AS); Harald Takle (Marine Harvest ASA)

COLLABORATORS: Guy Claireaux, Exercise training Atlantic Salmon (Salmo salar) A closer look of exercise training Atlantic Salmon Florian Mauduit (UBO); Katja Anttila (University of in the Brett-type two-channel swimming tunnel. (Salmo salar) in motion in the Brett-type two-channel Turku); Torstein Kristensen (Nord University) Photo: Yangfan Zhang (UBC) swimming tunnel. Photo: Yangfan Zhang (UBC) CONTACT: [email protected]

n this project we address the possibility were given either an 18-day exercise-training WEBSITE: http://www.zoology.ubc.ca/person/ that the Norwegian Atlantic Salmon (Salmo regime (an incremental water current of yangfan salar) breeding program which focuses 2.0–2.8 FL s−1), or were maintained at the I −1 on commercially beneficial traits, such as rapid control water current (0.5 FL s ) for 18 days. growth, may compromise the cardiorespiratory While exercise training produced several system. This may contribute to the mortality tangible benefits for the wild fish, it produced of smolts after seawater transfer. very few for the domesticated fish. This shows A suite of respiratory indices (including that the domesticated strain was athletically standard metabolic rate, maximum rate of less robust than the wild strain. These results oxygen uptake, absolute aerobic scope, imply that approximately ten generations excess post-exercise oxygen consumption, of selective breeding for rapid growth in critical oxygen level, and incipient lethal commercial aquaculture have reduced the oxygen saturation) was used to evaluate overall athletic robustness of domesticated aerobic capacity and hypoxia tolerance to salmon as compared to their wild test the hypothesis that exercise training conspecifics. Given the success in improving improves the athletic robustness in both athletic robustness of the wild strain, it still Atlantic Salmon (Salmo salar) are swimming in the Brett-type two-channel swimming tunnel. domesticated and wild strains of Atlantic remains to be seen whether an exercise Video: Sven Martin Jørgensen (Nofima AS) Salmon. These hypotheses were tested with training protocol can be developed that will Atlantic Salmon parr of domesticated and wild provide benefits to the salmon aquaculture strains that were reared under identical industry. hatchery conditions. The two strains of fish

What is a Farmed Salmon? Understanding the Life of a Seafood Commodity from Ocean to Table

armed Atlantic Salmon is one of the regarding farmed salmon. Research Salmon farmed in BC. This information will world’s most valuable and widely traded about farmed salmon can be widely found increase our understanding of social-cultural Fseafood commodities. Its consumption in the ecological, economic, and business issues along the entire value chain, contributing is driven by increased global consumer literature; however, there is a noteworthy to the social license dialogue by providing demand that can no longer be met by wild gap in the social sciences literature. greater understanding of the broader social-­ fisheries alone. It is now the fastest growing This research uses multi-sited ethnographic cultural perspectives about farmed salmon, food production system in the world. It also methodology (observation, conversational at a time when the sector is pursuing new and provides jobs and revenue for many coastal interviews, and document analysis) to ‘follow increased opportunities in Canada and abroad. communities, including in BC where the the fish’ along the commodity chain–recording, sector is a significant economic driver in comparing, and contrasting ideas, beliefs and DATE: OCT. 2015–SEP. 2018 some rural, largely resource-dependent knowledge about the product, both positive FUNDED BY: MITACS Accelerate (PhD Fellowship) communities, including some First Nations and negative, amongst people who engage villages. However, despite its significant with it on its path from production to CO-FUNDED BY: Grieg Seafood BC Ltd.; economic contributions, and the ever consumption. Research sites include fish Marine Harvest Canada Limited; BC Jobs Plan increasing global demand for the product, farms, processing plants, sales and PROJECT LEAD: Michele Patterson (UVic) both current operations and growth of distribution centres, and restaurants in Tofino, PROJECT TEAM: Rosaline Canessa (UVic); the sector in BC have been consistently Port Hardy, Campbell River, and San Francisco. Grant Murray (Duke U) challenged by social license constraints This research will produce rich, qualitative Marilyn Hutchinson (community intolerance for new and information from employees, customers, COLLABORATORS: (Grieg Seafood); Sharon DeDominicis increased aquaculture development) stakeholders, and others about the production, (Marine Harvest Canada Limited) that reflect, among other things, the processing, transport, culinary preparation, deeply embedded plurality of perspectives sales, and consumption practises for Atlantic CONTACT: [email protected] 16 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

Growth Performance of AquAdvantage® Salmon Using Genetic and Genomic Impacts Two Different Diets of Escaped Farmed Salmon in Atlantic Canada: Evaluating ttempts to enhance salmon DATE: MAY 2015–DEC. 2015 productivity by improving diets, the Use of Archived Atlantic FUNDED BY: National Research Council–Industrial Salmon Scales as a Source A while maintaining low production Research Assistance Program (NRC–IRAP) costs, has been a challenge for the of Pre-Impact DNA PROJECT LEAD: Dawn Runighan aquaculture industry. The possibility of (Aqua Bounty Canada Inc.) using triploid salmon (having an extra set quaculture escapes are a threat to the of chromosomes) instead of the naturally PROJECT TEAM: Armando Heriazon, persistence and stability of wild salmon Christina Bullerwell (Aqua Bounty Canada Inc.); occurring diploids has increased the populations; however, the presence and Rachid Ganga (Tyson Foods Inc.); André Dumas A magnitude of these genetic impacts are difficult challenge for providing an adequate diet. (Center for Aquaculture Technologies) AquAdvantage® salmon is a rapidly growing, to quantify in practice, largely due to a lack CONTACT: [email protected] all female, and triploid line of Atlantic Salmon. of pre-impact genetic baseline. Historically, The objective of the current study was to WEBSITE: https://aquabounty.com/ monitoring activities for Atlantic Salmon have examine the productivity impact of a premium collected scales for aging purposes, and these diet on AquAdvantage® salmon compared archived scales could represent a powerful to a commercial diet. For this study, source of pre-impact DNA. The main objective 300 AquAdvantage® salmon received two of this project was to explore the use of various different diets during two different stages of extraction methodologies to maximize DNA development established by weight, while yield and estimate genotyping success rate 300 AquAdvantage® salmon received only from archived Atlantic Salmon scales. Extracted a commercial Atlantic Salmon feed for the DNA was quantified and used for microsatellite whole experimental period (~7 months). genotyping to demonstrate the utility of AquAdvantage® salmon fed experimental this approach. The ultimate goal was future comparison of pre- and post-aquaculture diets had significantly (P ≤ 0.05) increased Difference in size of AquAdvantage® Salmon and thermal growth coefficient (TGC) and specific conventional Atlantic Salmon. Photo: Berni Wood DNA samples from Atlantic Salmon in growth rate (SGR) than those fish fed the (Reel Media Studio) Atlantic Canada to quantify the presence commercial feed. Results showed that the and magnitude of genetic impacts due to growth rate of AquAdvantage® salmon was escaped farmed salmon, thereby directly significantly (P ≤ 0.05) improved in fish fed informing mitigation strategies through a both starter and grower experimental diets quantification of impacts in space and time. (TGC > 2.65) as compared to the commercial feed (TGC < 2.50). At the end of the seventh DATE: APR. 2014–MAR. 2016 month, the average weight gain difference FUNDED BY: DFO–Program for Aquaculture was 184.3 g in favour of the experimental Regulatory Research (DFO–PARR) diet (P ≤ 0.05). This study suggests an opportunity to further improve growth PROJECT LEAD: Ian Bradbury (DFO) performance in new improved diets even PROJECT TEAM: Lorraine Hamilton, in a rapidly growing line. Performance of Patrick O’Reilly, Geoff Perry (DFO) the experimental groups and effects on CONTACT: [email protected] body composition will be discussed. Aqua Bounty Canada Inc. molecular laboratory showing the types of feed that were prepared. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Photo: Berni Wood (Reel Media Studio) parr-prra/projects-projets/2014-NL-01-eng.html

Detecting Hybridization among Wild and Farmed Escaped Atlantic Salmon in Southern Newfoundland: Field Collections

he monetary value of aquaculture impacts associated with the developing hybridization and evaluate the potential production has now surpassed aquaculture industry cannot be ruled out genetic impact of aquaculture escapees Tthe total value of wild fisheries. as a contributing factor. The aim of this on wild populations in Newfoundland Balancing the rapid industry expansion study was to collect young-of-the-year and Labrador. with environmental sustainability remains Atlantic Salmon following a large a challenge, with impacts for both wild (>20,000 individuals) escape event in 2013 in DATE: APR. 2014–MAR. 2015 populations and industry production. southern Newfoundland. This escape event FUNDED BY: DFO–Program for Aquaculture Aquaculture escapees represent a was equal to or greater than the estimate of Regulatory Research (DFO–PARR) continued threat to the genetic integrity wild salmon abundance in the region. Given of wild populations, and have been shown the magnitude of this release event, and PROJECT LEAD: Ian Bradbury (DFO) to interbreed with wild fish, eroding local reports of mature escapees in freshwater, PROJECT TEAM: Lorraine Hamilton, adaptation. In southern Newfoundland, wild these samples are expected to contain a Patrick O’Reilly, Geoff Perry (DFO) Atlantic Salmon populations remain at record mixture of wild and hybrid individuals. In total, CONTACT: [email protected] lows and are considered ‘threatened’ by the 2000 juvenile Atlantic Salmon were collected. Committee on the Status of Endangered Future genomic screening of these samples WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2014-NL-02-eng.html Wildlife in Canada (COSEWIC). Potential will be used to quantify the rates of successful CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 17

Fundy Salmon Recovery: Recovering Endangered Atlantic Salmon through Innovation and Collaboration with Atlantic Canada’s Aquaculture Industry

onservation sea cages–marine aquaculture sites designed to rear Cwild salmon–have the potential to return adults to their native rivers in numbers rivalling historic highs, provided sufficient smolts can be collected. This model could improve not only depressed numbers of wild Atlantic Salmon, but freshwater ecosystems impacted by reduced nutrient input caused by collapsed returns of diadromous fish. The Fundy Salmon Recovery project is a collaborative approach to species recovery that includes government, nongovernment, industry, academic, and First Nation partners. Building on the success of a pilot project (2009-2012), an innovative yet practical rearing strategy has been implemented to Specially designed smolt pen utilised by the Wild Salmon Conservation Farm at Dark Harbour. Pens use a boost endangered inner Bay of Fundy (iBoF) smaller mesh to accommodate smaller sized wild fish, and allow for feeding of smaller numbers of fish than Atlantic Salmon populations in two native typical salmon rearing operations. Photo: Nigel Fearson rivers. Wild smolts collected from rivers by Fundy National Park and Fort Folly First Nation are transported to Dark Harbour on Grand Manan Island, site of the world’s first wild salmon marine conservation farm. Maintained and operated by Cooke Aquaculture Inc. with support from the Atlantic Canada Fish Farmers Association, smolts are held at Dark Harbour until reaching sexual maturity. In early October, mature adults are transported to their natal rivers and released to allow for wild spawning, producing progeny free of captive exposure and associated domestication effects. Since releases of marine reared iBoF Atlantic Salmon began in 2015, over 1000 adults have been returned to the wild to spawn throughout the Upper Salmon River in Fundy National Park and the Petitcodiac River. Ongoing research through the University of New Brunswick tracks movement patterns and nutrient contributions of adults throughout the Becky Graham (DFO) passes a dip net of wild exposed smolt to Garrett Momberquette (PC). These fish have period of spawning activity. been held at the DFO Mactaquac Biodiversity Facility until ready for transport to the Cooke Aquaculture Inc. operated Wild Salmon Conservation Farm at Dark Harbour on the island of Grand Manan. Photo: Nigel Fearson The potential impacts of sea cage rearing are: 1) post-smolts mature in a semi-natural marine environment in the Bay of Fundy; DATE: MAR. 2014–MAR. 2019 2) significant numbers of adults produced for FUNDED BY: Environment and Climate Change release to native rivers to spawn; 3) increase Canada (ECCC)–National Conservation Plan in river ecosystem productivity through marine CO-FUNDED BY: Atlantic Canada Fish Farmers nutrient inputs; and 4) increased offspring Association (ACFFA); Cooke Aquaculture Inc.; New fitness through reduced captive exposure. Brunswick Department of Agriculture, Aquaculture and Fisheries (NBDAAF); Fort Folly First Nations; University of New Brunswick (UNB)

PROJECT LEAD: Corey Clarke (PC)

PROJECT TEAM: Betty House (ACFFA); Tom Taylor (Cooke Aquaculture Inc.); Michael Beattie (NBDAAF); Tim Robinson (Fort Folly First Nations); John Whitelaw (DFO); Kurt Samways (UNB) Staff from Department of Fisheries and Oceans, Parks Canada Agency, University of New Brunswick, Fort CONTACT: [email protected] Folly First Nations, and Cooke Aquaculture Inc. load wild exposed Inner Bay of Fundy Atlantic Salmon http://www.fundysalmonrecovery.com/ WEBSITE: smolt into transport trucks. Staff started before dawn to make the first ferry to the island of Grand Manan where smolt will be grown at the Dark Harbour Wild Salmon Conservation Farm. Photo: Nigel Fearson 18 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

Identification of Genetic High Density SNP Linkage Map for North American Atlantic Salmon Markers Associated with Growth (Salmo salar) Performance in a Soybean Meal DATE: JAN. 2016–AUG. 2018 Based Diet for Salmon tlantic Salmon continue to be a commercially and ecologically FUNDED BY: Genome Canada; Genome Atlantic; o date, soybean meal (SBM) inclusion Aimportant species. In regards to Ontario Genomics aquacultural practices, understanding where in salmon feed has been rather limited CO-FUNDED BY: NRC–Industrial Research due to poor performance and negative genes that influence commercially important Assistance Program (NRC–IRAP); Kelly Cove T traits (such as growth and disease resistance) Salmon Ltd. physiological impacts in fish fed SBM-containing are located on the genome as well as diets. However, studies have shown that there is PROJECT LEADS: Elizabeth Boulding significant individual and family variation in the determining how often genes from the (U Guelph); Keng Pee Ang (Kelly Cove Salmon Ltd.) ability to use SBM derived protein, and that this same chromosome are inherited together is of growing importance for improving the PROJECT TEAM: Melissa MacLeod-Bigley, trait has moderately high heritability. It is thus Forest Dussault, Jane Tosh, Melissa Holborn, development of selective breeding programs. possible to develop lines of salmon with Larry Schaeffer (U Guelph); Jake Elliott, increased efficiency in utilizing SBM. Marker Creating genetic linkage maps and using Frank Powell (Cooke Aquaculture Inc.) genetic markers such as single nucleotide assisted selection (MAS), using genetic markers Matthew Kent, Harald Grove, polymorphisms (SNPs) to trace inheritance COLLABORATORS: such as single nucleotide polymorphisms (SNPs) Sigbjørn Lien, Thomas Moen (Norwegian U Life associated with traits of interest, can be used from parents to offspring between individuals Sciences) is a necessary first step before quantitative to compliment traditional breeding and reduce CONTACT: [email protected] the time required to achieve genetic gains. traits can be mapped onto the genome. https://www.uoguelph.ca/ib/boulding This study is aimed at using genome-wide We used 220K and 50K SNP chip WEBSITE: association studies (GWAS) to identify Atlantic genotypes from the parents and offspring Salmon SNPs associated with increased of seven large families for constructing efficiency or tolerance to SBM as a protein sex-specific genetic linkage maps through source. A 60-day feeding trial was conducted the “onemap” package in R (a software to evaluate the effects of two different SBM and coding language commonly used for inclusion levels (Control and Test diets with statistical computing and data analysis). The 5% and 30% SBM, respectively) on weight initial male and female maps for each of the gain, feed efficiency, body composition, and 27 chromosomes were created using 11K nutrient deposition. Thirty full-sib families (initial SNP genotypes from three families of North body weight: 12.3 ± 1.0 g) of Atlantic Salmon American Atlantic Salmon (Saint John River (Saint John River strain) were utilized for the strain). We currently aim to create consensus trial. Six fish per family were allocated to linkage maps that would merge individual six different 325-liter tanks so that all families chromosomes between families for all were represented equally in each tank. Each 45,000 SNPs that overlap both custom fish was tagged with passive integrated SNP chips. In addition to benefitting selective transponders (PIT) and each diet was breeding programs, the consensus linkage allocated to three tanks. maps will also be compared to the newly The expected outcome of this project is a set published physical map for European Atlantic of SNPs associated with increased tolerance Salmon. This will facilitate the identification of and/or efficiency in utilizing SBM as a protein genes for commercially important traits that source. These novel markers will play a key may differ in genomic location between role in the development of improved genetic geographically distinct populations. lines that will allow for a significant increase in Creating highly informative consensus SBM inclusion in aquafeeds for Atlantic Salmon. maps for North American S. salar will enable selective breeding programs to identify causal loci that influence important traits such DATE: MAY 2016–DEC. 2016 as growth or disease resistance. It will also “Chromosome 1”–Linkage maps for chromosome 1 of FUNDED BY: Soy Aquaculture Alliance facilitate research in salmon conservation by male (left) and female (right) North American Atlantic Salmon. PROJECT LEAD: Jason Stannard (CAT) identifying functional genetic differences among stocks. PROJECT TEAM: John Buchanan (CAT); Debbie Plouffe, Tiago Hori, André Dumas (CATC)

COLLABORATORS: Cooke Aquaculture Inc.

CONTACT: [email protected]

WEBSITE: http://aquatechcenter.com/ CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 19

Using a Genomics Approach to Identify Atlantic Salmon Aquaculture Escapees and Hybrids

he cultivation of Atlantic Salmon has increased exponentially since the late T1960s with expansion into new geographic areas (e.g., Newfoundland) and the use of new selectively bred strains from North America and Europe. Coincident with this expansion has been an increased risk of farmed salmon escapes, which has the potential to impact the diversity of wild Atlantic Salmon populations. This project attempts to identify and apply targeted groups of genetic markers to quantify the genetic impacts of farmed Atlantic Salmon on wild populations and the frequency of interbreeding in the wild. This proposal directly targets client needs and is a first step towards identifying impacts and strategies for alleviating those impacts that result from interactions between wild and farmed salmon Sampling for possible offspring of escaped farmed Atlantic Salmon. Photo: Chris Hendry (DFO) escapees in Atlantic Canada. This project extends earlier work that Use of Hydro-Acoustic Methods to Assess the Migration Timing and developed expertise for genome wide marker development in non-model species. Distribution of Juvenile Salmon in Discovery Islands and Johnstone Strait In this proposal, the impact of farmed uring their migration to the Northern • Provide information in addressing critical escapees on wild populations will be Pacific, juvenile wild salmon from the uncertainties and recommendations as quantified by: 1) combining existing genomic Strait of Georgia pass through the identified in the Cohen Report with respect data and modern DNA sequencing methods D Discovery Islands and Lower Johnstone to: 1) marine survival in their early marine to develop a group of genetic markers (single Strait, where salmon farming occurs. life; 2) disease transfer and interactions nucleotide polymorphisms or SNPs) for rapid This project seeks to inform the risk of between wild and farm salmon; and and accurate identification of farmed salmon disease transfer associated with interactions 3) assessing the cumulative impacts escapees, including all strains in use, or between wild and farmed salmon in this area of multiple stressors on Fraser River under consideration for use, in Atlantic by studying wild salmon migratory pathways Sockeye Salmon productivity. Canada; and 2) applying this genomic and the duration of their residency in the screening tool to rapidly and accurately • Inform operational decisions and best vicinity of these fish farms. quantify, both, the presence of escapes practices engaged in by the BC salmon In conjunction with traditional survey/ and recent hybrids in the wild focusing aquaculture industry. sampling methods (including purse seining, on Newfoundland and Maritimes regions. beach seining, and trawling) using hydro-­ Research has confirmed that escaped acoustics offers a cost-effective way of DATE: MAY 2015–JUN. 2017 farmed salmon are breeding with wild monitoring fish abundance, behaviours, salmon and producing offspring in many FUNDED BY: DFO–Aquaculture Collaborative and distribution for extended and continuous rivers in Newfoundland. Research and Development Program (DFO–ACRDP) periods of time. This will enable observation BC Salmon Farmers Association and data collection on juvenile wild salmon CO-FUNDED BY: (BCSFA) DATE: APR. 2014–MAR. 2017 migration in the area of fish farms, thus gaining PROJECT LEAD: Stéphane Gauthier (DFO) FUNDED BY: DFO–Genomics Research and insights into potential impacts of wild salmon Development Initiative (DFO–GRDI) on farmed salmon and vice versa. PROJECT TEAM: Stewart Johnson, Marc Trudel, Chrys-Ellen Neville (DFO) CO-FUNDED BY: DFO–Program for Aquaculture The results of this project will: Regulatory Research (DFO–PARR) • Assist in informing a risk assessment COLLABORATORS: Joanne Liutkus (BCSFA) process to investigate the risks of PROJECT LEAD: Ian Bradbury (DFO) pathogen transfer from farmed to wild CONTACT: [email protected] PROJECT TEAM: Lorraine Hamilton, salmon, particularly in the Discovery WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Patrick O'Reilly (DFO) Islands. acrdp-pcrda/projects-projets/15-1-P-02-eng.html COLLABORATORS: Geoff Perry, • Improve our understanding and inform and Dounia Hamoutene, Martha Robertson (DFO); Elizabeth Barlow (DFA); Jon Carr (Atlantic Salmon support the development of evidence-based Federation); Ross Hinks (Aboriginal Government– aquaculture management approaches. Miawpukek First Nation)

CONTACT: [email protected]

WEBSITE: http://dfo-mpo.gc.ca/science/rp-pr/ grdi-irdg/projects-projets/016-eng.html 20 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

The Historical and Social Dimensions of Salmon Aquaculture Science

or three decades, salmon aquaculture Fourth, I am examining the prospects has been a focus of environmental for effective science that is able to contribute Fresearch. In this project I am applying the to help resolve controversies regarding tools of environmental history and science and this industry. technology studies to understand how this While this project is examining the full research has developed, as well as the roles it range of environmental science relating has played in public discussions regarding the to salmon aquaculture, a special focus is industry. Several more specific objectives are on research relating to sea lice. also being pursued. This project is providing a better First, I am writing an environmental history understanding of how salmon aquaculture of salmon aquaculture science. This history science has developed in relation to will explore the relations between scientific the growth of the industry in its varied research and the evolving environmental, environmental and social contexts. social, and political dimensions of the industry. Second, I am examining how the diverse DATE: JUN. 2007–DEC. 2018 institutions engaged in environmental FUNDED BY: Social Sciences and Humanities research–governments, universities, industry, Research Council of Canada (SSHRC) and public interest organizations–have shaped research priorities, research results, and the PROJECT LEAD: Stephen Bocking (Trent U) application of these results. CONTACT: [email protected] Third, I am investigating the movement of WEBSITE: http://people.trentu.ca/sbocking/ scientific knowledge of salmon aquaculture Bocking-Salmon.html Salmon farm near Campbell River, British Columbia. among research sites in Canada, Norway, Photo: Stephen Bocking (Trent U) Ireland, and Scotland.

Migration Timing and Distribution of Juvenile Salmon in Discovery Islands and Johnstone Strait

his research is determining how juvenile salmon utilize the Strait of TGeorgia, including the Discovery Islands area, with a focus on Fraser River Sockeye Salmon and to a lesser extent, Chinook Salmon. It will also provide the information required to fully assess the risks of disease transfer from salmon arms to the wild, understand the potential consequences of such transfers, and inform farm management policies. Purse seines and DFO trawl surveys have greatly increased the understanding of the migration and health of juvenile salmon within the Strait of Georgia, BC, especially for Sockeye Salmon. Surveys conducted in 2010–2012 revealed that Fraser River Sockeye Salmon do not enter the Discovery Islands area (a fish farming area) until the end of May, and that they are widely distributed throughout this area for at least part of June. Discovery Islands. Photo: Dan McPhee (DFO) To further assess risks associated with interactions between farmed and wild fish, salmon are present in the vicinity of fish farms, DATE: APR. 2014–JUN. 2017 information in the following key areas is as well as to describe migration timing of FUNDED BY: DFO–Aquaculture Collaborative needed: 1) knowledge of migratory pathways juvenile Fraser River Sockeye Salmon out Research and Development Program (DFO–ACRDP) of salmon and the duration of their residency of the Strait of Georgia. To gain this required in the vicinity of fish farms; 2) knowledge of information, sampling will be performed using CO-FUNDED BY: Marine Harvest Canada Limited; the prevalence of pathogens and diseases a three-year trawl survey in the Strait of Grieg Seafood BC Ltd.; Cermaq Canada Ltd. within wild and farmed populations; and Georgia and a three-year purse seine PROJECT LEAD: Stewart Johnson (DFO) 3) knowledge of environmental and host combined with hydroacoustic surveys PROJECT TEAM: Marc Trudel, Chrys-Ellen Neville conditions during the periods wild salmon in Johnstone Strait. (DFO); Diane Morrison (Marine Harvest Canada reside in the vicinity of fish farms. Additionally, Limited); Patrick Whittaker (Grieg Seafood BC Ltd.); more information is required to further Barry Milligan (Cermaq Canada) understand when and for how long juvenile CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/P-14-01-001-eng.html CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 21

Spatial and Temporal Distribution and Survival of Farmed Atlantic Thermal and pH Tolerance Salmon after Experimental Release from Sea Cage Locations of Farmed, Wild, and First Generation Farmed-Wild he expansion of the aquaculture as well as residency patterns and how they industry in Newfoundland and the vary with the timing of the escape event Hybrid Salmon Tdecline in wild salmon stocks have (seasonal effects), will help in designing n Newfoundland and Labrador (NL), all raised questions regarding the possible more efficient recapture strategies. farmed Atlantic Salmon (Salmo salar) impacts escaped farmed salmon may have The research results from this study will originate from the Saint John River strain on local wild populations. Despite increased inform federal and provincial ecosystem-­ I (New Brunswick). It is believed that wild industry awareness and the implementation based management of the industry and stocks have developed adaptations to their of a code of containment, escape events provide key information for the development local environment; therefore the vulnerability can still occur. Spawning between of strategies to minimize potential impacts of these local, genetically distinct stocks to aquaculture-­origin Atlantic Salmon and of escaped farmed Atlantic Salmon on the farmed escapees through interbreeding is wild Atlantic Salmon has been scientifically environment and wild salmon populations. a concern. Studies on interactions between documented in Newfoundland. Further wild and farmed salmon have shown that this research is needed to better understand the DATE: APR. 2014–MAR. 2017 issue is area-specific and therefore these potential risk of escapees on wild salmon FUNDED BY: DFO–Program for Aquaculture interactions need to be further explored populations. The objective of this project Regulatory Research (DFO–PARR) within Newfoundland and Labrador. is to determine the residency time, locations, This research sought to clarify the ability PROJECT LEAD: Dounia Hamoutene (DFO) migratory routes, and survival rates of of F1 hybrids (offspring of local wild and escaped farmed Atlantic Salmon by PROJECT TEAM: Curtis Pennell, domesticated strains) to survive under local monitoring the movements of acoustically- Kimberley Marshall, Dwight Drover, environmental conditions (i.e., reduced pH Sebastien Donnet, Keith Clarke, Geoff Perry (DFO) tagged smolts, post-smolts, and adults, level of river waters and low spring seawater following a simulated escape of a group of CONTACT: [email protected] temperatures) occurring in Newfoundland fish at different times of the year. Identifying http://dfo-mpo.gc.ca/aquaculture/rp-pr/ and Labrador. The results of this research the migratory routes followed by escapees, WEBSITE: parr-prra/projects-projets/2014-NL-04-eng.html provide information on the potential impact of farmed escapees on wild stocks. We found that after a 90-day exposure to low pH water, no differences were observed between pure wild parr and F1 hybrids in Studying Effects of Atlantic Salmon Broodstock Age and Egg Size on survival, growth, and gill enzymes indicative of Later Performance of Progeny seawater readiness, but pure farmed parr had lower survival than the F1 hybrids. Additionally, tlantic Salmon broodstock that have resulted from 4 x 4 year old crosses despite we found no significant differences in total not matured after four years might having the smaller egg size. It appears that mortality among wild, farmed, and hybrids A be culled or retained for use the the growth potential of juveniles is based after transfer to seawater and exposure to following year for various reasons. For on inherent genetic variation or essentially very cold temperatures. example, families of Atlantic Salmon that genetic growth potential rather than egg size. While pure farmed salmon might be have a higher than average prevalence for Various factors are considered when affected in river conditions, this research late sexual maturation may be bred to try to retaining broodstock based on age or eggs suggests that hybrids (most likely the outcome delay sexual maturation within production based on average egg size from a batch. of farm-wild reproductive interactions) would fish. Female broodstock that mature at five This line of research has direct commercial not experience a significant mortality due years of age have significantly larger eggs relevance within production or selection to low pH in Newfoundland rivers. The (on average) compared with eggs from of broodstock even in the absence of a findings also suggest that hybrids resulting four-year-old females. Anecdotally, it is pedigreed broodstock program. from crossing wild salmon and farmed often believed that this larger egg size Saint John River salmon are as likely provides an advantage to the same DATE: FEB. 2016–APR. 2020 to survive seawater migration in cold individuals throughout the production FUNDED BY: Atlantic Canada Opportunities temperatures as their wild counterparts. cycle–larger eggs yield larger progeny that Agency–Atlantic Innovation Fund (ACOA–AIF) is carried on through to harvest. We are DATE: APR. 2014–JUN. 2015 comparing egg sizes from all donor female CO-FUNDED BY: New Brunswick Innovation Foundation; Northern Harvest Sea Farms Ltd.; broodstock and resulting growth performance FUNDED BY: DFO–Aquaculture Collaborative Huntsman Marine Science Centre (HMSC) of progeny at various ages at the time of Research and Development Program (DFO–ACRDP) measurement where female and male PROJECT LEAD: Amber Garber (HMSC) CO-FUNDED BY: Cold Ocean Salmon Inc.; broodstock of different ages were crossed PROJECT TEAM: Chris Bridger, Northern Harvest Sea Farms Ltd. (four-year-old female x four-year-old male, Susan Hodkinson, Philip Wiper, Jamie Carpenter, PROJECT LEAD: Dounia Hamoutene (DFO) 4 x 5, 5 x 4, and 5 x 5). These crosses are Danny Craig, Esther Keddie, Brooke Barrett, Erica Harvey, Chantal Audet (HMSC) PROJECT TEAM: Lynn Lush, controlled within the same production cycle Kimberley Burt (DFO) and at the same physical location thereby COLLABORATORS: Aaron Craig (Northern reducing and/or removing environmental Harvest Sea Farms Ltd.) COLLABORATORS: Julia Jensen (Cold Ocean Salmon Ltd.); Jennifer Caines (Northern Harvest Sea variation. To date, egg size has not defined CONTACT: [email protected] Farms Ltd.) juvenile size (assessed up to a post-smolt, WEBSITE: http://www.huntsmanmarine.ca/ pre-harvest stage). With the first year of data CONTACT: [email protected] evaluated, the largest progeny, on average, WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/N-14-01-002-eng.html 22 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

Reduction of Ammonia and Solids from Chinook Salmon Family Variation and Heritability Culture Facilities of Male and Female Atlantic Salmon Fitness Traits n farmed fish, metabolic processes produce The results of this research indicate the nitrogenous (principally ammonia) wastes possibility for using cyclical feeding to reduce here is minimal information published Iwhich are released into the environment. nitrogen excretion during salmon farming. This associated with the heritability of male That fish are not efficiently utilizing the feed would be especially beneficial at land-based or female Atlantic Salmon broodstock for growth and maintenance represents a salmon farms with systems where the water T fitness traits. Documenting relevant data potential economic loss. Additionally, the discharge is focused to a single outflow, requires tracking individuals from known release of nitrogenous wastes into the recirculating aquaculture, and multiple families through maturation and gamete environment can have implications for the net-pens or tanks. collection. During the 2014 and 2015 ecosystem and the fish farm, and regulatory spawning seasons of mature Atlantic consequences for culture facilities. DATE: AUG. 2012–SEP. 2015 Salmon, 1056 milt samples were assessed This study explored how feed regimes FUNDED BY: DFO–Aquaculture Collaborative from 529 males and egg samples were designed to stimulate compensatory Research and Development Program (DFO–ACRDP) assessed from 1139 females. These growth may be used during Chinook broodstock originated from 130 different CO-FUNDED BY: Agrimarine Industries Inc. Salmon production to reduce nitrogen families over two year classes with various excretion into the environment and increase PROJECT LEAD: Ian Forster (DFO) levels of relatedness among families. food utilization by the fish. When faced with PROJECT TEAM: Lawrence Albright (AgriMarine Heritability and genetic correlations were modest periods of food deprivation, the Industries Inc.) assessed considering various traits including: salmon were found to maintain growth and Lawrence Albright, for both males and females total body weight excrete less nitrogen, despite the similarity COLLABORATORS: Robert Walker (AgriMarine Industries Inc.) (kg) and gamete volume (mL); for males only of their final weights to the control group. sperm density, milt volume from repeated [email protected] This indicates that repeated short-term CONTACT: stripping (repeatability); and for females only food deprivation of two days duration WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ egg size. From collected data, fecundity and over a seven week cycle may provide a acrdp-pcrda/projects-projets/P-12-01-001-eng.html total number of gametes by individual were useful strategy for reducing nitrogen loss calculated. Data continues to be collected to the environment, while minimizing the with each new spawning season. In addition, loss of growth potential of the fish. effect of age (primarily four and five year old broodstock) and photo-thermal manipulation of spawning time on male and female Determination of the Potential Spatial Overlap and Interaction gamete production related traits is under Between Commercial Fisheries (American Lobster, Snow Crab) evaluation. and Finfish Aquaculture Activities in Connaigre Bay, Newfoundland Knowledge of fitness traits and heritability may inform decisions within a broodstock he objective of this project was to DATE: APR. 2012–JUN. 2017 program related to selection, numbers of provide valuable information to inform FUNDED BY: DFO–Aquaculture Collaborative each sex to maintain, and expected number Tfuture site development initiatives and Research and Development Program (DFO–ACRDP) of eggs resulting from the Atlantic Salmon contribute to the sustainability of the fishing CO-FUNDED BY: Fish, Food, and Allied Workers retained for spawning. and aquaculture industries on the south Union (FFAW); Cold Ocean Salmon Inc. coast of Newfoundland and Labrador. DATE: NOV. 2014–APR. 2020 There is rarely an opportunity to collect PROJECT LEAD: Dounia Hamoutene, Pierre Goulet (DFO) and compare ecological data before, during, FUNDED BY: Atlantic Canada Opportunities Agency–Atlantic Innovation Fund (ACOA–AIF) and after a salmon farming site has been PROJECT TEAM: Andry Ratsimandresy, approved and is under production. This Dwight Drover, Darrell Mullowney, Don Stansbury CO-FUNDED BY: New Brunswick Innovation (DFO); Jeff Barrell, Jon Grant (Dalhousie U) collected environmental and biological data Foundation; Northern Harvest Sea Farms Ltd.; at two newly approved salmon aquaculture COLLABORATORS: Harvey Jarvis (FFAW); Huntsman Marine Science Centre (HMSC) Jennifer Woodland (Cold Ocean Salmon Inc.) sites in Connaigre Bay, Newfoundland and PROJECT LEAD: Amber Garber (HMSC) Labrador–a bay that has not yet held salmon [email protected], CONTACT: PROJECT TEAM: Chris Bridger, production sites. Unfortunately, the [email protected] Susan Hodkinson, Philip Wiper, Jamie Carpenter, aquaculture sites were not stocked according WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Danny Craig, Esther Keddie, Brooke Barrett, to the expected time-frame, thus, the project acrdp-pcrda/projects-projets/N-12-02-001-eng.html Erica Harvey, Chantal Audet (HMSC) was terminated prematurely. Data collected COLLABORATORS: Aaron Craig (Northern over the course of the project are currently Harvest Sea Farms Ltd.) being employed to establish habitat CONTACT: [email protected] preferences and species distribution mapping. This can be used as a tool to WEBSITE: http://www.huntsmanmarine.ca/ advise on potential spatial overlap between aquaculture sites and local fisheries. CANADIAN AQUACULTURE R&D REVIEW 2017 FINFISH: SALMON 23

Hybridization of Farmed Escaped and Wild Atlantic Salmon: Probability of Detecting Escaped So What? An Empirical and Model Based Exploration of the Aquaculture Salmon is Related Consequences for Wild Populations throughout the North Atlantic to Distance Between Production Areas and Rivers he farming of Atlantic Salmon now aquaculture escapees is necessary for exceeds two million tonnes worldwide the successful conservation of wild salmon almon that escaped from sea cage T which exceeds the natural production populations, the stability of recreational and aquaculture facilities have been of wild populations. Interbreeding between Aboriginal fisheries, and continued growth detected in a large number of rivers in wild and escaped farmed salmon has been of a sustainable aquaculture industry. S Eastern North America with the detection of reported both in Europe and North America Through an examination of the presence of escapees seemingly related to the distance and can alter wild population characteristics, interbreeding and introgression, this work of the river from the production areas. Morris eroding local adaptation and causing wild will help identify strategies for maintaining et al. (2008) compiled the existing information population declines. However, the extent the rapid growth of the aquaculture industry available to 2007 on aquaculture escapees and magnitude of these genetic impacts without altering population structure or local in rivers of Eastern North America but did not are difficult to predict. The resiliency of wild adaptation of wild salmon populations. By provide any quantitative analysis that could populations, the recovery time following doing so, this work will directly assist DFO in be used to link the detection of escapees hybridization, and the efficacy of possible meeting Canada’s commitment to ensure the relative to the distance of the rivers from the mitigation strategies remain unclear. aquaculture industry develops sustainably. production areas. This project proposes to The overall goal of this international update the compilation of observations from collaborative research project is to provide DATE: MAR. 2016–MAR. 2019 Morris et al. (2008) to 2015, to review the the basis for robust scientific advice regarding literature on the behaviour of escaped salmon, the genetic impacts of escaped farmed Atlantic FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR) and based on these components, to examine Salmon on wild populations both locally (i.e., a series of models with differing assumptions Newfoundland) and across the North Atlantic. PROJECT LEAD: Ian Bradbury (DFO) on behaviour and diffusion, for their ability As well, potential successes of various COLLABORATORS: Ian Flemming, Matt Rise to generate the empirical observations of mitigation strategies will be explored by using (MUN); Kjetil Hindar (Norwegian Institute for Nature escapees in monitored rivers. The objective data collected in parallel research projects from Research); Kevin Glover (Institute of Marine Research, is to examine models that would provide Norway); Mark Coulson, Eric Verspoor (The Rivers across the North Atlantic. This work will directly probability statements of observing an complement existing studies and will: 1) quantify and Lochs Institute, Scotland); Phil McGinnity (School of Biological, Earth, and Environmental Sciences, escaped salmon in a river based on the the magnitude of hybridization between wild Ireland); Einar Nielsen (Technical University of distance of the river from the escape location, and escaped farmed salmon and explore Denmark); Kristen Gruenthal (NOAA Fisheries) the intensity of the escape event, and the river growth, survival, and biological differences CONTACT: [email protected] monitoring effort. This knowledge will inform between wild and hybrid individuals; and aquaculture management siting decisions. 2) develop an international collaborative project WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Reference: Morris, MRJ., Fraser, D.J., parr-prra/projects-projets/2016-NL-11-eng.html focused on evaluating different models used Heggelin, A.J., Whoriskey, F.G., Carr, J.W., throughout the North Atlantic. O’Neil, S.F., and Hutchings, J.A. 2008. Identifying risks and potential mitigation Prevalence and recurrence of escaped strategies associated with Atlantic Salmon farmed Atlantic Salmon (Salmo salar) in Eastern North American rivers. Can. J. Fish. Quantifying Direct Genetic Impacts of Escaped Farmed Salmon Aquat. Sci. Vol. 65: 2807-2826. on Wild Salmon in Atlantic Canada DATE: MAY 2016–MAR. 2017 quaculture escapes are a threat to This study will begin to quantify the FUNDED BY: DFO–Program for Aquaculture the persistence and stability of wild extent of genetic impacts from farm escaped Regulatory Research (DFO–PARR) salmon populations, with impacts Atlantic Salmon on wild populations over A PROJECT LEAD: Ian Bradbury (DFO) occurring through both genetic and time and in different areas in Atlantic Canada. ecological interactions. The goal of this study PROJECT TEAM: Brian Dempson, Ross Jones, Alex Levy (DFO) is to quantify the presence and magnitude of DATE: APR. 2016–MAR. 2019 direct genetic impacts that escaped farmed CONTACT: [email protected] FUNDED BY: DFO–Program for Aquaculture salmon have on wild salmon populations in Regulatory Research (DFO–PARR) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ order to inform management decisions and parr-prra/projects-projets/2016-NL-14-eng.html advise on mitigation strategies. Specifically, PROJECT LEAD: Ian Bradbury (DFO) this study addresses three objectives: 1) to PROJECT TEAM: Lorraine Hamilton, Carole Grant, quantify the magnitude of low level chronic Chris Hendry, Brian Dempson, Ross Jones (DFO) escapes through an annual targeted survey; COLLABORATORS: Ian Fleming (MUN); 2) to quantify annual variation in hybridization Jon Carr (Atlantic Salmon Federation); Ross Hinks among wild and farm escaped Atlantic (Miawpukek First Nation); Tony Blanchard, Salmon; and 3) to evaluate at sea survival Derek Tobin, Gerald Cline, Lloyd Slaney, of hybrids in Newfoundland. Helen Griffiths (DFO) Identifying risks and potential mitigation CONTACT: [email protected] strategies associated with Atlantic Salmon WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ aquaculture escapees is critical to both the parr-prra/projects-projets/2016-NL-02-eng.html successful continued growth of the aquaculture industry and the conservation of wild salmon populations. 24 FINFISH: SALMON CANADIAN AQUACULTURE R&D REVIEW 2017

Heritability of Blood Parameters as Health Indices for an Atlantic Salmon (Salmo salar) Selective Breeding Program

he Atlantic Salmon broodstock program at the Huntsman Marine Science Centre T(HMSC), with commercial partner Northern Harvest Sea Farms Ltd., is selecting for traits that are important to commercial production. Many of these traits cannot be measured directly on breeding candidates but have to be recorded on close relatives (e.g., progeny from the same families), thereby selecting based on performance of the family versus the individual. One limitation of this approach is that it is possible to select an individual that does not possess enhanced performance for the desired trait (e.g., disease resistance/susceptibility). Use of genomic markers in a broodstock program mitigates this issue after the molecular markers are demonstrated to be reliable for predictive purposes. Alternatively, biological proxy indicators may be discovered that are readily measurable and closely correlate with specific commercial traits of interest to increase selection efficiency as well. As an example, during the 2016 spawning season, 1217 blood samples were collected from individual male and female broodstock Fish blood (stained with Diff-Quik™) illustrating predominantly erythrocytes (orange arrows), with few lymphocytes representing 195 families from three ages, (green arrows) and one neutrophil (red arrow). Image captured at 1000X. Photo: Duane Barker (HMSC) multiple rearing conditions, and at various points during and after typical spawning. DATE: OCT. 2016–DEC. 2020 Blood parameters recorded from samples FUNDED BY: Atlantic Canada Opportunities included lymphocyte and neutrophil density, Agency–Atlantic Innovation Fund (ACOA–AIF) erythrocyte size, and hematocrit. Heritability of these parameters, their reliability as health CO-FUNDED BY: New Brunswick Innovation Foundation; Northern Harvest Sea Farms Ltd.; indicators, and correlations among these Huntsman Marine Science Centre (HMSC) traits and other commercial traits are under evaluation. Preliminary analysis indicates PROJECT LEADS: Duane Barker, Amber Garber significant differences in hematocrit (HMSC) among broodstock reared under ambient PROJECT TEAM: Anne McCarthy, Chris Bridger, conditions compared to those receiving Susan Hodkinson, Esther Keddie, Rebecca Eldridge, photo-thermal-advanced conditions. Erica Harvey, Ellen Fanning, Chantal Audet, Brooke Barrett (HMSC) The encouraging preliminary research complements the extensive data array for COLLABORATORS: Aaron Craig (Northern the Atlantic Salmon broodstock program Harvest Sea Farms Ltd.) and may provide another monitoring tool in CONTACT: [email protected] the production of salmon. WEBSITE: http://www.huntsmanmarine.ca/ CANADIAN AQUACULTURE R&D REVIEW 2017 SEA LICE 25

SEA LICE

Characterizing the Mechanism of Salmon Louse Defining the Risk of Sea Lice Infections Through An Investigation of the Relationship Between (Lepeophtheirus salmonis) Rejection by Coho the Development of an Understanding of the Environmental Parameters, Oceanographic Zones Salmon (Oncorhynchus kisutch) Using a Novel Early Life History Population Dynamics of Sea Lice of Influence, and the Prevalence of Parasitic Dual RNA-Sequencing Approach Associated with Atlantic Salmon Aquaculture Sites Copepods on Three-Spine Stickleback in Bay in the Bay of Fundy D’Espoir Newfoundland with Specific Reference The Use of Kelp Perch and Pile Perch to Control to Salmonid Aquaculture Sites Sea Lice (Lepeophtheirus salmonis) on Infested Development of Bacterial Biomarkers of Salmon Atlantic Salmon Smolts Microbiota Mediated Resistance Against the Studies of Sea Lice Infection Levels on the Sea Louse Lepeophtheirus salmonis Health of Juvenile Salmon in the Strait of Wild Salmon Sea Lice Data Integration–Sea Lice Georgia and Adjacent Waters Monitoring Network Development for Wild Salmon Safety Assessment of an Oxygen Gas Infusion in Vancouver Island Coastal Waters System Used During Various Hydrogen Peroxide Refining the Use of Warm Water Showers to

(H2O2) Treatments on Atlantic Salmon (Salmo salar) Remove Sea Lice from Atlantic Salmon and Susceptibility of Farmed and Wild Atlantic Salmon Understanding the Fish Health Implications (Salmo salar) to Experimental Infestations with Developing a Non-Chemical Means to Effectively of the Technique Sea Lice (Lepeophtheirus salmonis) Remove All Forms of Sea Lice from Aquaculture Salmon Using Warm Water The Effects of Sea Lice in Modulating Salmonid Susceptibility to Viruses 26 SEA LICE CANADIAN AQUACULTURE R&D REVIEW 2017

Characterizing the Mechanism of Salmon Louse (Lepeophtheirus salmonis) Rejection by Coho Salmon (Oncorhynchus kisutch) Using a Novel Dual RNA-Sequencing Approach

fter infection with larval sea lice (Lepeophtheirus salmonis), juvenile ACoho Salmon are able to rapidly reject the parasite. This rejection is associated with aggressive hyperplasia and infiltration of cellular effectors; however, the molecular mechanisms of this response have not been characterized. This project aims to explore the response of both salmon and sea louse simultaneously by leveraging high-throughput modern sequencing technologies (dual RNA-seq). Samples of Coho Salmon fins with and without visible sea lice infestation were used to generate a pool of transcripts originating from both the sea lice and the salmon. Reads arising from either organism were separated using publicly available transcriptome/genome information for both species. Differential expression was analyzed for both the host and the parasite comparing different Sea lice are encapsulated by an aggressive host response in the skin (right) and fin (left) of Coho Salmon time-points throughout the progression (shown here at 6 days post-infection). Photo: Laura Braden (UPEI-AVC) of the infection. Several pathways of the immune response were shown to be activated in Coho Salmon such as the complement cascade, tissue remodelling, and an acute phase response, while a concomitant response in the sea louse featured activated oxidative stress and cell death pathways. The analysis also revealed that mRNA expression reached basal levels after 18 days post-infection, indicating that rejection mechanisms were most likely completed by that time. To our knowledge, this is the first time the transcript expression of both host and parasite has been simultaneously investigated in salmonids using RNA-seq. The results of this project demonstrates the feasibility of dual RNA-seq while also putting forward many hypotheses related to the molecular mechanism behind sea lice resistance.

DATE: DEC. 2015–DEC. 2017

FUNDED BY: Natural Sciences and Engineering Research Council (NSERC)–Postdoctoral Fellowship Program

CO-FUNDED BY: Elanco Animal Health

PROJECT LEAD: Mark Fast (UPEI–AVC) A micrograph (H&E, 200X magnification) showing a sea louse attached to Coho Salmon fin, with massive PROJECT TEAM: Laura Braden (UPEI–AVC); recruitment of cellular responders (small round blue cells) below attachment site at four days post-infection. Tiago Hori (CAT); Phil Byrne (DFO)

CONTACT: [email protected] CANADIAN AQUACULTURE R&D REVIEW 2017 SEA LICE 27

The Use of Kelp Perch and Pile Perch to Control Sea Lice (Lepeophtheirus salmonis) on Infested Atlantic Salmon Smolts

ea lice infestations in farmed Atlantic The goal of this research was to cohabitating perch gastrointestinal tracts and Salmon require regular monitoring demonstrate if Kelp Perch (Brachyistius in fecal casts recovered from experimental Sand, sometimes, treatments with frenatus) and Pile Perch (Rhacochilus vacca) tanks. Salmon body condition and health chemicals such as SLICE®. Alternative would clean sea lice off infested Atlantic showed no observable differences between methods to control sea lice infestations are Salmon. Several cohabitation trials have experimental and control tanks, indicating needed to improve the sustainability of been performed whereby Kelp or Pile Perch that active sea lice predation by perch does Atlantic Salmon farming. Biological controls were placed in tanks with sea lice infested not result in negative health impacts to as a method to control sea lice infestations salmon. While variation in feeding activity infested salmon. have been considered as viable mitigation exists, perch of both species actively cleaned This research addresses a large issue tools to reduce sea lice infestations for many infested salmon of parasitic sea lice within facing the salmon farming industry in BC by years and are now being successfully used 48 hours of cohabitation. Video evidence conducting research to find a sustainable in Norway and Scotland, with cleaner fish supports this result showing perch actively way to reduce the environmental, economic, such as wrasse and lumpfish. feeding on parasitic sea lice. Additionally, and public perception issues related to digested sea lice were found within sea lice infestations in farm raised Atlantic Salmon. The use of cleaner fish to reduce sea lice infestations is an environmentally friendly solution to this issue of protecting wild salmon populations.

DATE: DEC. 2014–ONGOING

FUNDED BY: Sea Pact; BCSFA–Marine Environment Research Program (BCSFA–MERP)

CO-FUNDED BY: Marine Harvest Canada Ltd.

PROJECT LEAD: Shannon Balfry (Vancouver Aquarium)

PROJECT TEAM: Maureen Finn (Living Elements Ltd.); Sam Ferguson, Selina Thorberg (Vancouver Aquarium)

COLLABORATORS: Diane Morrison (Marine Harvest Canada Ltd.); Simon Jones (DFO)

CONTACT: [email protected]

Kelp Perch (Brachyistius frenatus) cleaning sea lice off of an Atlantic Salmon (Salmo salar) smolt. (A) Kelp Perch approaching the left side of the tail of an Atlantic Salmon. (B) The instant the Kelp Perch picks a sea louse off of the salmon, notice the jaw protrusion. (C) and (D) The moments after the pick as the perch begins to retreat from the salmon. Photo: Sam Ferguson (Vancouver Aquarium) 28 SEA LICE CANADIAN AQUACULTURE R&D REVIEW 2017

Wild Salmon Sea Lice Data Integration–Sea Lice Monitoring Network Susceptibility of Farmed Development for Wild Salmon in Vancouver Island Coastal Waters and Wild Atlantic Salmon (Salmo salar) to Experimental Infestations with Sea Lice (Lepeophtheirus salmonis)

ea lice (Lepeophtheirus salmonis) are common pests on farmed Atlantic SSalmon and can have large economic consequences for the salmon industry. These consequences can include treatment costs, increased mortalities, and negative public perception. Sea lice originating from aquaculture farms may also negatively impact wild stocks of salmonids, although the extent of the impact is unclear. Salmonid species have been shown to have different susceptibilities to sea lice infection. Atlantic Salmon have been shown to exhibit substantial genetic variation (in addition to phenotypic variation) in resistance to sea lice. This project will utilize controlled sea lice laboratory infestations to determine variations in sea lice susceptibility of three groups of fish: wild salmon from two origins (Garnish River, The coastal waters of British Columbia. Photo: BCSFA Conne River) and farmed salmon. Results from this project will: 1) aid the aquaculture industry in understanding and monitoring any potential ea lice monitoring programs on wild The program is currently synthesizing wild-farmed interactions to ensure sustainable Pacific smolts have served to broaden existing sea lice data sets into a useful format production of fish; 2) better inform on potential the understanding of sea lice ecology to communicate historical data trends, while S differences in sea lice susceptibility between and help to further develop sea lice also collecting and storing data from current farmed and wild salmon; and 3) provide management protocols on salmon farms. industry-sponsored sea lice monitoring information on stress levels for salmonids Studies where a large amount of annual programs. This includes ongoing monitoring following sea lice infestations in all groups data has been collected present a novel of sea lice on wild fish. By bringing these of fish. opportunity to study patterns over time, data together, new opportunities will arise particularly where such studies offer to conduct further analyses, report on trends structured snap-shots in space and/or noted in various regions, and increase DATE: APR. 2015–JUN. 2017 time. To fully capture the value of these transparency as well as the potential FUNDED BY: DFO–Aquaculture Collaborative types of studies, it is essential that they for information sharing. Research and Development Program be integrated for the purposes of By integrating data sets from conservation (DFO–ACRDP) comparison and aggregation. groups, academia, First Nations, government, CO-FUNDED BY: Cold Ocean Salmon Inc. This program aims to create a single and salmon farming companies, greater PROJECT LEAD: Dounia Hamoutene (DFO) repository for sea lice monitoring data from analytical and modelling opportunities arise. wild fish in British Columbia (BC), collected This should ultimately benefit all contributing PROJECT TEAM: Harry Murray, Lynn Lush, by the salmon farming industry, and parties and the sustainability of the aquatic Kimberley Burt (DFO) supplemented by additional data sets ecosystem along the BC coast. COLLABORATORS: Julia Bungay (Cold Ocean generated from conservation groups, Salmon Inc.) academics, First Nations, and government. DATE: APR. 2016–MAR. 2017 CONTACT: [email protected] Large sets of consistent, annual data can be FUNDED BY: BC Salmon Farmers WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ used in sea lice population studies, not only to Association (BCSFA) acrdp-pcrda/projects-projets/16-1-G-02-eng.html determine abundance and intensity, but also to help map clustering patterns in predicting PROJECT LEAD: Crawford Revie (UPEI) where sea lice will likely be most prevalent in PROJECT TEAM: Thitiwan Patanasatienkul (UPEI) a particular area by stage and time of year. CONTACT: [email protected]

WEBSITE: http://www.upei.ca/avc/crawford-revie CANADIAN AQUACULTURE R&D REVIEW 2017 SEA LICE 29

The Effects of Sea Lice Defining the Risk of Sea Lice Infections Through the Development in Modulating Salmonid of an Understanding of the Early Life History Population Dynamics Susceptibility to Viruses of Sea Lice Associated with Atlantic Salmon Aquaculture Sites in the Bay of Fundy he sea louse, Lepeophtheirus salmonis, is a naturally occurring parasite and a ea lice continue to be a challenge salmon farms, suggesting a specialised Tserious pest of farmed Atlantic Salmon in for Atlantic Salmon farmers worldwide internal mechanism for retention. A better both Eastern and Western Canada. As sea lice despite the development of various understanding of the early life history of sea are found on a number of wild host species in S chemo-therapeutant treatments and advanced lice in the Bay of Fundy will allow for insights the marine environment and co-occur with application measures (e.g., well boats). While on when to intervene in the lifecycle of the endemic viruses, mixed infections of sea lice some chemicals can be effective at controlling animal. Also, by assessing the degree to which and viruses are likely. Despite the widespread sea lice populations on the farm, they can aquaculture farms retain sea lice larvae and occurrence of sea lice in both wild fisheries sometimes affect other invertebrate groups how they leave the site, we can begin to and aquaculture, there have been no controlled and therefore need to be part of an Integrated assess the risk to other farms and whether studies that have explicitly examined the effect Pest Management Plan (IPMP) that includes a or not they could affect wild species in of L. salmonis on disease caused by viral variety of treatments to address various life their spread. pathogens. Sea lice infected salmon may be stages of sea lice and are suited to varying Through this work, it may be possible to more likely to develop severe infections with environmental conditions. Nonchemical determine where the critical points are in the second pathogens, either because the sea measures such as genetic selection for farming operation that may promote sea lice louse serves as a vector, transmitting the resistance or mechanical devices that can infestations and what may be done to reduce secondary pathogens, or because the sea remove sea lice are currently being actively the infestations through protocol changes louse infection compromises the host immune examined. All management techniques are and engineering applications. response. The latter possibility is supported ultimately premised on the ability to control the by the observation of reduced expression of lifecycle of the sea lice from larvae to adult. DATE: APR. 2014–MAR. 2017 genes associated with anti-viral responses and However, there has been surprisingly little adaptive immunity in several salmon species FUNDED BY: DFO–Program for Aquaculture empirical field work done on the planktonic Regulatory Research (DFO–PARR) during laboratory infections with L. salmonis. early life history stages of sea lice where the This research project will focus on two viral largest numbers of individual animals exist and PROJECT LEAD: Shawn Robinson (DFO) pathogens, the Infectious Hematopoietic the infection first spreads. This is due to the PROJECT TEAM: Emily Nelson, Steve Neil, Necrosis Virus (IHNV) and the Infectious logistic difficulties of working in the field on Craig Smith (DFO) Salmon Anemia Virus (ISAV). IHNV infects wild commercial sites where production priorities COLLABORATORS: Joel Halse and cultured salmonids throughout the Pacific take priority over scientific requirements, (Kelly Cove Salmon Ltd.) Northwest of North America. ISAV infects and making it difficult to sample. Previous studies CONTACT: [email protected] causes disease in farmed Atlantic Salmon in from this team conducted in the Bay of Fundy Eastern Canada. For both viral pathogens, have revealed that the highest densities of WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ there is a need to better understand if sea lice sea lice larvae are consistently found around parr-prra/projects-projets/2014-M-02-eng.html parasitism influences virus transmission and susceptibility of salmon to infection. This research project addresses this issue by integrating parallel investigations into IHNV and ISAV interactions with sea lice in Western and Eastern Canada, respectively. The goal of the study is to determine level of sea lice infestation at which intervention or pest management strategies may be needed to prevent further damage from viral infection. This research will provide scientific information for management decisions regarding sea lice infestation thresholds for use in salmon aquaculture.

DATE: APR. 2014–MAR. 2017

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Simon Jones (DFO)

PROJECT TEAM: Kyle Garver (DFO)

COLLABORATORS: Mark Fast (UPEI–AVC)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2014-P-12-eng.html Plankton net with flow meter used to sample sea lice larvae (inset) in and around salmon farms in the Bay of Fundy. Photo: Shawn Robinson (DFO) 30 SEA LICE CANADIAN AQUACULTURE R&D REVIEW 2017

Development of Bacterial Biomarkers of Salmon Microbiota Mediated Resistance Against the Sea Louse Lepeophtheirus salmonis

ea lice, Lepeophtheirus salmonis, smolt was surveyed and population changes This project provided a survey of the parasitism of salmon represents an in response to L. salmonis infestation were microbial ecology of farmed Atlantic Salmon. Sanimal health issue for both wild and examined. Study results suggest that sea lice It also showed how the microbial community farmed salmon. Existing treatments are infestation drives imbalances in salmon mucus structure changed with respect to sea lice generally experiencing a loss of efficacy microbiota, which could underlie some of the exposure and how the change increases or variable results. Current research is morbidity associated with sea louse infection. with time post exposure as compared to exploring strategies such as vaccines, Principle component analysis and frequency non-infested salmon. selective breeding, novel drugs, and distributions suggested that, over the course non-chemical and biological control for of the experiment, the sea lice exposed mucus DATE: APR. 2013–MAR. 2015 the treatment, reduction, and removal of sea microbiome became increasingly different over FUNDED BY: DFO–Aquaculture Collaborative lice from farmed fish. This study represents a time, while water and biofilm remained similar. Research and Development Program (DFO–ACRDP) first step in developing strategies to reduce Although the control and treatment microbiome infections resulting from sea lice prevalence composition differed at the outset of the trial CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS); U Laval (NSERC–Engage) and sea lice landing by employing a making strong assertions difficult, infected probiotic approach. salmon microbiome changed more over time. PROJECT LEAD: Steven Leadbeater (DFO) Atlantic Salmon smolts were designated as This work demonstrates how a disrupted PROJECT TEAM: Martin Llewellyn (Glasgow U); non-exposed or exposed to a sea lice infection microbial community structure could allow for Keng Pee Ang (KCS); Nicolas Derome (U Laval) pressure of 40 copepodids per fish and potential secondary infection to occur. Future CONTACT: [email protected] monitored at regular time points as the sea lice research could examine ways to stabilize developed from chalimus to large pre-adult. the community structure, reducing this risk. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ The mucosal and gut microbiome of salmon acrdp-pcrda/index-eng.html

Safety Assessment of an Oxygen Gas Infusion System Used During Various Hydrogen Peroxide

(H2O2) Treatments on Atlantic Salmon (Salmo salar)

umerous strategies have been The Huntsman Marine Science Centre This research is innovative and quite developed to control sea lice (HMSC) is currently evaluating the safety timely. New strategies to mitigate sea lice Ninfestations within the farmed Atlantic and efficacy of using a gas infusion system infestations, especially those that will have Salmon industry. Unfortunately, sea lice (to create 150% ± 10% O2 saturation while minimal to no impact on fish welfare, are resistance to many chemotherapeutants maintaining total gas pressure of 100%) when needed globally. has now been reported globally. Thus, the exposing Atlantic Salmon to H2O2 at varying exploration of new therapeutants for sea lice treatment dosages (0-1500 ppm and DATE: JAN. 2017–ONGOING is warranted and timely. Hydrogen peroxide exposure times 15-40 mins). Subsequent FUNDED BY: GIS Gas Infusion Systems Inc. (H2O2) has been used in combination with investigations will explore: 1) histological other products (e.g., SLICE, Salmosan) as part analysis of cellular and tissue-level sub-lethal CO-FUNDED BY: New Brunswick Innovation of a sea lice integrated pest management effects; 2) additional dosages and exposure Foundation (NBIF) plan, but there are concerns regarding fish times; 3) the impact of using freshwater PROJECT LEAD: Duane Barker (HMSC) welfare when temperatures are high (>14°C) (e.g., bath treatment for amoebic gill PROJECT TEAM: Anne McCarthy, Chris Bridger, and fish are excessively stressed during disease, AGD); 4) the effect of various Rebecca Eldridge, Esther Keddie, Ellen Fanning treatment. One solution to minimize fish environmentally relevant temperatures; and (HMSC) stress during treatment is to increase the 5) sea lice removal efficacy. Initial results are COLLABORATORS: Mike Beattie (GIS Gas dissolved oxygen saturation (via the GIS Gas encouraging, with no ill-effects observed on Infusion Systems Inc.) Infusion System Transport Module) in the commercially-sized salmon exposed to CONTACT: [email protected] surrounding water, thereby creating a slight H2O2 dosages and exposure times that narcosis among the treated fish. reflect industry practices. WEBSITE: http://www.huntsmanmarine.ca/ CANADIAN AQUACULTURE R&D REVIEW 2017 SEA LICE 31

Developing a Non-Chemical Means to Effectively Remove All Forms of Sea Lice from Aquaculture Salmon Using Warm Water

An adult egg-bearing female (gravid) of the salmon sea lice (Lepeophtheirus salmonis) removed using a warm water shower from an adult salmon. Photo: Shawn Robinson (DFO)

he sea louse (Lepeophtheirus Specifically, the following results were found: engineers, healthcare professionals, and salmonis) remains a global challenge • The use of a warm water shower will farm staff. The results are being applied to Tfor salmon farming, with considerable remove over 95% of all attached mobile the next generation commercial prototype resources expanded to manage this pest. stages of the sea lice at temperatures that is currently being designed. Sea lice are becoming resistant to many over 30°C. This project supports the DFO objectives of the traditional treatment chemicals which of environmental performance and optimal • Mortality rates of fish going through the are also lethal to non-target organisms. fish health. treatment are close to 0% for healthy fish, Consequently, many non-chemical alternative but slightly higher for fish that are in poor treatments are being tested, including condition due to heavy infections. DATE: JUN. 2014–JUN. 2016 predators (cleaner-fish), traps (physiological • A small amount of surface mucus from the FUNDED BY: DFO–Aquaculture Collaborative or biological), and physical exclusion Research and Development Program (DFO–ACRDP) devices (nets, electrical fields). fish is removed during the process, but this A promising technique uses warm water is not significant. CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS) showers to remove all attached stages of • Lower salinities of the treatment water PROJECT LEAD: Shawn Robinson (DFO) sea lice and prevent the detached sea lice do not improve the removal efficiency. PROJECT TEAM: Steve Neil, Craig Smith (DFO); from being returned to the ocean. This Joel Halse (KCS) project aims to develop protocols for safe • A technique was developed to quickly and Keng Pee Ang (KCS) and effective showers to remove sea lice easily quantitatively measure the mucus COLLABORATORS: from Atlantic Salmon, and to understand layer on a fish without harming the animal. CONTACT: [email protected] why it works. Research results are expected Developing a new, environmentally benign WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ to provide the required information for treatment option for industry will significantly acrdp-pcrda/projects-projets/M-14-02-001-eng.html ongoing modification of the commercial increase the sustainability of the sector. The sea lice warm water shower device, as well research is being done in close hands-on as inform sea lice management strategies. collaboration with the industry’s design 32 SEA LICE CANADIAN AQUACULTURE R&D REVIEW 2017

An Investigation of the Relationship Between Environmental Parameters, Oceanographic Zones of Influence, and the Prevalence of Parasitic Copepods on Three-Spine Stickleback in Bay D’Espoir Newfoundland with Specific Reference to Salmonid Aquaculture Sites

ea lice infestation has increased This project supports the DFO objective of Further monitoring is necessary to track with farmed salmon expansion in optimal fish health. Specifically, the following the status of each parasite and continued SNewfoundland and Labrador’s Bay results were found: diligence on the part of industry will be D’Espoir and Fortune Bay. The gill louse • These bays can be divided in distinct required to successfully manage the (Ergacilus labracis) was the most abundant zones based on environmental conditions. parasites prominent in each region. sea lice species observed, but their impact • These zones are characterized by on farmed salmonids has not yet been distinct populations of sea lice. DATE: JUL. 2014–MAR. 2016 characterized. This study investigates the • Upper Bay D’Espoir is defined primarily FUNDED BY: DFO–Aquaculture Collaborative potential correlation between the distribution Research and Development Program (DFO–ACRDP) of sea lice on Three-Spine Stickleback and by the presence of the parasite Ergasilus farmed salmonids in the region. labracis and its relationship with CO-FUNDED BY: Cold Ocean Salmon Inc. The results of this research will help Three-Spine Stickleback. PROJECT LEAD: Harry Murray (DFO) provide information on the potential of • Upper Hermitage Bay region is defined PROJECT TEAM: Andry Ratsimandresy, wild non-salmonid fish species to act as sea by the presence of the parasite Alexandra Eaves, Sebastien Donnet, Dwight Drover, lice reservoirs (with the potential to re-infect Lepeophtheirus salmonis and its Sharon Kenny (DFO); Keng Pee Ang (Cold Ocean farmed fish), as well as a potential predictor relationship with farmed Atlantic Salmon. Salmon Inc.) of infestation levels in Bay Management COLLABORATORS: Cold Ocean Salmon Inc. Areas. The bays investigated in this study are • The ecological needs of these different defined by specific environmental conditions species likely act as partial biological CONTACT: [email protected] which can dictate how the sea lice community barriers to their successful movement WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ is partitioned. This study is one of the first to across zones. acrdp-pcrda/projects-projets/N-14-02-001-eng.html draw correlations between environmental conditions and sea lice ecology in the region.

Studies of Sea Lice Infection Levels on the Health of Juvenile Salmon in the Strait of Georgia and Adjacent Waters

o assess risk associated with sea lice mid-June. Caligus clemensi was the dominant DATE: APR. 2010–MAR. 2017 and microbe transfer between farmed species of sea lice present, but was in low FUNDED BY: DFO–Program for Aquaculture and wild salmon, we have undertaken abundance on juvenile salmon, Pacific Herring, Regulatory Research (DFO–PARR); T DFO–Aquaculture Collaborative Research and a detailed study on the: 1) migratory pathways and Three-spined Sticklebacks. There was no of wild salmon and the duration of their significant increase in the numbers of sea lice Development Program (DFO–ACRDP); residency in the vicinity of fish farms; on juvenile salmon in the vicinity of salmon Pacific Salmon Commission (PSC) 2) the prevalence of pathogens and diseases farms in the Discovery Islands. Infections with PROJECT LEADS: Stewart Johnson, within wild and farmed populations; and 3) the the Hematopoietic Necrosis Virus (IHNV) and Marc Trudel (DFO) overall physiological well-being and health the parasites Parvicapsula minibicornis and PROJECT TEAM: Chrys Neville, Kyle Garver, of wild populations as this impacts their Myxobulus articus have been seen in Simon Jones (DFO) susceptibility to infection. Using net-based samples collected in the lower Fraser River CONTACT: [email protected], surveys we have examined the duration of and throughout the Strait of Georgia. The [email protected] juvenile Fraser River Sockeye Salmon prevalence of infection of these agents is www.dfo-mpo.gc.ca/aquaculture/rp-pr/ residency within the Strait of Georgia, as highly variable among years and stock of WEBSITE: parr-prra/projects-projets/2010-P-02-eng.html well as in the vicinity of salmon farms in the origin. We have neither found Piscine Discovery Islands. We have found that the Orthoreovirus (PRV) nor Renibacterium majority of juvenile Fraser River Sockeye salmoninarum in any of the fish that Salmon pass through the Discovery Islands we tested. over a two to three week period in early to CANADIAN AQUACULTURE R&D REVIEW 2017 SEA LICE 33

Refining the Use of Warm Water Showers to Remove Sea Lice from Atlantic Salmon and Understanding the Fish Health Implications of the Technique

onsiderable effort is expended and also control the release of larvae and was found to be very effective at removing (via chemo-therapeutants and mobile parasitic stages within the farm which mobile stages of sea lice (over 90%) and was Canimal husbandry practices) to seem to contribute to the magnification of able to retain virtually all of the removed sea manage parasitic infections by the sea the infection cycles on the salmon leases lice, preventing them from being reintroduced louse, Lepeophtheirus salmonis, a globally for Southwest New Brunswick. into the water column near the salmon cages acknowledged challenge for salmon Over the last two years, a new technology and re-infecting the fish. This project will farmers. The parasite is gaining resistance to was introduced to salmon farming in the Bay refine and build on the results gathered from treatments and new approaches are urgently of Fundy in which salmon were exposed to previous research through investigations on needed. Recent research suggests that any a warm water shower. Through a series of the effect of fish health on the efficiency of technique must remove parasites from fish laboratory and field trials, this technology removal as well as the dynamics of the removal process itself. Adding a new, environmentally benign treatment option for industry will significantly increase the sustainability of the sector and reduce the substantial investment in management controls by the regulatory sector. The research will be done in close hands-on collaboration with the industry’s design engineers, healthcare professionals, and farm staff. The results will be immediately applied to the next generation commercial prototype currently being designed. This project supports the DFO objectives of environmental performance and optimal fish health.

DATE: JUL. 2016–JUN. 2018

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS)

PROJECT LEAD: Shawn Robinson (DFO)

PROJECT TEAM: Steve Neil, Craig G. Smith (DFO); Joel Halse (KCS)

COLLABORATORS: Keng Pee Ang (KCS); Duane Barker (HMSC)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/16-1-M-01-eng.html

Testing the efficiency of the lab-based model of the warm water shower in the field with industry partners in the Bay of Fundy. Photo: Shawn Robinson (DFO) 34 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH

Study of Genomic Diversity in Aeromonas Net Pen Liver Disease Project–Developing a Physiological Consequences of Piscine salmonicida, the Etiological Agent that Causes Fluorescent Antibody Test to Prove the Orthoreovirus (PRV) Infection of Atlantic and Furunculosis, to Establish its Resistome, Causative Agent Pacific Salmonids Epidemiological Markers, and Potential Treatments Improving the Survival, Health, Quality, and Food- Does Infection with Piscine Reovirus (PRV) Affect The Effect of Dietary Camelina Oil on the Health Safety of Post-Transported Tilapia and Barramundi How Salmon Respond to Challenge with Infectious of Salmon Hematopoietic Necrosis Virus (IHNV)? Piscine Reovirus (PRV): Characterisation, Atlantic Prophylactic Effect of Haslea ostrearia Culture Salmon Susceptibility, and Initial Survey in Farmed Addressing the Question of Sturgeon Nucleo- Supernatant Containing the Pigment Marennine and Wild Salmonids in Atlantic Canada Cytoplasmic Large DNA Virus (sNCLDV) Systematics Against the Pathogenic Bacteria Vibrio splendidus Salmon Gill Poxvirus-Like (SGPV-Like): Stage 1 Validation of Real-Time PCR (qPCR) in Bivalve Hatcheries Characterisation, Atlantic Salmon Susceptibility, and Assay for the Detection of Bonamia spp. Investigating Probiotic Bacteria and Their Initial Survey in Farmed and Wild Salmon Development and Diagnostic Validation of a Bacteriocins as Part of a Disease Management Description of Oceanographic Conditions within qPCR Assay to Detect Mikrocytos mackini and its Strategy in Salmon Aquaculture Hermitage Bay, Newfoundland, at Sites with and Application in Understanding the Transmission The Effects of Smolt Size on the Intensity of Kudoa without the Occurrence of an ISA Outbreak Risks and General Biology of the Pathogen thyrsites Infections in Atlantic Salmon Investigations into Ulcerative Skin Disease Agents, Effects of Pooling Animals on the Probability of Comparison of Field Isolates of Moritella viscosa: Moritella viscosa and Tenacibaculum spp. in Detection: MSX and ISAV Characterization and in Vivo Challenge Model Atlantic Salmon: Interactions and in Vivo Identification of Vectors of MSX to Support Development to Address Winter Ulcer Mitigation Challenge Development Introductions and Transfers Decisions Related to in Canada Cyprinid Herpes Virus 3 (CyHV-3) in Wild Common Inter-Provincial Movements of Mussels: Is Mussel Estimating the Potential for Waterborne Carp (Cyprinus carpio L.) in Manitoba, Canada Intra-Valvular Liquid a Vector for MSX Transmission? Transmission of Infectious Haematopoietic Necrosis Marine Reservoirs of Infectious Agents Associated Effect of Water Temperature on the Immune (IHN) Disease between Salmon Farms and Wild with Proliferative Gill Disorders in Farmed Salmon Response of American Lobster (Homarus Sockeye Salmon in the Discovery Islands, americanus) Experimentally Infected with British Columbia Pathogen Susceptibility of Sockeye Salmon– White Spot Syndrome Virus Phase 1: Infectious Salmon Anemia Virus (ISAV) Optimizing the Fish Health Reporting and Data and Salmon Alphavirus (SPDV or SAV) Developing a Genomics Tool (FIT-CHIP) for Management System In-Season Information on Salmon Health The Transfer Potential of Fish Pest and Screening of Cultured Atlantic Salmon for Pathogen from Farmed to Wild Salmon: Susceptibility of Sockeye Salmon to Viral Resistance and Susceptibility to Infection by Sea Stocking Density Effect Hemorrhagic Septicemia Virus Lice (Lepeoptheirus salmonis) and Renibacterium salmoninarum, the Causative Agent of Bacterial Reverse Transcription Quantitative Polymerase Epidemiology of Ulcer Disease in Salt Water Kidney Disease (BKD) Chain Reaction (RT-qPCR) Assays For Detection Atlantic Salmon of Spring Viremia of Carp Virus–Phases IV and V Microbial Impacts on Shellfish Aquaculture in Infectious Salmon Anemia Virus Susceptibility Diagnostic Validation Relationship to Ocean Acidification and Health Status of Wild Versus Farmed Atlantic Marine Reservoirs of Infectious Agents Associated Salmon: A Comparative Study Low Pathogenic Infectious Salmon Anemia Virus with Proliferative Gill Disorders in Farmed Salmon (ISAV) in Vivo: A Comparative Genomic Study Rapid Detection of Replicating Infectious Epidemiological Analysis and Modelling of Salmon Anemia Virus (ISAV) The Effects of Prior Exposure and Body Size on the Aquatic Pathogens Intensity of Kudoa thyrsites Infections in Farmed Disease and Parasite Resistance Genomics in a Atlantic Salmon Diagnostic Validation of Three Test Methods for Commercial Strain of North American Atlantic Salmon Detection of Cyprinid Herpesvirus 3 Development of Artificial Reference Material for Assessing IHNV and VHSV RT-qPCR Assays CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 35

Study of Genomic Diversity in Aeromonas salmonicida, the Prophylactic Effect of Etiological Agent that Causes Furunculosis, to Establish its Haslea ostrearia Culture Resistome, Epidemiological Markers, and Potential Treatments Supernatant Containing the Pigment Marennine Against he Aeromonas salmonicida bacterium Increased knowledge of the pathogen, is the infectious agent that causes A. salmonicida, will aid Canadian aquaculture the Pathogenic Bacteria Vibrio Tfurunculosis in salmonids (salmon, productivity while enabling fish farmers to: splendidus in Bivalve Hatcheries trout, Arctic Charr, etc.). Controlling this 1) make appropriate use of antibiotics during primary requisite in any shellfish disease, which is very harmful to the treatment; 2) better track the pathogen’s culture or farming operation is an aquaculture industry, can prove to be quite location; and 3) suggest alternatives to abundant, reliable, and inexpensive demanding and fruitless, mainly due to the antibiotics as treatment. Ultimately, our work A supply of juveniles. Hatchery-produced logistic constraints of the vaccination and the will offer an integrated approach to follow, seed is increasingly becoming the standard very frequent resistance of A. salmonicida to control, and treat A. salmonicida infections. raw material for aquaculture. However, several antibiotics. We are therefore studying repeated bacterial infections result in the genomic diversity of A. salmonicida to DATE: NOV. 2012–MAR. 2019 heavy mortalities, causing major losses and better understand its virulence and its FUNDED BY: Natural Sciences and Engineering great expenses for shellfish growers. This antibiotic resistome (all genes conferring Research Council (NSERC) project explores the possibility of using the resistance to antibiotics). Through supernatant of cultured diatoms (Haslea familiarization with this diversity, tools and CO-FUNDED BY: Ressources Aquatiques Québec (RAQ); Ministère de l’Agriculture, des Pêcheries et de ostrearia) containing marennine, a natural alternative treatments for preventing or curing l’Alimentation du Québec (MAPAQ) microalgal pigment, as an antimicrobial furunculosis can be created. In concrete terms, agent in bivalve hatcheries. The Blue we are developing a kit for quickly diagnosing PROJECT LEAD: Steve Charette (U Laval) Mussel (Mytilus edulis) and the Sea Scallop antibiotic resistance. We are also studying the PROJECT TEAM: Antony Vincent, (Placopecten magellanicus) were used as action of mobile DNA elements in the Valérie Paquet, Katherine Tanaka, Sabrina Attéré, model animals, and the pathogenic marine evolution, host adaptation, and geographic Alex Bernatchez, Mélanie Trudel, bacteria, Vibrio splendidus, was used to distribution of A. salmonicida, and their Jean-Guillaume Edmond-Rheault (U Laval) induce larval mortality. The hypothesis potential activation by various treatments, COLLABORATORS: Nicolas Derome, tested was that V. splendidus pathogenicity including the effect of certain essential oils, Michel Frenette, Sylvain Moineau (U Laval); in larval rearings can be controlled by with a view to developing a treatment. It is Andrée Lafaille (UdeM) using marennine-containing culture also our intent to verify the potential of CONTACT: [email protected] supernatants. The effect of three marennine bacteriophages (viruses that infect bacteria) WEBSITE: www.amibe.org concentrations was tested on a larval as a cure for furunculosis. It is a recurrent rearing over 20 days for M. edulis and disease, hard to control and, as such, all of 9 days for P. magellanicus. At a low dose these approaches must be considered. (0.1 mg/L), survival and physiological condition were both higher than in the control. In bacterial challenges, larvae were The Effect of Dietary Camelina Oil on the Health of Salmon exposed to V. splendidus for 72 hours, with or without marennine. The bacterial raditional salmon feeds use high By using Camelina oil to trigger gut challenge caused significant mortality levels of fishmeal and fish oil to meet inflammation in Chinook Salmon, results when compared to control, while the Tthe nutritional needs of the fish, but from this project will increase knowledge marennine-treated larvae showed a these ingredients face large fluctuations in and understanding of these effects in order significantly higher survival. The results price and availability. Lower-cost alternatives to develop better management practices show that marennine is an interesting have been investigated, including canola oil, surrounding disease impacts on cultured molecule for pathogen control in hatcheries soy oil, and poultry fat. Oil from the plant finfish species. as it is active at low concentrations and can species Camelina sativa is another promising significantly enhanced larval survival and option that is already able to replace fish oil START DATE: SEP. 2015–OCT. 2016 physiological condition. in diets for Atlantic Cod, Atlantic Salmon, FUNDED BY: DFO–Aquaculture Collaborative and Rainbow Trout with little or no reduction Research and Development Program (DFO–ACRDP) DATE: MAY 2013–FEB. 2016 in growth or feed efficiency. However, substitution of dietary fish oil with vegetable CO-FUNDED BY: Creative Salmon Co. Ltd. FUNDED BY: Natural Sciences and Engineering Research Council (NSERC) oils (such as Camelina oil) in fish feed may PROJECT LEAD: Ian Forster (DFO) elicit inflammatory changes due to the CO-FUNDED BY: Ressources Aquatiques PROJECT TEAM: Simon Jones (DFO); Québec (RAQ); Fermes Marines Inc. different fatty acid profiles. There are limited Marije Booman (UVic); Barb Cannon, data available on changes to the gut, and Tim Rundle (Creative Salmon Co. Ltd.); PROJECT LEAD: Réjean Tremblay no data for vegetable oil’s health effects Jack Grushcow (Linnaeus Plant Sciences Inc.); (UQAR–ISMER) Brad Hicks (Taplow Ventures, Ltd.) on Chinook Salmon. PROJECT TEAM: François Turcotte, This project seeks to examine the COLLABORATORS: Barb Cannon, Tim Rundle Bertrand Genard, Karine Lemarchand, influence of fish oil substitution by Camelina (Creative Salmon Co. Ltd.) Réjean Tremblay (UQAR–ISMER); Jean-Luc Mouget (U Maine); oil on susceptibility to intestinal inflammation CONTACT: [email protected] of Chinook Salmon under culture conditions. Jean-Sébastien Deschênes (UQAR) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Inflammation is energetically demanding and CONTACT: [email protected] acrdp-pcrda/projects-projets/15-2-P-03-eng.html stressful, thus influencing disease resistance. 36 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Investigating Probiotic Bacteria and Their Bacteriocins as Part Comparison of Field Isolates of of a Disease Management Strategy in Salmon Aquaculture Moritella viscosa: Characterization and in Vivo Challenge Model n salmon farms, diseases caused • No significant effect of the probiotic by bacterial infections are managed diets was found on the survival rate Development to Address Winter Oby minimizing the risk of exposure of salmon after exposure to the Ulcer Mitigation in Canada to pathogens, vaccination, and ensuring the pathogen Vibrio anguillarum. he bacteria Moritella viscosa is availability of sufficient high quality water • P. terrae survived in salmon intestines associated with cold-water ulcer and feed. There are concerns regarding the but did not colonize the gut. disease in farmed Atlantic Salmon at effectiveness and long term sustainability T sea. Over the past decade, skin ulcers have of using antibiotics to treat bacteria, so • The results suggested that the live also been noted in warmer water in Eastern to help further reduce antibiotic use, this P. terrae diet may cause changes in the Canada. The role of M. viscosa remains study focused on the therapeutic potential abundance and/or the diversity of the unclear due to its infrequent recovery from of probiotics in aquaculture. intestinal microbiota. This is currently summer ulcers, however, suspicion of its Probiotic bacteria can enhance the being examined in more detail. involvement persists. At the onset of this immune system of the fish, and can change • Increased knowledge of the effect of research, there was no vaccine for ulcer the composition of the intestinal microbiota, P. terrae on fish health will help determine disease based on Canadian isolates. Salmon which function in overall fish health. Probiotic its suitability as a therapeutic probiotic feed producers had limited tools to manage this bacteria may also secrete antimicrobial additive for salmon, which will benefit the disease, and though commercial vaccines compounds that kill other bacteria, including aquaculture industry. used in Europe existed, no information fish pathogens. This project used probiotic existed with regard to their efficacy bacteria and antimicrobials with activity against Canadian isolates. against common salmon pathogens, DATE: APR. 2014–JUN. 2015 For this project, Canadian field isolates and evaluated their application as feed FUNDED BY: DFO–Aquaculture Collaborative were collected and characterized by additives to improve fish health. Research and Development Program (DFO–ACRDP) establishing in vitro growth curves at This project supports the DFO objective CO-FUNDED BY: Mainstream Canada (Cermaq different temperatures. Differences in of optimal fish health. Canada Ltd.); Marine Harvest Canada Limited protein profiles and immunogenic proteins Specifically, this project found the Simon Jones (DFO) through gel electrophoresis and Western following results: PROJECT LEAD: blotting methods were examined. Ultimately, • Paenibacillus terrae and Paenibacillus PROJECT TEAM: Marije Booman, the characterization steps allowed for the polymyxa showed antimicrobial activity Steve Cho (DFO) development of an in vivo challenge model against five salmon pathogens. P. terrae Peter McKenzie (Mainstream COLLABORATORS: using an isolate of adequate virulence with was selected for further trials as it showed Canada (Cermaq Canada Ltd.)); Diane Morrison appropriate culturing and challenge exposure a stronger activity. (Marine Harvest Canada Limited) methodologies. When employed at 8°C, the • There was no evidence that the probiotic CONTACT: [email protected] model was successful in inducing lesions diets caused a reduction in feed attraction WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ consistent with clinical cold-water sores or appetite. acrdp-pcrda/projects-projets/P-14-01-003-eng.html found on sea cage Atlantic Salmon. In addition, the live challenge model also verified that a recent Atlantic isolate, originating from a summer ulcer field case, was virulent at 12°C The Effects of Smolt Size on the Intensity of Kudoa thyrsites and caused lesions in unvaccinated animals Infections in Atlantic Salmon at this warmer temperature. Diagnostically, M. viscosa can be recovered by bacteriology tlantic Salmon infected with Kudoa An understanding will be gained in the relative with a high success rate from all stages thyrsites do not exhibit clinical signs importance of fish size (smolts) in influencing of lesions present on challenged fish. The of disease. However, protease the development of K. thyrsites. Data obtained developed challenge model can be used A for evaluating and developing potential secretion from this parasite rapidly from the project will help inform K. thyrsites deteriorates affected muscle in the salmon management strategies. commercial vaccines and was shown to when the fillet is processed, resulting in be an excellent model for the study of ulcerative disease progression. economic loss for the grower. Earlier START DATE: OCT. 2015–JUN. 2017 research suggested the risk of K. thyrsites DFO–Aquaculture Collaborative FUNDED BY: DATE: AUG. 2014–MAR. 2016 was reduced when salmon were transferred Research and Development Program (DFO–ACRDP) to sea as larger smolts. This research FUNDED BY: DFO–Aquaculture Collaborative project involves a more robust test of the CO-FUNDED BY: Marine Harvest Canada Limited; Research and Development Program (DFO–ACRDP) Cermaq Canada Ltd. size hypothesis by conducting trials that CO-FUNDED BY: Cooke Aquaculture Inc.; examine how smolts of a range of size PROJECT LEAD: Simon Jones (DFO) Novartis Animal Health Canada Inc. classes respond to exposure to the Diane Morrison COLLABORATORS : PROJECT LEAD: Steven Leadbeater (DFO) K. thyrsites parasite. (Marine Harvest Canada Limited); The results of this project may help to Kathleen Frisch (Cermaq Canada Ltd.) PROJECT TEAM: Anthony Manning (RPC); Leighanne Hawkins (Cooke Aquaculture Inc.); improve the competitiveness of the Canadian CONTACT: [email protected] salmon aquaculture industry by assessing a Allison MacKinnon (Novartis Animal Health Canada Inc.) problem that greatly affects the marketability of WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/15-2-P-01-eng.html Atlantic Salmon produced in British Columbia. CONTACT: [email protected] WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/M-14-01-003-eng.html CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 37

Estimating the Potential for Waterborne Transmission of Infectious Optimizing the Fish Health Haematopoietic Necrosis (IHN) Disease between Salmon Farms and Reporting and Data Wild Sockeye Salmon in the Discovery Islands, British Columbia Management System

nfectious Haematopoietic Necrosis • The model simulations demonstrated that he Centre for Coastal Health (CCH) Virus (IHNV) is responsible for major using commercially available IHN vaccines is conducting a utility assessment Ieconomic losses in British Columbia greatly reduces the risk of transmission by T of the current BC Salmon Farmers salmon aquaculture operations. Viral lowering the overall number of susceptible Association (BCSFA) fish health database, transmission patterns and oceanographic fish. It also reduced the virus shedding which houses fish health data contributed circulation models for the Discovery Islands capacity of the vaccinated farm population by industry members from 2001-2016. The region provide estimates for the potential if it were to become infected with IHNV. results of the utility assessment will be used of IHNV outbreak and spread to To date, vaccinated farmed Atlantic Salmon to determine how the database can be used neighbouring farms. populations have not developed IHN to generate useful fish health information for This study quantified the transmission disease, while unvaccinated populations BCSFA members and other stakeholders, potential of IHN disease between farms and have been declared INHV positive. including the public. The CCH is also wild Sockeye Salmon. It also determined the developing a portfolio of fish health reports • With some modifications, the modelling capacity of vaccinated Atlantic Salmon and from data contained within the database. tools can be applied to other diseases IHNV-carrying Sockeye Salmon to transmit The overall objectives of this project are and to simulate transmission from farmed the virus to naïve hosts (ones who have to: 1) understand fish health information and to wild populations and vice versa. It never before been infected). accessibility needs, and to determine the will be possible to estimate the risk of Specifically this project found the uses and limitations of the BCSFA fish health infection for fish swimming in proximity following results: database; 2) design new fish health reports to diseased farms and assess the • Neighbouring naïve farms can become from the BCSFA database that assist farm relative effectiveness of disease and infected via waterborne transmissions. management and aid in communications; farm management practices such as Adherence to the stringent disease and 3) identify changes that could be made vaccination, quarantine, depopulation, management practices (such as to the database to expand its utility. and determining optimal locations for immediately quarantining an infected farm The current fish health database functions aquaculture sites. site) reduces transmission of infectious as a repository of data, from which limited doses to other farms. analysis can be conducted. The outcomes DATE: JUN. 2013–JUN. 2015 from this project should improve the FUNDED BY: DFO–Aquaculture Collaborative functionality of the database, and enable Research and Development Program (DFO–ACRDP) improved reporting of fish health events.

CO-FUNDED BY: Marine Harvest Canada Limited; Grieg Seafood BC Ltd.; Mainstream Canada (Cermaq DATE: APR. 2015–MAR. 2016 Canada Ltd.) FUNDED BY: BC Salmon Farmers Association

PROJECT LEAD: Kyle Garver (DFO) PROJECT LEAD: Carl Ribble (CCH)

PROJECT TEAM: Mike Foreman, Darren Tuele, PROJECT TEAM: Tyler Stitt, Theresa Burns, Ming Guo, Dario Stucchi, Peter Chandler (DFO) Stefan Iwasawa (CCH)

COLLABORATORS: Diane Morrison (Marine COLLABORATORS: Kyle Garver (DFO) Harvest Canada Limited); Barry Milligan (Grieg Seafood BC Ltd.); Peter McKenzie (Mainstream CONTACT: [email protected] Canada (Cermaq Canada Ltd.)) WEBSITE: www.centreforcoastalhealth.ca CONTACT: [email protected]

Aerial photo of the Discovery Islands in British WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Columbia. Photo: Kyle Garver (DFO) acrdp-pcrda/projects-projets/P-13-01-001-eng.html 38 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Screening of Cultured Atlantic Salmon for Resistance and Microbial Impacts on Shellfish Susceptibility to Infection by Sea Lice (Lepeoptheirus salmonis) Aquaculture in Relationship to and Renibacterium salmoninarum, the Causative Agent of Bacterial Ocean Acidification Kidney Disease (BKD) cean acidification (characterized hile vaccination is one approach DATE: SEP. 2015–JUN. 2018 by high dissolved carbon dioxide (pCO2) levels) can affect shellfish to impart disease resistance, FUNDED BY: DFO–Aquaculture Collaborative O there is significant variation Research and Development Program (DFO–ACRDP) fertilization rates, hatching success, larval W development, shell deformation, seed among Atlantic Salmon in terms of vaccine CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS) responsiveness. It is imperative to assess the production, and survival. However, it is not genetic stocks of salmon for their robustness PROJECT LEAD: Steven Leadbeater (DFO) clear whether high pCO2 levels alone are against disease. PROJECT TEAM: Keng Pee Ang (KCS); responsible for poor performance in some This research project will test family Jake Elliott, Frank Powell (Cooke Aquaculture Inc.); West Coast shellfish operations. While crosses of farmed salmon for resistance Anthony Manning (RPC) hatcheries have successfully controlled to Lepeoptheirus salmonis (sea lice) and COLLABORATORS: Keng Pee Ang (KCS) levels of pCO2 for larval and nursery production Renibacterium salmoninarum (the causative through the use of buffering systems, there CONTACT: [email protected] agent of Bacterial Kidney Disease, BKD). have continued to be high variations in batch Testing of more than one disease agent WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ to batch survival. This suggests that other (in this case, L. salmonis and R. salmoninarum) acrdp-pcrda/projects-projets/15-1-M-01-eng.html uncontrolled aspects of the seawater will help assess what resistance to one agent composition during high pCO2 events type may mean for resistance to another may be at play, most notably bacterial common agent. Information resulting from this compositions. Researchers are applying project will aid in broodstock selection with a metabarcoding approach to assess the the goal of enhancing resistance of farmed shifts in bacterial community composition fish to both sea lice and BKD infections. This that occur in sea water coming into a Pacific will serve to reduce losses to farmed fish and Northwest shellfish hatchery, post pCO2 improve the sustainability of the Canadian buffering, and throughout larval culture and aquaculture industry. comparing bacterial compositions in larvae and water between batches of good and poor performance. Ultimately, the project will identify

the degree to which initial pCO2 levels impact bacterial communities of cultured shellfish and identify whether certain bacterial species are more common in seed batches demonstrating poor survival. The knowledge obtained through this research will be useful in the development of a mitigation strategy to reduce the impact of ocean acidification on the shellfish industry Project team members collecting gravid female sea on Canada’s West Coast. Additionally, the lice on a harvest boat. Egg strings will be hatched to be used in exposure challenges. Clockwise from top identification of factors that contribute to left, Cindy Hawthorne, Steven Leadbeater (DFO), and farmed shellfish mortality may lead to the Melissa Holborn (U Guelph). Photo: DFO development of monitoring tools. This would ultimately assist the industry in enhancing environmental sustainability and economic viability of shellfish aquaculture. This project supports the DFO objective of optimal fish health.

DATE: JUN. 2014–JUN. 2017

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: Island Scallops Ltd.; Fanny Bay Oysters Ltd.

Post mortem examination of salmon from PROJECT LEAD: Kristi Miller-Saunders (DFO) Renibacterium salmoninarum exposure challenge. From foreground Melissa Holborn (U Guelph), Steven COLLABORATORS: Barb Bunting, Rob Saunders Leadbeater, and Ann Kinney (DFO). (Island Scallops Ltd.); Brian Yip (Fanny Bay Oysters Ltd.) Photo: Cindy Hawthorne (DFO) CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/P-14-02-001-eng.html Cindy Hawthorne (DFO) collecting samples from fish following a sea lice exposure challenge. Photo: Melissa Holborn (U Guelph) CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 39

Low Pathogenic Infectious Salmon Anemia Virus (ISAV) in Vivo: A Comparative Genomic Study

nfectious Salmon Anaemia (ISA) is a threat • Low virulence ISAV strains showed little to the salmon aquaculture industry. This to no fish mortalities, thus confirming Istudy investigated different Infectious observations in the field about their Salmon Anemia Virus (ISAV) strains with varying low pathogenicity. degrees of virulence (harmful effects). The virus • The high virulence ISAV strains produced was observed in vivo in Atlantic Salmon and between ~40% and 80% mortalities. the infectious potential of surviving/carrier fish The differences in observed mortality was evaluated. Tested fish showed significant using this strain shows the possibility differences in susceptibility. Specifically, this of selecting fish with specific genotypes project found the following results: that might be associated with favourable • Fish exposed to a low pathogenic ISAV traits such as disease resistance, which had detectable viral RNA in their tissues is beneficial for breeding programs and 18 months past exposure. the aquaculture industry. Necropsy of Atlantic Salmon to detect the presence of Infectious Salmon Anemia. Photo: (DFO) • Fish surviving a high pathogenic ISAV returned to a near negative state rapidly after the end of mortalities, but are also DATE: DEC. 2011–JUN. 2016 potential long term carriers of ISAV. FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP) • Low pathogenic ISAV can be transmitted horizontally and create a state similar to CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS) “herd immunity”, where a proportion of PROJECT LEAD: Nellie Gagné (DFO) fish were exposed and are thus naturally PROJECT TEAM: Francis Leblanc, immune to ISAV infections, thus reducing Steven Leadbeater, Mélanie Roy, the risk of an outbreak caused by a virulent Mark LaFlamme (DFO) ISAV. Still, those fish could continue to COLLABORATORS: Keng Pee Ang (KCS) transmit infections due to their long term carrier state. CONTACT: [email protected] WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Atlantic Salmon infected with Infectious Salmon acrdp-pcrda/projects-projets/MG-11-01-004-eng.html Anemia–operculum removed to show pale gills. Photo: Nellie Gagné (DFO)

The Effects of Prior Exposure and Body Size on the Intensity of Kudoa thyrsites Infections in Farmed Atlantic Salmon

he parasite Kudoa thyrsites is and wild-farmed interactions. Additionally, • No consistent relationship between fish the cause of soft-flesh syndrome in this information will allow for better finfish size and susceptibility to K. thrysites was Tpost-harvest Atlantic Salmon farmed cage siting and decision making and the observed. Further research will explore in British Columbia. Infected fish exhibit no development of tools to help further alternative methods of testing the size clinical signs of disease, but affected muscle manage this disease. hypothesis. deteriorates after processing depending on This project supports the DFO objective the severity of infection. The industry in BC is of optimal fish health. subject to substantial economic loss because Specifically, the following results DATE: JUN. 2013–JUN. 2015 of Kudoa-associated changes to fillet quality. were found: FUNDED BY: DFO–Aquaculture Collaborative Currently, there are no vaccines or approved • Ultraviolet irradiation of seawater Research and Development Program (DFO–ACRDP) strategies for treatment for K. thyrsites. significantly reduces risk of infection CO-FUNDED BY: Marine Harvest Canada Limited; This study investigated three management in Atlantic Salmon. UV-irradiation is not Mainstream Canada (Cermaq Canada Ltd.) options for K. thyrsites infections: practical in current net pen production PROJECT LEAD: Simon Jones (DFO) • The efficacy of ultraviolet irradiation systems, but would prove valuable in of seawater as a method to inactivate a closed-containment system. PROJECT TEAM: Diane Morrison (Marine Harvest Canada Limited); Peter McKenzie (Mainstream K. thrysites in the laboratory. • Previous infection with K. thyrsites reduces Canada (Cermaq Canada Ltd.)) • The influence of prior exposure to the risk of a severe subsequent infection. CONTACT: [email protected] K. thyrsites on parasite development This is consistent with observations made during subsequent exposure. by industry that initial rearing of smolts at a WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/P-13-01-002-eng.html low-risk site reduces the severity of infection • The influence of fish size on the following transfer to high-risk sites. It would prevalence and severity of the infection. be valuable to further investigate alternative The knowledge gained through this methods of simulating an earlier exposure. research project will lead to a greater understanding of disease transmission 40 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Net Pen Liver Disease Project–Developing a Fluorescent Antibody Test to Prove the Causative Agent

n incidence of Net Pen Liver Disease positive for NPLD; feed rate and mortality determining both the level of sensitivity of (NPLD) was diagnosed in a population remained normal. Water samples were the antibody and the strength of antibody A of adult Atlantic Salmon at a Grieg taken from the affected site and a site required for accurate testing. This study Seafood farm site in Nootka Sound, British located geographically distant from the provides proof of concept for the causative Columbia, June 25, 2014. Previous affected site both tested positive for agent for Net Pen Liver Disease. presentations of the disease at company sites the presence of MC. were limited to poor performers, three to Atlantic Salmon were experimentally DATE: AUG. 2016–MAR. 2017 four months post sea water entry. This new exposed to the microcystin toxin thought to FUNDED BY: Grieg Seafood BC Ltd. presentation was different as it affected well be the causative agent of the disease. Liver established grow out fish of approximately tissue samples were harvested over various PROJECT LEAD: Tim Hewison 3.6 kg. Based upon historical information, timescales and the tissues were sent to the (Grieg Seafood BC Ltd.) the disease had been associated with a Animal Health Centre in Abbotsford, BC for PROJECT TEAM: Matthew Patterson, hepatotoxic mycrocystin–LR (MC). Phase 1 histological processing and evaluation. Patrick Whittaker, Graeme Cooper of the project was to develop a fluorescent Samples with lesions attributed to toxin (Grieg Seafood BC Ltd.) antibody test to positively identify the exposure were used to develop a COLLABORATORS: Heindrich Snyman microcystin toxin present in affected fish. fluorescent antibody which was able to (BC Ministry of Agriculture) Histological surveys of smolts (500 g) detect the presence of the toxin. Future CONTACT: [email protected] growing within an adjacent inlet did not test work will optimize the test including

Histological pictures of normal liver tissue from an Atlantic Salmon stained by H&E (left) and stained by IHC–anti–Microcystin–LR (right). Photo: Heindrich Snyman (BC Ministry of Agriculture)

Histological pictures of liver tissue from an Atlantic Salmon exposed to the toxin Microcystin stained by H&E (left) and stained by IHC–anti-Microcystin-LR (right). Photo: Heindrich Snyman (BC Ministry of Agriculture) CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 41

Improving the Survival, Health, Quality, and Food-Safety of Post-Transported Tilapia and Barramundi

he market demand for live Tilapia (Oreochromis niloticus) and Barramundi T(Lates calcarifer) in Metro-Vancouver is steadily increasing. The stress and physical injury that occurs to fish during transport from USA to Langley, B.C. for acclimation and maintenance prior to retail sales have resulted in high fish mortalities and large economic losses to Viva Aquaculture and Seafood Distribution Ltd. (Viva). Developing viable and sustainable protocols to improve the survival, health, and quality of post-transported fish will benefit the company and retailers economically, and will also provide consumers with better food safety and quality fish products. It will Tilapia (Oreochromis niloticus). Photo: Jesse Ronquillo (UBC) also lead to new economic and employment opportunities locally, as well as be a source of diversified and nutritious seafood products for consumers in British Columbia. The University of British Columbia (UBC) and Viva have established a research collaboration to improve the survival and quality of fish transported from USA to Langley, BC. The specific objectives of this collaborative project were: 1) to increase the survival rate of adult Tilapia transported from Idaho, USA, by improving water quality through the manipulation of salinity, alkalinity, hardness, pH, temperature, and dissolved oxygen, and the elimination of toxic nitrogenous wastes; and 2) to improve the quality and food safety of fish during the Barramundi (Lates calcarifer). Photo: Jesse Ronquillo (UBC) post-transport recuperation and acclimation period using government-approved therapeutants and prophylactics, as well as indigenous microalgae, to eliminate potential Piscine Reovirus (PRV): Characterisation, Atlantic Salmon Susceptibility, microbial pathogens that might be present in and Initial Survey in Farmed and Wild Salmonids in Atlantic Canada the source water used to transport the fish from USA. The piscine reovirus or PRV is a or that factors other than the presence of PRV The results of this research project will recently identified virus that has been are required to cause the disease. lead to the development of post-transport Tlinked to Heart and Skeletal Muscle A survey and characterisation of the local protocols that are applicable in a commercial Inflammation (HSMI) in Atlantic Salmon. HSMI PRV are important in order to know the scale; are viable, efficient, safe, and was demonstrated as an infectious disease, current distribution of the virus on the East sustainable for the maintenance rearing of however, the role of PRV in HSMI continues Coast, and the potential for PRV to adult fish destined for the retail market and to be studied, as PRV is often found without compromise wild and farmed Atlantic human consumption in Canada. symptoms of HSMI. Although the host range Salmon. This research builds on other of this virus appears primarily restricted to studies about PRV. salmonids, it has been occasionally detected DATE: FEB. 2015–DEC. 2018 in a few non-salmonid species. DATE: APR. 2016–MAR. 2020 FUNDED BY: Viva Aquaculture and Seafood In 2015, a small sample of Atlantic Salmon Distribution Ltd. (Viva) FUNDED BY: DFO–Aquaculture Collaborative from different sources on the East Coast Research and Development Program (DFO–ACRDP) PROJECT LEAD: Jesse Ronquillo (UBC; Viva) was tested and the presence of PRV was detected for the first time. During genetic CO-FUNDED BY: Kelly Cove Salmon Ltd. PROJECT TEAM: Chang Lin Ye, Kai Chen (Viva) sequencing, it was discovered that the strain PROJECT LEAD: Nellie Gagné (DFO) COLLABORATORS: David Kitts, Siyun Wang (UBC) of virus found on the East Coast bore a PROJECT TEAM: Delphine Ditlecadet, CONTACT: [email protected] close resemblance to the West Coast strain Crystal Collette-Belliveau, Jean-René Arseneau, of PRV. As there are no reports of HSMI-like Francis Leblanc, Steven Leadbeater, WEBSITE: www.vivaseafood.com syndromes in salmon on the East coast, the Philip Byrne (DFO) significance of PRV detection is unclear. COLLABORATORS: Keng Pee Ang (KCS) HSMI was recently diagnosed for the first time on the Pacific Coast; given that no WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/index-eng.html cases of HSMI have been diagnosed on the Atlantic Coast, this suggests that PRV on the East Coast of Canada may not be harmful, 42 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Salmon Gill Poxvirus-Like (SGPV-Like): Characterisation, Atlantic Investigations into Ulcerative Salmon Susceptibility, and Initial Survey in Farmed and Wild Salmon Skin Disease Agents, Moritella viscosa and Tenacibaculum spp. oxviruses are large DNA viruses are anecdotal reports that salmon gill diseases of vertebrates and insects causing of unknown etiology were previously detected in Atlantic Salmon: Interactions Pdisease in many animal species. on the East Coast of Canada. A survey and and in Vivo Challenge In the spring of 2006, a new poxvirus, characterisation of the local SGPV are needed Development the salmon gill poxvirus (SGPV), was to determine the extent of the virus distribution discovered on the gills of salmon suffering on the East Coast, and its potential to his project examines two pathogens from proliferative gill disease (PGD) in compromise the health of salmon. of concern to the salmon farming freshwater in Northern Norway. Later the Tindustry, Moritella viscosa and Tenacibaculum spp., and their roles in same year, this virus was also found on DATE: APR. 2016–MAR. 2020 salmon gills at two marine sites in Western skin ulcerative diseases. The primary focus FUNDED BY: DFO–Aquaculture Collaborative is to study bacterial isolates of the genus Norway where all farms suffered high losses Research and Development Program (DFO–ACRDP) associated with the presence of this virus. Tenacibaculum which causes a condition Clinical disease symptoms are lethargy, CO-FUNDED BY: Kelly Cove Salmon Ltd. (KCS) called tenacibaculosis. Recent experience respiratory distress, and mortality. PROJECT LEAD: Nellie Gagné (DFO) in developing immersion challenge models In 2015, an unknown virus was isolated from with M. viscosa will be applied to produce a PROJECT TEAM: Delphine Ditlecadet, disease challenge model for tenacibaculosis tissues sampled from a suspected escaped Valérie Godbout, Jean-René Arseneau, farmed Atlantic Salmon caught in a river in Francis Leblanc, Steven Leadbeater, using a Canadian Tenacibaculum isolate. The New Brunswick. Using Next Generation Philip Byrne (DFO) secondary focus is to study in vitro interactions among M. viscosa and Tenacibaculum isolates Sequencing, researchers found that there COLLABORATORS: Keng Pee Ang (KCS) was an 80-90% similarity to Norwegian SGPV, and other bacteria associated with skin ulcers. hence “SGPV-like”. The significance of CONTACT: [email protected] The project focuses on isolates found on the SGPV-like detection is unclear, although there WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ East Coast of Canada in the context of the acrdp-pcrda/projects-projets/16-1-G-02-eng.html range of environmental temperatures at which pathogenicity is observed in clinical cases. The project develops a basis for reproducing tenacibaculosis in Atlantic Salmon within a Description of Oceanographic Conditions within Hermitage Bay, lab environment, and will provide a challenge Newfoundland, at Sites with and without the Occurrence of an model for testing diagnostic techniques for recovery of Tenacibaculum spp. during disease ISA Outbreak progression. This information could provide the aquaculture industry with improved nfectious Salmon Anemia (ISA) is an The occurrence of ISA events in the region techniques for early identification of potential important viral disease in the salmon could be the result of a combination of causative agents of skin diseases. In addition, farming industry. The ISA virus (ISAV) has various factors including the environmental I a reproducible live challenge model could also been found on wild fish and can be conditions reported in the present study as be used for testing efficacy of treatments transmitted to farmed fish through a number well as other processes (e.g., water and and vaccines. of vectors. ISA outbreaks have been reported particle, ISA virus, movement between sites). Results of the study can be used by in Newfoundland salmon farms between Due to the limitation of the data and cases the aquaculture industry for research on December 2012 and November 2013. (only four ISA occurrences), further research genetic selection for disease resistance, This study aimed to understand how is required should more cases of ISA events help the fish health community apply better environmental conditions (e.g., temperature, occur in the area. diagnostic methodology for confirming salinity, and dissolved oxygen) at farm sites This project supports the DFO priority of and treating ulcerative skin diseases, might favour ISA outbreaks. The link between optimal fish health. and improve understanding of naturally conditions and ISA outbreaks would help occurring diseases that impact wild and identify other areas at risk of potential START DATE: JUN. 2014–MAR. 2015 farmed salmon. outbreaks, assist the aquaculture industry FUNDED BY: DFO–Aquaculture Collaborative in mitigating the risk, and improve the Research and Development Program (DFO– ACRDP) sustainability of salmon farming. DATE: APR. 2016–JUN. 2018 CO-FUNDED BY: Cold Ocean Salmon Inc.; This project found that ISA outbreaks FUNDED BY: DFO–Aquaculture Collaborative Newfoundland Aquaculture Industry Association in Bay d’Espoir occurred in spring/early Research and Development Program (DFO–ACRDP) PROJECT LEAD: Andry Ratsimandresy (DFO) summer and late autumn and that the CO-FUNDED BY: Cooke Aquaculture Inc. general conditions at sites with ISA PROJECT TEAM: Sebastien Donnet, PROJECT LEAD: Steven Leadbeater (DFO) outbreaks were similar to those without. Steve Snook, Kevin Le Morzadec (DFO) At the sites with ISA occurrences, the PROJECT TEAM: Allison MacKinnon (Elanco Julia Bungay (Cold Ocean COLLABORATORS : Canada Ltd.); Anthony Manning (RPC) environmental conditions prior to outbreaks Salmon Inc.); Miranda Pryor (Newfoundland were different between the spring and Aquaculture Industry Association) COLLABORATORS: Leighanne Hawkins autumn cases. However, a common range (Cooke Aquaculture Inc.) CONTACT: [email protected] of temperature, salinity, and dissolved oxygen CONTACT: [email protected] concentration has been observed two weeks WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ prior to the ISA events. A clear link could not acrdp-pcrda/projects-projets/N-14-01-003-eng.html WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/16-1-M-02-eng.html be established between the environmental conditions, their variability, and the occurrence of ISA in the outer Bay d’Espoir area. CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 43

Cyprinid Herpes Virus 3 (CyHV-3) in Wild Common Carp (Cyprinus carpio L.) in Manitoba, Canada

ake Manitoba was the site of a 2008 Koi herpes virus disease (KHVD) outbreak Ldue to the presence of the aetiological agent CyHV-3 in resident Common Carp populations. This study was designed to test whether CyHV-3 is enzootic in Common Carp in Lake Winnipeg and Lake Manitoba. Test methods included quantitative PCR (qPCR), enzyme-linked immunosorbent assay (ELISA), duplex conventional PCR, and DNA sequence and phylogenetic analysis. Over the course of four years, carp from Netley Marsh (23.5%; n=17) and Delta Marsh (27.2%; n=235) tested positive for CyHV-3 by qPCR. Virus loads ranged from <5 to 2.9x104 equivalent plasmid copies per µg of DNA (average 7.2x102 copies/ µg of DNA ± 3.6x103). Sequence analysis of two variable regions of CyHV-3 DNA located between ORF29 and ORF31 (marker I) and near the 5’ end of ORF133 (marker II) identified a single virus genotype in Manitoba. The marker II allele contained the same novel 13 base pair deletion associated with isolates from East Asia and Southeast Asia. Aerial view of Clair Lake of Delta Marsh with the southern tip of Lake Manitoba evident in the foreground. Phylogenetic analysis using the thymidine Photo: Dale Wrubleski (Ducks Unlimited Canada) kinase DNA sequence showed that the Manitoba CyHV-3 isolate shared a closer relationship to isolates from the Asian lineage than with those from the European lineage. Marine Reservoirs of Infectious Agents Associated with Proliferative Analysis of the ELISA test results suggested Gill Disorders in Farmed Salmon that 66.9% (n=239) of the carp sampled were DATE: APR. 2016–JUN. 2018 CyHV-3 seropositive. Together, these results ill diseases and disorders among suggest that CyHV-3 is now enzootic in Atlantic Salmon raised in seawater net FUNDED BY: DFO–Aquaculture Collaborative Common Carp populations Gpens are an emergent and important Research and Development Program (DFO–ACRDP) cause of losses. There is a need to better residing in the two largest lakes in Manitoba. CO-FUNDED BY: BC Salmon Farmers Association This study examines subsequent changes describe the causes, distribution, and possible (BCSFA) control of gill diseases, which have been in carp population dynamics, reports on the PROJECT LEAD: Simon Jones (DFO) distribution, transmission and genetics of attributed to infections with parasites, bacteria, Gary Marty (BC Ministry of CyHV-3 and provides evidence of a carrier viruses, as well as exposure to algal blooms, PROJECT TEAM: Agriculture); Sonja Saksida, Marc Trudel (DFO); state in convalescent carp. The results provide jellyfish, and other non-infectious agents. This project focuses on associations of Diane Morrison, Sharon DeDominicis (Marine insight into CyHV-3 ecology and are useful to Harvest Canada Limited) regulators considering the use of CyHV-3 as viruses and parasites such as Paramoeba perurans and Desmozoon lepeophtherii with COLLABORATORS: Jeremy Dunn, a biocontrol mechanism for feral Common Joanne Liutkus, Rachel Saraga (BCSFA) Carp populations causing widespread water proliferative gill disorders (PGD) in order to habitat destruction. improve understanding of reservoirs of CONTACT: [email protected] infections. Infectious causal factors will be WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ studied in populations of wild and farmed DATE: JUL. 2009–FEB. 2017 acrdp-pcrda/projects-projets/16-1-P-02-eng.html salmon sharing common bodies of water FUNDED BY: DFO–Centre for Aquatic Animal to better understand the epidemiology of Health Research and Diagnostics (DFO–CAAHRD) proliferative gill disorders. PROJECT LEAD: Sharon Clouthier (DFO) This project will develop knowledge related to the distribution and causes of PROJECT TEAM: Tamara Schroeder, Melissa Lindsay (DFO): Darius Khambatta (U Manitoba) PGD in British Columbia, which will inform further development of farmed fish health COLLABORATORS: Dale Wrubleski, management strategies and improve the Bob Emery (Ducks Unlimited Canada); Eric Anderson (Ste. Anne, MB) understanding of the role of gill disorders in the conservation of wild salmon. CONTACT: [email protected] 44 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Pathogen Susceptibility of Sockeye Salmon–Phase 1: Infectious Salmon Anemia Virus (ISAV) and Salmon Alphavirus (SPDV or SAV)

n recent years, Sockeye Salmon populations DATE: JUL. 2014–JUN. 2018 in Canada have been experiencing declines FUNDED BY: DFO–Aquaculture Collaborative Iin productivity; of particular note is the Fraser Research and Development Program (DFO–ACRDP) River Sockeye Salmon stock. The reasons CO-FUNDED BY: Marine Harvest Canada Limited for this decline remain speculative but it is thought the susceptibility of Sockeye to PROJECT LEAD: Nellie Gagné (DFO) pathogens may be a key contributing factor. PROJECT TEAM: Francis Leblanc, Philip Byrne, However, the susceptibility of Sockeye Steven Leadbeater (DFO) Salmon to Infectious Salmon Anemia Virus COLLABORATORS: Diane Morrison (ISAV) or Salmon Alphavirus (SPDV or SAV) (Marine Harvest Canada Limited) has never been tested. These pathogens CONTACT: [email protected] are known to affect cultured Atlantic Salmon DFO’s Gulf Biocontainment Unit – Aquatic Animal Health Laboratory in Charlottetown, PEI. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ in various salmon producing regions and Photo: Nellie Gagné (DFO) countries (e.g., ISAV on the east coast of acrdp-pcrda/projects-projets/G-14-01-003-eng.html Canada, ISAV and SPDV in Norway). This project examines the disease resistance or susceptibility of Sockeye Salmon to pathogens known to affect Atlantic Salmon and the potential transmission of disease for a priority list of pathogens (ISAV, SPDV). Additionally, this project compares the viral response to ISAV at a cellular level (e.g., using gill tissue) between Sockeye and Atlantic Salmon, and their long-term immunity in response to exposure. This research is necessary in order to predict the consequences of an introduction or outbreak of these pathogens at an aquaculture site to the health and sustainability of Sockeye Salmon. The outcome of this work will allow Fisheries and Oceans Canada to improve disease surveillance, detection and management strategies, and help to minimize the impacts of pathogens on Immunostained ISAV infected cells. Photo: Mélanie Roy (DFO) cultured and wild fish.

The Transfer Potential of Fish Pest and Pathogen from Farmed to Wild Salmon: Stocking Density Effect

almon farms can become infected produce new experimental information: DATE: APR. 2014–MAR. 2017 with the Infectious Salmon Anemia 1) quantifying the transfer rates of ISAV from FUNDED BY: DFO–Program for Aquaculture SVirus (ISAV) from wild fish stocks. farmed Atlantic Salmon; 2) new information Regulatory Research (DFO–PARR) Should this occur, farms could potentially on the minimum exposure dose needed to PROJECT LEADS: Fred Page, become an amplified source of ISAV that infect naïve salmon; 3) virus shedding rate of Nellie Gagné (DFO) could, in turn, impact wild fish. ISAV is infected fish; 4) ultraviolet (UV) and survival transported and dispersed by water currents, of virus in water; as well as 5) models for PROJECT TEAM: Blythe Chang, Francis Leblanc, Steve Leadbeater, Kyle Garver (DFO) and the resulting plumes or ISAV zones may predicting the potential for waterborne contribute to the transfer of ISAV between transfer of ISAV from commercial salmon COLLABORATORS: Michael Beattie (NBDAAF); farms and to migrating wild salmon that farms under a range of stocking and farm Ian Gardner, Larry Hammel, Crawford Revie, Sophie St. Hilaire, Raphael Vanderstichel (UPEI-AVC) intersect the plumes. density scenarios. The information will help Fisheries and Oceans Canada (DFO) inform regulators, as well as the aquaculture CONTACT: [email protected], regulators in the Maritimes Region are and recreational salmon industries who are [email protected] particularly interested in the role of stocking working toward developing and implementing WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ density in pest and pathogen transfer from strategies and actions aimed at mitigating parr-prra/projects-projets/2014-m-01-eng.html existing farms to endangered wild Atlantic the potential for transfer of ISAV from farmed Salmon populations. This project aims to to wild salmon. CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 45

Reverse Transcription Marine Reservoirs of Infectious Agents Associated with Proliferative Quantitative Polymerase Chain Gill Disorders in Farmed Salmon Reaction (RT-qPCR) Assays For ill diseases contribute to economically 4) conduct laboratory transmission Detection of Spring Viremia of important production losses in Atlantic studies to identify and quantify Carp Virus–Phases IV and V GSalmon aquaculture. This project will (host and environmental) parameters Diagnostic Validation improve our understanding of reservoirs of surrounding transmission of the infections with infectious agents associated causative agent between candidate pring viremia of carp virus (SVCV) is with these disorders. One of these, amoebic reservoir species and Atlantic Salmon. the aetiological agent of an aquatic gill disease (AGD), was diagnosed for the first These objectives reflect the knowledge animal disease that is listed as time in BC in 2014 and the causative agent, S gaps concerning PGI and causal agents in notifiable to the World Organization for Animal Paramoeba perurans, has been detected in farmed salmon in BC. The key anticipated Health (OIE) and reportable to the Canadian BC. Another agent that is associated with project outcome will be knowledge related Food Inspection Agency (CFIA). In this proliferative gill inflammation (PGI) in Europe, to the distribution and causes of PGI in BC. This multi-year study, two RT-qPCR tests targeting the microsporidian, Desmozoon lepeophtherii, knowledge will inform further development of either the glycoprotein or nucleoprotein has been detected in BC and Washington farmed fish health management strategies. gene were designed and optimized for State. Several cases of a PGI-like condition their analytical performance. They were then were reported in farmed salmon in BC in 2015. evaluated along with the virus isolation by cell This project capitalizes on an opportunity to DATE: APR. 2016–MAR. 2018 culture test in a diagnostic validation study benefit from a unique set of samples; juvenile FUNDED BY: DFO–Program for Aquaculture to assess their fitness as diagnostic tools for salmon collected by industry as part of their Regulatory Research (DFO–PARR) detection of SVCV. Test performance metrics sea lice certification program. Specifically, PROJECT LEAD: Simon Jones (DFO) of diagnostic precision were repeatability these samples will be examined for evidence and reproducibility. Sensitivity and specificity PROJECT TEAM: Anne-Marie Flores, of their involvement as reservoirs of infection Sonja Saksida (DFO) were measured to assess diagnostic accuracy. with agents associated with proliferative gill Estimates of test accuracy, in the absence of a disorders in farmed salmon. COLLABORATORS: Diane Morrison, gold standard reference test, were generated Sharon DeDominicis (Marine Harvest Canada Limited); The objectives of this project are to: Marc Trudel (DFO) using latent class models. Test samples 1) determine distribution of P. perurans originated from domesticated koi that were and D. lepeophtherii in wild Pacific CONTACT: [email protected] either virus free or experimentally infected Salmon and salmon lice collected WEBSITE: http://www.dfo-mpo.gc.ca/aquaculture/ with the virus. Two tissues, kidney and brain, in proximity to marine netpens; parr-prra/index-eng.html were evaluated for their relative suitability as target tissues for the RT-qPCR assays. Four 2) describe the occurrence of proliferative laboratories in Canada participated in the gill lesions in wild fish; precision study. Estimates of test precision 3) characterize the genomic sequence and accuracy are being evaluated in the of BC variants of P. perurans and final two phases of the project. The results D. lepeophtherii; and will determine if any of the three tests are suitable diagnostic tools for detection of SVCV. Epidemiological Analysis and Modelling of Aquatic Pathogens Canada is a member of the OIE and the World Trade Organization and as such is ne of the big questions concerning this project will: 1) gather and assemble a obligated, for trade purposes, to implement disease processes of aquatic comprehensive dataset of fish health analyses OIE standards for disease diagnosis. The OIE pathogens is what factors influence and salmon population metrics across multiple has SVC on its list of notifiable diseases and O pathogen prevalence in wild and cultured river systems; 2) examine and compare in Canada it is currently designated as a CFIA fish populations. The prevalence and intensity annual pathogen prevalence among wild reportable disease. The diagnostic tools of pathogens can vary annually within and sockeye populations from multiple river developed in this project will be used by between fish stocks, yet the drivers behind systems; and 3) explore host, pathogen member laboratories of the National Aquatic such annual fluctuations remain unresolved. and environmental factors for potential Animal Health Laboratory System to help Some fish populations can be free of virus correlates with pathogen variability in Canada meet its obligations to protect the one year, yet be greater than 80% positive wild sockeye populations. health of wild and cultured aquatic animals in subsequent years. The occurrence of within the country and globally. such dramatic “on and off periods” begs DATE: APR. 2016–MAR. 2018 the questions “Why now?” and “Why was FUNDED BY: DFO–Program for Aquaculture APR. 2013–MAR. 2018 DATE: there an absence of virus in previous years?” Regulatory Research (DFO–PARR) FUNDED BY: DFO–Centre for Aquatic Animal To better understand variations in aquatic PROJECT LEAD: Kyle Garver (DFO) Health Research and Diagnostics (DFO–CAAHRD) pathogen prevalence in wild and farmed populations, this project will use PROJECT TEAM: Christine MacWilliams (DFO) Sharon Clouthier (DFO) PROJECT LEAD: epidemiological analytical approaches to COLLABORATORS: Carl Ribble (Centre for Tamara Schroeder, PROJECT TEAM: study the patterns of aquatic pathogens in Coastal Health Society) Shaorong Li, Crystal Collette-Belliveau, Jason Allen, wild and cultured fish populations with the [email protected] Melissa Lindsay, Sandra Aldous, Philip Byrne (DFO) goal of identifying the factors that influence CONTACT: COLLABORATORS: Carol McClure (AquaEpi the occurrence of pathogens and disease. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Research); Eric Anderson (Ste. Anne, MB) To help understand the main drivers of parr-prra/projects-projets/2016-P-02-eng.html CONTACT: [email protected] pathogen epidemiology in aquatic systems, 46 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Diagnostic Validation of Three Test Methods for Detection Does Infection with Piscine of Cyprinid Herpesvirus 3 Reovirus (PRV) Affect How Salmon Respond to Challenge yprinid herpesvirus 3 (CyHV-3) is the for VI/qPCR were 90% for DSe and 88% for aetiological agent of koi herpes virus DSp. Collectively, the results show that with Infectious Hematopoietic Cdisease (KHVD) in Common Carp the CyHV-3 qPCR test is a suitable tool for Necrosis Virus (IHNV)? (Cyprinus carpio L.) and Koi. The disease surveillance, presumptive diagnosis, and iscine reovirus (PRV) is a virus common is notifiable to the World Organization for certification of individuals or populations in wild and farmed salmon in BC and Animal Health (OIE). Three tests [quantitative as CyHV-3 free. likely establishes long term infections polymerase chain reaction (qPCR), Canada is a member of the OIE and the P in its host. It is inevitable that mixed infections conventional PCR (cPCR), and virus isolation World Trade Organization and as such is of PRV and known pathogens will occur. One by cell culture (VI)] were validated obligated, for trade purposes, to implement pathogen that is in the same geographical to assess their fitness as diagnostic tools for OIE standards for disease diagnosis. The OIE area with PRV is the infectious hematopoietic detection of CyHV-3. Test performance metrics has KHVD on its list of notifiable diseases and necrosis virus (IHNV) which occurs naturally in of diagnostic accuracy were sensitivity (DSe) in Canada it is designated as reportable to Pacific Northwest waters. With the appropriate and specificity (DSp). Repeatability and the Canadian Food Inspection Agency. The virus strain, host condition, and environmental reproducibility were measured to assess diagnostic tools developed in this project for parameters, IHNV can cause an acute disease diagnostic precision. Estimates of test accuracy, detection of CyHV-3 will be used by member (IHN) in all five species of Pacific salmon, in the absence of a gold standard reference laboratories of the National Aquatic Animal Atlantic Salmon, and Rainbow Trout. test, were generated using latent class models. Health Laboratory System (NAAHLS) to help This project seeks to examine the The test samples originated from wild Canada meet its obligations to protect the consequences of viral co-infections of PRV Common Carp naturally exposed to CyHV-3 health of wild and cultured aquatic animals and IHNV in Sockeye Salmon. The study will or domesticated Koi, either virus-free or within the country and globally. address how Sockeye Salmon hosts, infected experimentally infected with the virus. Three with viruses with no or low pathogenic effect, laboratories in Canada participated in the DATE: JUL. 2009–NOV. 2016 respond to challenge with other viruses. precision study. Moderate to high repeatability FUNDED BY: DFO–Centre for Aquatic Animal Challenge trials will be used to examine IHN (81% to 99%) and reproducibility (72% to 97%) Health Research and Diagnostics (DFO–CAAHRD) disease progression in naïve (never before were observed for the qPCR and cPCR tests. infected) and PRV-infected Sockeye Salmon. The lack of agreement observed between PROJECT LEAD: Sharon Clouthier (DFO) This challenge trial will determine if there some of the PCR test pair results was attributed PROJECT TEAM: Tamara Schroeder, are differences between groups in morbidity to cross contamination of samples with Megan Desai, Laura Hawley, Sunita Khatkar, associated with IHNV challenge, and to CyHV-3 nucleic acid. Accuracy estimates for Melissa Lindsay, Geoff Lowe, Jon Richard (DFO) generate biological samples for gene and the PCR tests were 99% for DSe and 93% for COLLABORATORS: Carol McClure (AquaEpi microRNA expression studies. This research DSp. Poor precision was observed for the virus Research); Eric Anderson (Ste. Anne, MB) will help to determine what, if any, additional isolation test (4% to 95%). Accuracy estimates CONTACT: [email protected] risk is posed to wild and/or farmed fish due to changes in their ability to respond to exposure to IHNV, thereby contributing to the knowledge base important for the Physiological Consequences of Piscine Orthoreovirus (PRV) Infection sustainable management of the salmon of Atlantic and Pacific Salmonids aquaculture industry.

iscine Orthoreovirus (PRV) commonly This research builds on other studies DATE: APR. 2014–MAR. 2017 occurs in healthy salmon which are about PRV. The outcome of this study will asymptomatic of heart and skeletal provide a better understanding of whether FUNDED BY: DFO–Program for Aquaculture P Regulatory Research (DFO–PARR) muscle inflammation (HSMI) disease. The PRV infections are associated with capacity of PRV to establish long-term physiological consequences. Results of the PROJECT LEADS: Stewart Johnson, infections and the potential association study will inform Fisheries and Oceans Kyle Garver (DFO) with the HSMI disease in fish has raised Canada management strategies for PRV. PROJECT TEAM: Jon Richards, concerns towards its ability to impact Julia Bradshaw (DFO) salmon physiology and overall fish health. DATE: AUG. 2016–JUN. 2018 COLLABORATORS: Matthew Rise (MUN); As such, the role of PRV in HSMI continues Rune Adnreassen (Oslo and Akershus University FUNDED BY: DFO–Aquaculture Collaborative to be studied. Research and Development Program (DFO–ACRDP) College of Applied Sciences) This project aims to determine if PRV CONTACT: [email protected], infections have physiological consequences CO-FUNDED BY: BC Salmon Farmers Association (BCSFA) [email protected] and whether the virus can directly impact http://www.dfo-mpo.gc.ca/science/rp-pr/ salmon health. This laboratory study PROJECT LEAD: Kyle Garver (DFO) WEBSITE: parr-prra/projects-projets/2014-P-13-eng.html addresses these questions by evaluating the PROJECT TEAM: Mark Polinski (NSERC); cardiorespiratory performance (swimming Anthony Farrell, Colin Brauner (UBC) ability) of PRV-infected Atlantic and Sockeye COLLABORATORS: Jeremy Dunn (BCSFA) Salmon in comparison to uninfected controls. Oxygen binding potential and maximum CONTACT: [email protected] oxygen consumption will be measured WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ and compared between infected and acrdp-pcrda/index-eng.html non-infected individuals. CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 47

Addressing the Question of Sturgeon Nucleo-Cytoplasmic Large DNA Virus (sNCLDV) Systematics

turgeon nucleo-cytoplasmic major capsid protein sequence of five The study has been designed so that the large DNA viruses (NCLDV) are sNCLDVs suggested that the taxa formed a phylogeny outcomes would be taxonomically Sepitheliotropic viruses associated monophyletic group outside of the Iridoviridae informative to the International Committee with mortality in nine sturgeon species in family. NV genome sequence has been on Taxonomy of Viruses. The results of this North America and Europe. White Sturgeon determined for three non-overlapping contigs research may impact how WSIV and, by iridovirus (WSIV), a member of this group, with an overall length of 288.4 kb. A set extension, other sNCLDVs are regulated causes a disease that is reportable to the of 10 orthologous genes present in the by the CFIA and by regulators of national Canadian Food Inspection Agency (CFIA). genomes of all NCLDVs are being used to aquatic animal health programs in Europe When the virus was originally described in the build a series of phylogenetic trees for each and the United States. 1990’s, it was classified as a member of the gene and to construct a consensus tree. A Iridoviridae family based on its morphological total of 40 taxa representing genera from DATE: JAN. 2012–JUN. 2017 characteristics. In 2009, Namao virus (NV) was six virus families have been chosen. The FUNDED BY: DFO–Centre for Aquatic Animal discovered in populations of moribund lake sequences for each gene will be aligned Health Research and Diagnostics (DFO–CAAHRD) sturgeon in Manitoba, Canada and found to and the evolutionary relationship of NV with be genetically related to WSIV. This study was other NCLDVs will be examined using multiple CO-FUNDED BY: Manitoba Hydro undertaken to investigate the evolutionary phylogenetic software packages including PROJECT LEAD: Sharon Clouthier (DFO) relationship of NV to other NCLDVs. The goal coalescent analyses with the BEAST suite of COLLABORATORS: Rachel Breyta, Gael Kurath was to resolve the systematics of NV within programs and maximum likelihood analyses (US Geological Survey–Western Fisheries Research the proposed order Megavirales given that using MEGA. Center); Eric Anderson (Ste. Anne, MB) our initial phylogenetic analyses with the CONTACT: [email protected]

Stage 1 Validation of Real-Time PCR (qPCR) Assay for the Detection of Bonamia spp.

ssays for this pathogen vary in 1) A sybr-green based qPCR (based DATE: APR. 2016–MAR. 2017 their ability to detect one or both on the work of Hill et al., 2010 and 2014), FUNDED BY: DFO–Centre for Aquatic Animal Aof pathogens regulated by the capable of distinguishing between Bonamia Health Research and Diagnostics (DFO–CAAHRD) Canadian Food Inspection Agency (CFIA); spp. using melt-curve analysis, has been PROJECT LEADS: Cathryn Abbott, Bonamia ostreae and Bonamia exitiosa. The validated to OIE stage 1 requirements. Geoff Lowe (DFO) objectives of this project are: 1) to complete a 2) An artificial internal positive control (IPC) World Organization for Animal Health (OIE) has been created that is distinguishable from CONTACT: [email protected] stage 1 validation (determine the operating both ‘wild-type’ infections and demonstrates range, analytical specificity and sensitivity, the same reaction kinetics as natural repeatability and characterization of inhibition) infections of both B. ostreae and B. exitiosa. for a modified version of a previously 3) An existing conventional PCR confirmatory published real-time PCR (qPCR) assay assay (based on the work of Cochennec capable of detecting both of these et al., 2000) was optimized and tested on pathogens; 2) the design and characterization B. ostreae, B. exitiosa and the IPC and of an artificial internal positive control was able to distinguish between the two (G-block) for use with the assay; and 3) the pathogens but did not amplify the IPC (this verification of a previously published is by design to prevent false ‘detected’ conventional, PCR based, confirmatory results). However, it should be noted that assay which, along with Sanger based DNA the confirmatory assay was found to be sequencing, distinguishes between these less sensitive than the screening assay. species. The results of this validation and control development will be described in a validation dossier prepared for the National Aquatic Animal Health Program (NAAHP). 48 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Development and Diagnostic Validation of a qPCR Assay to Detect Identification of Vectors of Mikrocytos mackini and its Application in Understanding the MSX to Support Introductions Transmission Risks and General Biology of the Pathogen and Transfers Decisions Related to Inter-Provincial Movements of his project will finalize the validation Further investigation revealed limited process and produce a manuscript environmental stability of M. mackini, as most Mussels: Is Mussel Intra-Valvular Tand validation dossier for the recently material became non-infectious after a period Liquid a Vector for MSX developed qPCR diagnostic assay intended of 24 h in seawater. Mapping of infections Transmission? for routine shellfish screening. The validated within host tissues revealed that exposure to qPCR assay provided field data for the project M. mackini of naïve oysters in an aquatic ultinucleated sphere “X” (MSX) is an described below and publication of the data environment demonstrated gill associated infectious disease that causes heavy and a validation dossier is in progress. Once parasites within one day following exposure. Mmortalities in American Oysters completed, this will provide the international These results indicate that in natural environs, (Crassostrea virginica) although it does aquatic animal health community with a fully M. mackini may be shed into the water by not affect human health. The transfer of live validated and characterized assay for the infected oysters but the limited environmental shellfish, such as mussels, are regulated detection of this important shellfish pathogen. stability of the parasite likely restricts its spread under Section 56 of the Fisheries (General) The second part of this project will use the causing focal infection dynamics within a Regulations and are reviewed on a case by qPCR described above to: 1) determine the host population. case basis by the DFO Introductions and environmental stability of Mikrocytos mackini; Transfer Committees (ITC) of the receiving Province. Prior DFO analysis of mussels 2) assess the ability and practicality for DATE: APR. 2016–MAR. 2017 environmental diagnostic screening; 3) map collected from heavily infected MSX positive FUNDED BY: DFO–Centre for Aquatic Animal areas of the Bras d’Or Lakes, and from MSX M. mackini infections within host tissues so as Health Research and Diagnostics (DFO–CAAHRD) to better understand routes of transmission positive areas outside of the Lakes, had not that can be used to identify/manage disease PROJECT LEADS: Cathryn Abbott, detected MSX in the soft tissues/intra-valvular Mark Polinski (DFO) outbreaks; and 4) lead to a publication and liquid. In the absence of information, epifauna dissemination of these findings that will aid PROJECT TEAM: Gary Meyer, Geoff Lowe, on mussel lines was considered potentially in Canadian and international management Eliah Kim (DFO) positive for MSX and mitigation was of M. mackini (and likely, by extension, other CONTACT: [email protected] recommended by the ITCs. In this project, related parasites). targeted sampling of wild mussels and In this project we expanded the utility of this epifauna in an area with MSX infected wild assay to detect M. mackini from environmental oysters resulted in the detection of MSX by samples and demonstrated that M. mackini Real Time Polymerase Chain Reaction (qPCR) was shed into culture water from infected but the disease was not visually detected oysters following experimental injection. histologically. These results support industry concerns that although mussels are not believed to be a host of MSX, a life stage Effects of Pooling Animals on the Probability of Detection: of the parasite may be present in the MSX and ISAV intra-valvular fluid of the mussels or the intermediate host may be found within the lthough pooling of animals is not or five negative animals, for DNA extraction associated epifauna. Therefore, based currently used in the National methods (with MSX as a pathogen) and RNA on the results of this project, continued AAquatic Animal Health Laboratory extraction methods (ISAV pathogen); and mitigation to reduce the risk of the System (NAAHLS), it is often discussed, as it 2) in practice, the data produced in this inadvertent spread of MSX should be has the advantage of processing multiple project should be transferable directly to considered during risk assessments of animals at once. This can greatly reduce the other assays where pooling is desired. industry activities. processing time and increase the throughput Knowing the impact of pooling, clients will of a laboratory. By pooling two animals, one be able to decide if the decline in sensitivity is DATE: APR. 2013–MAR. 2015 doubles the throughput, and pooling more worth the trade-off, based on their reason for FUNDED BY: DFO–Program for Aquaculture than two animals is possible. However, there testing and the current disease prevalence. Regulatory Research (DFO–PARR) is a trade-off to pooling; when only one PROJECT LEAD: Mary Stephenson (DFO) animal is infected, and the animal is infected DATE: APR. 2015–MAR. 2016 at a level near the limit of detection, the PROJECT TEAM: Nellie Gagné, DFO–Centre for Aquatic Animal FUNDED BY: Marie-Line Cournoyer (DFO) dilution effect of the pooling process Health Research and Diagnostics (DFO–CAAHRD) reduces the probability of detection. This COLLABORATORS: Andrew Bagnall (NSDFA) reduction in diagnostic sensitivity needs to PROJECT LEAD: Nellie Gagné (DFO) CONTACT: [email protected] be carefully evaluated at the bench level. PROJECT TEAM: Francis Leblanc, This project will provide: 1) a set of Crystal Collette-Belliveau, Valérie Godbout (DFO) WEBSITE: http://www.dfo-mpo.gc.ca/aquaculture/ parr-prra/index-eng.html data (probability of detection) of a single CONTACT: [email protected] positive animal in a pool of two, three, four, CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 49

Effect of Water Temperature on the Immune Response of American Lobster (Homarus americanus) Experimentally Infected with White Spot Syndrome Virus

ater temperature influences but not at 10°C and 15°C. This suggests a model has been useful for enabling a many basic biological functions decrease in clinical condition of WSSV infected comparative examination of the lobster Wof the American Lobster (Homarus H. americanus at warmer temperatures. immune response to different kinds of americanus); yet, little is known about the Light and transmission electron microscopy pathogens (bacterial, protozoal, and viral). effects of temperature on the immune were used to elucidate tissue changes in response of H. americanus. White Spot the host and confirmed the antennal gland DATE: SEP. 2014–SEP. 2016 Syndrome Virus (WSSV) is one of the as a key target tissue for WSSV. A lobster FUNDED BY: University of Prince Edward largest impediments to shrimp aquaculture specific microarray identified 717 significantly Island–Atlantic Veterinary College (UPEI–AVC) worldwide; there are no reports of naturally differentially expressed genes between occurring WSSV infection in lobster. The infected and control animals at the various CO-FUNDED BY: Federal Student Work Experience Program (FSWEP); DFO–Centre for World Organization for Animal Health (OIE) temperatures. Microarray results highlighted Aquatic Animal Health Research and Diagnostics lists WSSV as a notifiable disease with the differential expression of various temperature DFO–CAAHRD) potential to infect all crustacean decapods. and immune-related genes. At 20°C, This project utilized a previously established H. americanus appears to produce a PROJECT LEADS: Philip Byrne (DFO); Spencer Greenwood (UPEI-AVC) infection challenge model to investigate the targeted immune response to injected WSSV. constraints imposed by a range of temperatures This project used a range of diagnostic PROJECT TEAM: Louise-Marie Roux (10°C, 15°C, 17.5°C, and 20°C) on the clinical, tools and experimental temperatures in (UPEI–AVC; DFO) tissue, and molecular immune responses of order to broaden our understanding of COLLABORATORS: Fraser Clark, Mark Fast, American Lobster experimentally infected how temperature influences host pathogen Glenda Wright, Dorota Wadowsk (UPEI-AVC) with WSSV. The infection model utilized interactions in the economically important CONTACT: [email protected] intramuscular injection inoculation of WSSV. crustacean species, the American Lobster This study found that WSSV amplification was (H. americanus). Although this project and associated with increased water temperatures other work done involving DFO and the (17°C and 20°C). Significant differences in total Lobster Science Centre collaboration haemocyte concentration between infected suggests that WSSV is not a threat to lobster, and control H. americanus at 17.5°C and 20°C, the use of the WSSV experimental infection

Louise-Marie Roux in the Gulf Biocontainment Unit (DFO) facility collecting a haemolymph sample from American Lobster (Homarus americanus). Photo: Phil Byrne (DFO)

Transmission Electron Micrograph of WSSV infected Homarus americanus antennal gland, two-weeks post inoculation at 17.5°C. Hypertrophic nuclei showing marginated host chromatin Heat map with hierarchical clustering of significantly differentially expressed genes identified between infected and containing WSSV viral particles within the nucleus Homarus americanus, two-week post inoculation at 10°C, 15°C, 17.5°C, and 20°C. identified by an electron dense nucleocapsid center and a trilaminar envelope. Virions ranged from 200-350 nm Red represents a threefold or greater decrease in gene expression whereas green represents a threefold or in length. Nucleus, apical microvilli, mitochondria (mt), greater increase in gene expression. and vacuole (va) labelled. 50 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Developing a Genomics Tool (FIT-CHIP) for In-Season Information on Salmon Health

limate change, genetic challenges, A text search will be conducted on The ultimate aim is to discover biomarkers ecological inconsistency, and disease abstracts or full papers for key protein predictive of the presence of specific stressors Ccan all be listed as potential stressors (biomarkers) word associations that have or conditions and to translate these into a tool to wild populations of salmon on Canada’s been linked to a given stressor. The project (FIT-CHIP) that can inexpensively and rapidly West Coast. This project plans to address the will then continue by data-mining the huge identify the presence of multiple stressors or physical states of wild populations through the in-house microarray databases produced conditions in a group of fish at once. development of a series of “salmon FIT-CHIPs” from dozens of studies that encompass more which will be used as a predictor of salmon than 4,900 microarrays and three salmon DATE: APR. 2014–MAR. 2017 condition. The system offers extreme flexibility, species (Chinook, Sockeye, and Coho) as FUNDED BY: DFO–Genomics Research and allowing biological markers to be easily well as over 60 stress-challenge microarray Development Initiative (DFO–GRDI) customized for stress or other conditional studies conducted across a broad range of states to different life-history stages, salmon species available in public databases. CO-FUNDED BY: Genome BC environments, and in different tissues. This Tests will be developed that should work PROJECT LEAD: Kristi Miller-Saunders (DFO) tool will provide the first in-season method to across all three species, and preferentially PROJECT TEAM: Norma Ginther, Tobi Ming, incorporate information on salmon condition across Atlantic Salmon and Rainbow Trout as Colin Wallace (DFO) into fisheries management decision making. well. In all, it is anticipated that five FIT-CHIPS Paul Pavlidis (UBC) will be developed through this project. COLLABORATORS: CONTACT: [email protected]

Susceptibility of Sockeye Salmon to Viral Hemorrhagic Epidemiology of Ulcer Disease Septicemia Virus in Salt Water Atlantic Salmon

s part of the sustainable management This study is investigating what effect, orking with the aquaculture of finfish aquaculture, there are if any, the occurrence of VHSV in farmed industry, we investigated A regulatory requirements that Atlantic Salmon may have on wild Sockeye Wthe pattern of ulcer disease are designed to minimize the transfer of Salmon. Previous studies have shown that occurrence in salt water Atlantic Salmon. pathogens from farmed finfish to wild fish. Coho, Chinook, and Chum Salmon are We also conducted a laboratory trial to: However, finfish cultured in ocean net natural hosts of VHSV, but less is known 1) evaluate waterborne transmission pens have the potential to be exposed to about the susceptibility of Sockeye Salmon of Moritella viscosa; 2) describe the naturally occurring pathogens and to transfer to VHSV. To address this knowledge gap, progression of the disease within a pathogens to wild fish. Viral Hemorrhagic this project will determine the susceptibility population; and 3) determine if skin ulcers Septicemia Virus (VHSV) has been identified of Sockeye Salmon smolts to VHSV using could be induced from exposure to the in farmed Atlantic Salmon, Salmo salar, laboratory exposure studies. The results of extracellular toxins produced by M. viscosa. in British Columbia. VHSV is a naturally this study will contribute to the development To effectively treat ulcer disease, our occurring pathogen in British Columbia and of adaptive management strategies in British research suggests that treatments would is a cause of serious disease in wild Pacific Columbia aimed at minimizing the transfer of likely have to be applied very early in the Herring, Clupea pallasii. Pacific Herring are pathogens between farmed Atlantic Salmon disease process because fish stop eating known to enter and remain in Atlantic Salmon and wild Pacific salmon. once they develop the ulcer. Further, it is net pens, thereby increasing the potential for relatively difficult to transmit M. viscosa the virus to be transferred to farmed Atlantic DATE: APR. 2015–MAR. 2017 via water, and the lesion associated with Salmon. Although the occurrence of VHSV M. viscosa can be induced by exposure FUNDED BY: DFO–Program for Aquaculture in farmed salmon is rarely accompanied with Regulatory Research (DFO–PARR) to the extracellular toxins of M. viscosa. significant disease and mortality, experimental The latter may explain why fish have a studies have shown that the VHS virus can PROJECT LEAD: Kyle Garver (DFO) strong tissue response when exposed persist in the tissue of farmed Atlantic Salmon. PROJECT TEAM: Paul Hershberger (United to M. viscosa, but bacteria are difficult This causes concern for potential host States Geological Survey); Jon Richard (DFO) to identify on histological evaluation. adaptation and viral spillback to fish sharing CONTACT: [email protected] the marine environment. DATE: MAR. 2015–OCT. 2016 WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2015-P-01-eng.html FUNDED BY: Natural Sciences and Engineering Research Council (NSERC)

PROJECT LEAD: Sophie St-Hilaire (UPEI)

PROJECT TEAM: Brett MacKinnon (UPEI)

CONTACT: [email protected] CANADIAN AQUACULTURE R&D REVIEW 2017 FISH HEALTH 51

Infectious Salmon Anemia Virus Susceptibility and Health Status of Wild Versus Farmed Atlantic Salmon: A Comparative Study

here are concerns about the potential for interaction between farmed and Twild Atlantic Salmon in areas where they coexist. The Committee on the Status of Endangered Wildlife in Canada (COSEWIC) has designated wild Atlantic Salmon populations in Atlantic Canada as threatened or endangered. While the health status and disease resistance of farmed Atlantic Salmon is well documented, the information for wild Atlantic Salmon is less abundant. For example, Infectious Salmon Anemia Virus (ISAV) remains a recurrent problem for cultured salmon in Atlantic Canada, with outbreaks detected in Nova Scotia and Newfoundland since 2012. There are knowledge gaps regarding the prevalence of this virus in wild populations as well as the potential transmission between wild and cultured stocks. As such, the aim of this project is to use in vivo disease challenges and next generation sequencing technologies to compare the susceptibility of wild Atlantic Salmon stocks (Saint John River, Inner Bay of Fundy, Miramichi, Margaree River Atlantic Salmon from the Miramichi River. Photo: Steven Leadbeater (DFO) stocks) and cultured stocks (Saint John River origin) to diseases such as ISAV and others. This study will examine genetic differences and measure immune responses, which could Rapid Detection of Replicating Infectious Salmon Anemia potentially explain any observed differences in Virus (ISAV) susceptibility of wild and cultured salmon to ISAV. It will also provide a general assessment n the diagnostic lab, the traditional methods particles, whether they are “alive” or “dead”. of the health status of wild stocks. The evolution of virus detection are based on the culture A few days later, a second PCR is done on rate of ISAV will be examined by looking at full or isolation of the virus. These methods are the cell culture. If the number of viral particles ISAV sequences in tissue of farmed and wild I quite sensitive, and very reliable. They are has increased, this can only be explained by Atlantic Salmon sampled throughout the course based on the observation that many viruses the fact that viruses were replicating. of the in vivo challenges. This project will will replicate in cells, and eventually rupture The combined use of two PCR reactions address the knowledge gap regarding the the cells. These burst cells can be seen under along with the infection of cell lines can identify susceptibility of wild Atlantic Salmon compared a microscope, and thus burst cells equal the replicating virus an average of 25 days faster to farmed Atlantic Salmon to ISAV. presence of a replicating (live) virus. However, than using the current virus isolation protocol this observation can take many days. alone. Currently, the detection of the ISA virus DATE: APR. 2014–MAR. 2017 Emerging, modern methods are based on can take over 40 days. Given the immense FUNDED BY: DFO–Program for Aquaculture the detection of virus nucleic acids through impact this virus can have on cultured fish, this Regulatory Research (DFO–PARR) amplification by polymerase chain reaction is simply too long. Our protocol can provide (PCR). These methods are ultra-sensitive, and decision makers with a much earlier warning. PROJECT LEAD: Nellie Gagné (DFO) very fast, but they are only indirectly detecting PROJECT TEAM: Francis LeBlanc, virus. In other words, it is debatable whether DATE: MAR. 2014–MAR. 2016 Mark Laflamme, Gérald Chaput, what is being detected can be associated to Steven Leadbeater, John Whitelaw (DFO) FUNDED BY: DFO–Centre for Aquatic Animal a replicating virus or just “dead” viruses. Health Research and Diagnostics (DFO–CAAHRD) COLLABORATORS: Mark Hambrook (Miramichi Our rapid detection protocol uses both Salmon Association) traditional and modern techniques in a “best PROJECT LEAD: Mark LaFlamme (DFO) CONTACT: [email protected] of both worlds” approach. Test material is put PROJECT TEAM: Jean-René Arseneau (DFO) in culture with cells, and a molecular PCR WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ CONTACT: [email protected] parr-prra/projects-projets/2014-G-11-eng.html assay is done at that time as well. The PCR assays determines the presence of all viral 52 FISH HEALTH CANADIAN AQUACULTURE R&D REVIEW 2017

Disease and Parasite Resistance Genomics in a Commercial Strain of North American Atlantic Salmon

acterial kidney disease (BKD), DATE: APR. 2014–MAR. 2018 infectious salmon anemia (ISA), and FUNDED BY: Genome Canada salmon lice (Lepeophtheirus salmonis) B CO-FUNDED BY: Cooke Aquaculture Inc.; are economically important pathogens to Genome Atlantic; Ontario Genomics; Atlantic Salmon aquaculture on the east DFO–Aquaculture Collaborative Research and coast of Canada. This research project aims Development Program (DFO–ACRDP); to detect molecular markers (SNPs) that Industrial Research Assistance Program (NRC); are associated with pre-existing genetic Atlantic Canada Opportunities Agency (ACOA) resistance in the Saint John River strain of PROJECT LEAD: Elizabeth Boulding (U Guelph) Atlantic Salmon for BKD, ISA, and L. salmonis. PROJECT TEAM: Melissa Holborn, Smolts from the breeding nucleus are Larry Schaeffer, Jane Tosh (U Guelph); exposed to each pathogen in separate Keng Pee Ang, Jake Elliott, Frank Powell (Cooke challenges to quantify the level of resistance Aquaculture Inc.); Steven Leadbeater (DFO); of siblings of potential broodstock. Challenged Brian Glebe (Genome Atlantic) fish were genotyped using a custom COLLABORATORS: Norwegian University 50,000 (50K) SNP chip designed specifically of Life Sciences for North American Atlantic Salmon. Analysis CONTACT: [email protected] of the SNP genotypes, resistance phenotypes, and the pedigree information can identify SNP WEBSITE: https://www.uoguelph.ca/ib/boulding markers associated with resistance to these pathogens. These markers can then be incorporated into breeding programs to Melissa Holborn (U Guelph) counting salmon lice on develop Atlantic Salmon lines that have Atlantic Salmon smolts. Photo: Cindy Hawthorne (DFO) an increased resistance to BKD, ISA, and L. salmonis.

Development of Artificial Reference Material for Assessing IHNV and VHSV RT-qPCR Assays

eference materials, commonly Results from small scale pilot studies characterization procedures for IHNV referred to as controls or standards, proved promising for proficiency testing of and VHSV bulk reference materials. Rare substances with extremely well IHNV and VHSV RT-qPCR in that the artificial Artificial positive controls are now an defined properties used in the assessment of transcripts mimicked the biological target, integral component of laboratory quality diagnostic methods. The Virology laboratory could be accurately quantified, and present management systems and a requirement at DFO’s Pacific Biological Station (PBS) has extremely low false positive risk due to of ISO 17025. By using APCs, the NAAHLS been experimenting with various control its unique identity. However, uncertainties eliminates the risk of false positives. materials that can be used to accurately remain concerning the large scale production Reference materials are distributed assess the validity of IHNV and VHSV of such panels. In particular, what are the among the NAAHLS as needed to molecular diagnostic tests. The Virology best manufacturing methods suitable for ensure compliance with national laboratory has initiated the use of an artificial generating large batches of homogenous protocols and certify testing competency. positive control (APC) for monitoring test aliquots? What preservation methods are performance. APCs have an advantage over best for large batches of proficiency panels DATE: SEP. 2014–MAR. 2015 traditional controls due to the fact that they and what is the expected stability? The aims FUNDED BY: DFO–Centre for Aquatic Animal are unrelated to the target pathogen and of this study was threefold: 1) establish Health Research and Diagnostics (DFO–CAAHRD) can be easily differentiated from each procedures for generating large batches other, facilitating the identification of of IHNV and VHSV artificial reference PROJECT LEAD: Kyle Garver (DFO) false positive results. material for use as standards, controls, and PROJECT TEAM: Laura Hawley, proficiency testing; 2) identify optimal storage Jon Richard (DFO) practices and best before dates of bulk CONTACT: [email protected] reference materials; and 3) develop CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 53 ENVIRONMENTAL INTERACTIONS

Developing Hard-Bottom Indicators from BC Study on the Sublethal Effects of the Sea Lice Evaluation of Benthic Far-Field and Site Recovery Archived Benthic Video Surveys Associated with Pesticide Salmosan® (Azamethiphos) on Adult Male Effects from Aquaculture within the Letang Inlet, Aquaculture Activities Lobsters (Homarus americanus) New Brunswick Development and Validation of a Biomonitoring Tool to Study of The Effects of Emamectin Benzoate or Freshwater Finfish Cage Aquaculture: Development Assess the Impacts of Salmon Aquaculture on Marine Ivermectin in Sediments on Juvenile American of Sediment Biogeochemical Indicators for Regulation Benthic Communities Using Metabarcoding Lobsters (Homarus americanus) of Freshwater Cage Aquaculture Assessment of Biodiversity and Functional Changes Validation of the Robustness of the Ecosystem Effect of Wind Forcing on the Oceanographic in Benthic Communities Associated with Aquaculture Carrying Capacity Models Being Developed for Conditions of Fortune Bay–Belle Bay: Identification Activities in Newfoundland St. Peters Bay of Changes in Water Physical Conditions and Ocean Currents, and Development of a Forecasting Tool Biochemical Oxygen Demanding (BOD) Dispersion Effects of Organophosphate Aquaculture Pesticide Model Validation Standards Azamethiphos on Stage I and Stage IV American Robustness of Alternative Benthic Impact Indicators: Lobster (Homarus americanus) Larvae Quantification of Spatial and Temporal Variability Exploration of Methodologies for Environmental Effects of Alternative Methods, and Application at Monitoring of Finfish Aquaculture Sites in Sandy Paving the Way for Salmon-Kelp Integrated Aquaculture Sites Across Different Farm and Bottom Environments with Natural Disturbances: Aquaculture in British Columbia: A Foundational Field Environmental Conditions Shelburne, Nova Scotia Trial Assessing Sugar Kelp (Saccharina latissima) Growth and Quality at BC Salmon Farms The Development of a Robust Methodology for Analysing the Impact of Freshwater Aquaculture on Sulfide Probe Calibration and Sediment Sampling Wild Fish Populations using DIDSON Technology The Effects of Sublethal Aquaculture Chemotherapeutant Exposure on Pink Salmon Sustainable Development of Offshore Bivalve Culture Oceanographic Study of the South Coast of in the Magdalen Islands: Production Capacity and Newfoundland (Baie D’Espoir and Fortune Bay) The Lethal, Physiological, and Behavioural Effects Interactions with Commercial Fisheries of Anti-Sea Lice Therapeutants in Non-Target Temporal Assessment of Organic Loading from Crustacean Species Developing the Benthic Component of Integrated Finfish Aquaculture on Hard Bottom Communities Multi-Trophic Aquaculture to Reduce the Impact of in Newfoundland The Effects of Anti-Sea Lice Chemotherapeutants Organic Nutrients from Fish Farms and Evolving on Sensitive Life Stages of Non-Target Crustacean Alternative Detection Methods for Performance Standard Operating Procedures Species in Combination with Environmental Stressors Indicators of the Oxic State of Bottom Sediments: Impact of Finfish Farms in Eastern Canada on Indicator Inter-Calibration and Thresholds The Environmental Fate and Non-Target Effects of Sea Lobster Distribution and Condition Lice Drugs and Pesticides Used in Salmon Aquaculture Feeding Pressure of Styela clava on Plankton Influence of Eastern Oyster (Crassostrea virginica) (Phytoplankton and Zooplankton) in Malpeque Bay, Structure and Function of the Salmon Farm “Reef” Aquaculture Overwintering on Eelgrass Prince Edward Island Identifying Critical Ecological Thresholds for Tunicate (Zostera marina) Can Hard Clams (Mercenaria mercenaria) Increase Infestations on Mussel Farms Evaluating the Effectiveness of Fallowing as a the Rate of Eelgrass (Zostera marina) Recovery in Co-Culture of Blue Mussel (Mytilus edulis) and Sugar Mitigation Tool at Predominantly Hard-Bottom Areas Impacted by Oyster Aquaculture? Kelp (Saccharina latissima): Exploring the Potential Aquaculture Sites in Newfoundland Recovery of Neural Function in Lobsters Following Effect of Seaweeds in Deterring the Effect of Duck Characterization of Pesticide Post-Deposit Sub-Lethal Salmosan® Exposure Predation on Mussels, Cascapedia Bay (Quebec) Exposure Zones Impact of Global Warming on Aquaculture Production Tracking in Situ Real-Time Responses of Ocean Effects of Cage Aquaculture on Freshwater in the Magdalen Islands: Blue Mussel, Atlantic Deep- Acidification Effects on Biological Organisms and Benthic Communities Sea Scallop, and American Oyster Influence on Plankton Diversity Comparing the Impact of Bottom and Suspended Study of the Effects on Adult American Lobsters Building an Understanding of the Mobile Wild-Farmed Oyster Culture on Bay-Scale Food Resources (Homarus americanus) Consuming Clams Exposed Interactions Occurring around Aquaculture Farms in (Foxley/Trout River, PEI) to Atlantic Salmon Sea Lice Therapeutants the Bay of Fundy Meta-Analysis of Freshwater Aquaculture Provincial Water Quality Monitoring Data 54 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Developing Hard-Bottom Indicators from BC Archived Benthic Video Development and Validation Surveys Associated with Aquaculture Activities of a Biomonitoring Tool to Assess the Impacts of Salmon nder the Aquaculture Activities Polychaete Complexes–OPC). Potential Regulations (AAR), and previously additional indicators that may warrant Aquaculture on Marine Uas a condition of licence, the Pacific further investigation include Giant Plumose Benthic Communities aquaculture industry has been required Anenomes as this species is tolerant to Using Metabarcoding to conduct seafloor monitoring of finfish organic enrichment and was observed as aquaculture sites. This project is applying co-occurring with Beggiatoa-like bacteria almon aquaculture causes organic a standard analytical approach to a large and OPCs at some farm sites, as well as enrichment of surrounding sediments collection of archived video surveys collected taxa that tend to occur at the transition Swhich has been shown to affect during a seven-year period (2004-2010) and between oxic states could be investigated biodiversity and biomass of benthic fauna over a wide range of coastal settings (fjordic (e.g., sea urchins, brittle stars, tube concomitant with sediment chemical changes. inlets, Broughton Archipelago, the west coast dwelling anemones, shrimp, etc.). Environmental impact assessments have of Vancouver Island, Johnstone Strait, etc.). generally focused on changes in macro-­ invertebrate communities based on manual The measurement of redox and sulphide from DATE: SEP. 2011–MAR. 2016 sediment samples is an accepted standard taxonomic identification, requiring a substantial FUNDED BY: DFO–Program for Aquaculture investment of labour and taxonomic expertise, practice for soft-bottom seabeds. However, Regulatory Research (DFO–PARR) past monitoring practices involving grab or have relied on abiotic proxies like sulfide sampling for redox and sulfide analyses PROJECT LEAD: Terri Sutherland (DFO) measurements with uncertain accuracy and have presented challenges at aquaculture PROJECT TEAM: Andrea Bartsch, reliability. Next-generation DNA sequencing sites located over hard bottom substrates. Michelle Ou (DFO) methods offer an efficient and reliable lower-cost alternative by cataloging the Section 10(2) of the AAR allows for visual COLLABORATORS: Bernie Taekema, Kerra Shaw, monitoring instead of sediment grab samples March Klaver, Jon Chamberlain (DFO) diversity and abundance of benthic if it is not possible to obtain benthic substrate communities through metabarcoding of CONTACT: [email protected] samples. Results supported the use of environmental DNA (eDNA). This approach primary and secondary indicator species WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ has been successful at identifying (Beggiatoa spp. and Opportunistic parr-prra/projects-projets/2011-P-13-eng.html environmental impacts associated with farming activities in Scotland, New Zealand, and Norway. This project will develop a new eDNA-based metabarcoding tool for assessing the impacts of farming on benthic metazoan and foraminiferan communities in BC and will validate its use for ongoing biomonitoring through comparisons with existing methods. This research will also address existing knowledge gaps about the impacts of salmon farming on benthic metazoans and foram communities and enrich DNA barcode databases for these taxa from BC inshore waters.

DATE: APR. 2016–MAR. 2019

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Cathryn Abbott (DFO)

PROJECT TEAM: Xiaoping He, Terri Sutherland, Kristi Miller-Saunders, Kara Aschenbrenner, Scott Gilmore, Kerra Shaw (DFO)

COLLABORATORS: Jan Pawlowski (U Geneva)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2016-P-06-eng.html

Sponge and Squat Lobster community on a rock cliff in British Columbia. Photo: Terri Sutherland (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 55

Assessment of Biodiversity and Functional Changes in Benthic Exploration of Methodologies for Communities Associated with Aquaculture Activities in Newfoundland Environmental Effects Monitoring of Finfish Aquaculture Sites in his research project builds on the work the natural benthic communities will be being completed through two ongoing completed. Third, species richness and Sandy Bottom Environments Tprojects funded through the Program for biodiversity data will be analyzed through with Natural Disturbances: Aquaculture Regulatory Research (DFO–PARR) linear mixed-effects (LME) models to examine Shelburne, Nova Scotia (Evaluating the efficacy of the fallowing period whether species richness on the seafloor as a mitigation tool at predominantly hard-­ beneath and adjacent to aquaculture sites he project will contribute to a better bottom aquaculture sites in Newfoundland; could be explained using available explanatory understanding of the limitations of and Development of a framework to assess variables (visual indicators, distance, depth, Texisting methods and models and the scale of year to year impacts from finfish and fallow period when applicable) treated provide the basis for better informed and aquaculture on hard ocean substrates in NL). as categorical variables. more extensive proposals focused on the This ongoing work allowed us to identify The results of this research will be used development of survey, monitoring, and knowledge gaps and highlight the importance to provide science advice to Fisheries and modelling approaches for this type of of linking biochemical oxygen demanding Oceans Canada’s Aquaculture Management environment. Existing and proposed finfish (BOD) fluxes with observed benthic indicators. Directorate on the impact of finfish aquaculture sites in parts of Nova Scotia are located First, a better knowledge of the natural over hard bottom substrates. on sandy bottoms that experience annual communities needs to be established through disturbance by near-bottom currents generated by offshore waves. Current completion of a reference database of the DATE: MAY 2016–MAR. 2018 natural Newfoundland benthic communities regulatory benthic sampling techniques FUNDED BY: DFO–Program for Aquaculture (cores and light weight grabs) and models in areas of aquaculture development. This Regulatory Research (DFO–PARR) will allow a better documentation of the (DEPOMOD) used to monitor and predict biodiversity hot spots and/or the areas with PROJECT LEAD: Dounia Hamoutene (DFO) deposition and benthic degradation have low natural richness. Through a paired/ PROJECT TEAM: Flora Salvo, Sebastien Donnet, been developed for muddy bottoms. The matched comparison of baseline data Shannon Cross, Dwight Drover, Fred Page (DFO) suitability of these approaches for sandy disturbed environments is scientifically (reference) with biodiversity data post-­ COLLABORATORS: Suzanne Dufour (MUN); aquaculture (gathered through the two Roberty Sweeney (SIMCorp Marine Environmental) uncertain and has been questioned by other PARR initiatives), an evaluation of the Nova Scotia provincial authorities and CONTACT: [email protected] 50% biodiversity loss areas and associated aquaculture consultants. indicator presence will be attempted. Second, WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ The purpose of this project was to a characterization of the functional change of parr-prra/projects-projets/2016-NL-09-eng.html test several benthic sampling approaches, including: grab samplers; Remotely Operated Vehicle (ROV) camera systems; acoustic echo sounder; side-scan sonar systems; monitoring Biochemical Oxygen Demanding (BOD) Dispersion Model the water current and wave environment during the anticipated disturbance season Validation Standards (autumn-winter); analyze sediments (and acoustic signals, where appropriate) for bottom he Aquaculture Activity Regulations The results of this project will help provide type, grain size, organic matter, and sulphide (AAR) under the Fisheries Act came information about the acceptability of models content; gather water column density profile into effect in July 2015. The AAR for the AAR requirements. T information (i.e., Conductivity, Temperature, Monitoring Standard for finfish marine and Depth (CTD) profiles); and run DEPOMOD aquaculture requires that dispersal models DATE: APR. 2016–MAR. 2018 scenarios for currents representing the be used to predict contours of the rate FUNDED BY: DFO–Program for Aquaculture disturbance season. As an extension to the of bottom deposited biochemical oxygen Regulatory Research (DFO–PARR) project, sediment re-suspension and transport demanding matter released from fish farms models will be incorporated into the FVCOM and that some form of an aquaculture waste PROJECT LEAD: Fred Page (DFO) and fine-tuned for the Shelburne area. The final deposition model be used to make these PROJECT TEAM: Adam Drozdowski, analyses for this project are currently underway. predictions. The model to be used is not Brent Law, Blythe Chang, Susan Haigh, specified. In an effort to help farm owners, Stacey Paul, Andry Ratsimandresy (DFO) DATE: APR. 2012–APR. 2016 operators, and regulators become sufficiently CONTACT: [email protected] aware of models that are potentially available, FUNDED BY: DFO–Program for Aquaculture WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Regulatory Research (DFO–PARR) along with an identification and evaluation of parr-prra/projects-projets/2016-M-13-eng.html how they function, what they assume, and PROJECT LEAD: Fred Page (DFO) what the accuracy of their predictions are, Blythe Chang, Mark McLean, this project will: 1) review existing literature PROJECT TEAM: Ed Parker, Randy Losier, Brent Law, on aquaculture deposition models, and Herb Vandermuelen, Sara Scouten (DFO) their applicability to AAR requirements and potential model audit criteria; 2) conduct COLLABORATORS: Mike Szemerda (Cooke Aquaculture Inc.) an initial evaluation of a new release of the popular DEPOMOD model; and 3) review CONTACT: [email protected] resuspension model literature and refine WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ some recent aquaculture motivated parr-prra/projects-projets/2012-M-06-eng.html resuspension models. 56 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Analysing the Impact of Freshwater Aquaculture on Wild Fish Populations using DIDSON Technology

e explored the distribution of wild fish surrounding aquaculture cages Wusing an innovative Dual-frequency IDentification SONar (DIDSON) in Lake Diefenbaker, Saskatchewan, Canada. The aim of this project was to test the DIDSON technology as a monitoring tool for the impact of freshwater aquaculture on wild fish populations. We collected DIDSON footage before (2011-2013) and after (2014-2015) the installation of net cages at a new aquaculture site in Kadla Coulee and at a reference site in Lake Diefenbaker. We assessed the efficacy of the DIDSON to detect changes in wild fish habitat use around fish farms. DIDSON technology is non-destructive towards fish habitat and allows for the non-intrusive detection of fish during both day and night, regardless of the turbidity. This multi-beam sonar technology uses 1.8 MHz frequency and 96 sub-beams to effectively fill the gap between underwater cameras and commonly used multi-frequency single-beam, dual-beam, or split-beam sonar equipment. We Image of the Kadla Coulee aquaculture site in Lake Diefenbaker, Saskatchewan, Canada. established an operational protocol and data Photo: Victoria Danco (DFO) analysis procedure for the niche-application­ of DIDSON within an aquaculture setting and provided advice for future DIDSON surveys. This research seeks to narrow the knowledge gap on the environmental interactions between cultured and wild fishes in order to make informed management decisions.

DATE: APR. 2015–MAR. 2016

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Eva Enders (DFO)

PROJECT TEAM: Victoria Danco, Cheryl Podemski, Cynthia Wlasichuk (DFO)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2015-CA-05-eng.html

A wild fish observed swimming towards the Rainbow Trout (Oncorhynchus mykiss) that are milling within the aquaculture cage. The video was captured using DIDSON (Sound Metrics Corporation, Lake Forest Park, Washington, USA) on October 21, 2015. Video: Victoria Danco and Adam Waterer (DFO). CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 57

Oceanographic Study of the Temporal Assessment of Organic Loading from Finfish Aquaculture South Coast of Newfoundland on Hard Bottom Communities in Newfoundland (Baie d’Espoir and Fortune Bay) isheries and Oceans Canada (DFO) finfish farm net-pens will be collected and he expansion of aquaculture activities recently developed and is now analyzed for changes in fauna and flora, and in new areas in Newfoundland’s south Fimplementing the Aquaculture specifically for the presence or absence of coast presents a challenge to the Activities Regulations (AAR) to clarify indicator species (i.e., Polychaete worms and T conditions under which aquaculture bacterial mats) known to occur near finfish biosecurity and the sustainability of this growth. This project sought to understand operators may treat their fish for disease farms. The study will also evaluate the use the oceanographic conditions (including and parasites, as well as deposit organic of remote video survey methods (ROVs) for circulation) in Newfoundland’s south coast matter (i.e., uneaten feed and faeces). monitoring benthic impacts, based on the and provide scientifically sound information These regulations permit aquaculture protocol used in British Columbia. The results to help establish Bay Management Areas. operators to deposit organic matter and from this study will support the development Building on these objectives, environmental treatments within certain restrictions while of science advice on the best practices for data (temperature, salinity, currents, sea level, avoiding, minimizing, and mitigating potential monitoring the effects of finfish aquaculture and wind speed and direction) collection, impacts of aquaculture on fish habitat and on the hard bottom benthic community. analysis, and modelling development were on commercial, recreational, and Aboriginal performed. The study first covered Bay fisheries. In support of the AAR, there is a need DATE: APR. 2015–MAR. 2018 to evaluate monitoring standards and protocols d’Espoir and Hermitage Bay, later extending FUNDED BY: DFO–Program for Aquaculture to Fortune Bay and Connaigre Bay where for biochemical oxygen demanding (BOD) Regulatory Research (DFO–PARR) aquaculture activity has expanded or will deposits (i.e., organic matter) in locations PROJECT LEAD: Dounia Hamoutene (DFO) expand. When possible, data collection where it is not possible to collect sediment was conducted in different seasons. samples (i.e., hard-bottom substrates). So far, PROJECT TEAM: Flora Salvo, Dwight Drover, This study’s results will provide insight into research findings suggest that video (i.e., visual) Kimberly Burt (DFO); Suzanne Dufour (MUN); Robert Sweeney (SIMCorp) the fundamental processes governing the monitoring should be the primary tool for ocean conditions and circulation in the area. environmental assessment; however, a better CONTACT: [email protected] understanding of its limitations is necessary. Such knowledge helps to develop a model to WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ simulate and map potential zones of influence To assess the impacts from unconsumed fish parr-prra/projects-projets/2015-NL-07-eng.html associated with finfish aquaculture. These feed and fish faeces on the benthic community, zones will be used to establish production it is necessary to validate video monitoring data management areas to support fish health with information on the benthic community. management for finfish aquaculture and Samples of the waste that builds up under will support the estimation of potential environmental zones of benthic influence associated with the aquaculture activity. The Alternative Detection Methods for Performance Indicators of the Oxic analysis of the observation data provides a comprehensive overview of the physical State of Bottom Sediments: Indicator Inter-Calibration and Thresholds environment of the area, showing temporal otential impacts associated with DATE: APR. 2016–MAR. 2017 and spatial variation leading to differences biochemical oxygen demanding (BOD) among bays driven by complex dynamics. FUNDED BY: DFO–Program for Aquaculture matter effluents at aquaculture sites Regulatory Research (DFO–PARR) Comparison of the observation with model P are currently assessed by monitoring the oxic data shows that the model is a good tool to PROJECT LEAD: Peter Cranford (DFO) state of the bottom sediment. Performance simulate the sea level variability in the area. indicators, including sulfide concentrations PROJECT TEAM: Lindsay Brager, Fred Page, However, the model is at an early calibration David Wong, Cathryn Abbott (DFO) and redox potential (Eh), are currently used stage with limited forcing physics to accurately to determine the effects of BOD matter CONTACT: [email protected] represent the complexity of the dynamics deposits on benthic organisms. Previous of the study area. This limits the possibility of WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ research has shown that the standard method parr-prra/projects-projets/2016-M-07-eng.html conducting full comparison and validation for quantifying total free sulfides in sediments between observed and modelled water can provide highly inaccurate results as a circulation. result of contamination with mineral sulfides, calibration variability, and inappropriate DATE: APR. 2010–APR. 2015 sample storage. Eh measurements are FUNDED BY: DFO–Program for Aquaculture also known to exhibit high variability. Regulatory Research (DFO–PARR) This project continues ongoing research PROJECT LEAD: Andry Ratsimandresy (DFO) designed to evaluate an alternative indicator (dissolved oxygen) and to develop accurate PROJECT TEAM: Sebastien Donnet, and practical methods for total free sulfides Dwight Drover, Shannon Cross, Fred Page, Randy Losier, Danny Ings, Mike Foreman (DFO) analysis. Results from several oxic state indicators will be compared with the intention COLLABORATORS: Newfoundland Department of identifying common thresholds that equate to Fisheries, Forestry, and Agrifoods the DFO management objective of no greater CONTACT: [email protected] than 50% biodiversity loss. This project will also Lindsay Brager (DFO) conducting field tests of a new WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ develop and evaluate sediment porewater method for rapidly and accurately measuring sediment parr-prra/projects-projets/2010-NL-09-eng.html sampling technologies as a potential alternative sulfide concentrations. Photo: Peter Cranford (DFO) to the traditional use of grabs and cores in aquaculture monitoring programs. 58 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Feeding Pressure of Styela clava on Plankton (Phytoplankton and Zooplankton) in Malpeque Bay, Prince Edward Island

raditionally, bivalve aquaculture carrying capacity has been viewed Tin the context of maximizing stocking biomass and profitability at the farm scale; however, ecological carrying capacity is now at the forefront. Ecological carrying capacity is defined as the most intensive aquaculture activity that can be supported in a given ecosystem without unacceptable changes in ecological processes. Most carrying capacity models do not integrate fouling organisms, such as tunicates, due to a lack of information on their biology and feeding physiology. Both industry and regulators recognize the need to evaluate the ecological impact of tunicates (such as Styela clava) within mussel farms to further improve carrying capacity numerical models. This project proposes five objectives: 1) assess the biomass and size structure of S. clava on mussel socks; 2) determine S. clava clearance rates on natural phytoplankton communities; 3) measure S. clava retention efficiency on zooplankton communities; 4) evaluate S. clava capacity to retain lobster larvae (stages I and IV); and 5) integrate results Reared lobster larvae. Photo: Luc Comeau (DFO) in a numerical model to provide new carrying capacity outputs inclusive of fouling S. clava. Results from this study will provide quantitative information on the S. clava biomass in mussel farms as well as its filtration pressure on plankton, including phytoplankton and zooplankton (such as lobster larvae). This study may also contribute to more detailed modelling exercises in tunicate infested mussel culture bays. The outcome will reinforce the quantitative framework for assessing carrying capacity scenarios (present or future) in Malpeque Bay, PEI.

START DATE: APR. 2015–MAR. 2017

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Rémi Sonier (DFO)

PROJECT TEAM: Luc Comeau, André Nadeau (DFO)

COLLABORATORS: Ramon Filgueira (Dalhousie U), Jeffrey Davidson (UPEI)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2015-G-10-eng.html

Mussels and Styela clava in metabolic chambers. Photo: Remi Sonier (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 59

Can Hard Clams (Mercenaria mercenaria) Increase the Rate acceptable treatments with this compound has of Eelgrass (Zostera marina) Recovery in Areas Impacted by focused on acute lethality to lobsters, but it is Oyster Aquaculture? also important to understand the non-lethal effects of exposure to this pesticide in order he strategies tested in this study to model, and thereby better predict, the may promote the development of environmental impacts of sea lice treatments. Tenvironmentally-friendly practices The objective of this research is therefore to for the aquaculture industry by mitigating conduct controlled experiments to determine the negative impacts of active leases and the rate at which lobsters recover from sub-lethal eliminating the impacts of sites no longer exposure to Salmosan®, using both behavioural in use. and biochemical endpoints. Eelgrass communities are declining in many This research will provide essential data to areas of the world, mainly due to increased support parallel oceanographic studies that inputs of nutrients and sediments from are modelling pesticide dispersal following land-based sources, but also due to shading sea lice treatments, with the goal of improving from aquaculture structures. Enhancement application protocols that maximize treatment Eelgrass (Zostera marina). Photo: Selma Pereira (DFO) activities such as manual seed dispersal and efficacy without undue harm to wild lobsters transplanting whole plants have been explored and their commercial harvesting and shipping. to help counter eelgrass habitat declines. This Recovery of Neural Function in has had limited success at a substantial cost. DATE: SEP. 2015–MAY 2017 Bivalves have been found to stimulate eelgrass Lobsters Following Sub-Lethal FUNDED BY: DFO–National Contaminants growth by clarifying the water column, thereby Salmosan® Exposure Advisory Group (DFO–NCAG) increasing light availability and increasing nitrogen levels through the production of rom a fish health and welfare perspective, CO-FUNDED BY: New Brunswick Department of Agriculture, Aquaculture and Fisheries (NBDAAF); waste products (faeces, pseudofaeces). the treatment of sea lice infestations is a critical component of managing New University of New Brunswick (UNB)–Environmental This project aims to determine whether the F Research Fund seeding of hard clams (Mercenaria mercenaria) Brunswick’s salmon farming industry. As with Tillmann Benfey (UNBF) can enhance eelgrass recovery in areas terrestrial farming, chemical pesticides are PROJECT LEAD: impacted by oyster aquaculture. Various often a key component of integrated pest PROJECT TEAM: Danielle Deonarine (UNBF) management for keeping such parasites densities of hard clams were introduced to COLLABORATORS: : Duane Barker (HMSC); areas with bare or sparse patches of eelgrass at bay. However, many pesticides that are Les Burridge (Burridge Consulting) due to shading from previous commercial effective against sea lice cannot be used CONTACT: [email protected] off-bottom oyster operations. Sediment for this purpose because of their toxicity to characteristics, such as porosity, organic non-target organisms. Salmosan® is one of WEBSITE: www2.unb.ca/biology/Faculty/Benfey.html content, and carbon/nitrogen levels will be the few pesticides approved for treating sea monitored along with the growth and recovery lice on farmed salmon in the Bay of Fundy, of the eelgrass over three years. Additionally, but it is known to be toxic to lobsters. clams were sown directly under lines Most research done to date on determining of suspended oyster bags at an active aquaculture site, to determine if their presence will encourage the growth of eelgrass in this heavily-impacted area. This project supports the DFO priority of environmental performance.

DATE: MAY 2014–JUN. 2017

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: L’Étang Ruisseau Bar Ltd.

PROJECT LEAD: Monica Boudreau (DFO)

PROJECT TEAM: Claire Carver (Carver Marine Consulting)

COLLABORATORS: André Mallet (L’Étang Ruisseau Bar Ltd.)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/G-14-01-004-eng.html

MSc. candidate Danielle Deonarine holding an experimental lobster. Photo: Anne McCarthy (HMSC) 60 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Impact of Global Warming on Aquaculture Production in the Magdalen Islands: Blue Mussel, Atlantic Deep-Sea Scallop, and American Oyster

Cages used to monitor mussel aquaculture yields. Photo: Pascale Chevarie (Merinov)

ariculture is an important economic were used to assess the status of the activity in the Magdalen Islands, bivalves. Relationships established Mwhich produce Blue Mussels among the environmental characteristics (Mytilus edulis), Atlantic deep-sea scallops of aquaculture sites, aquaculture yields, (Placopecten magellanicus), and American trophic conditions of the environment, and Oyster (Crassostrea virginica). However, the physiological status of individuals will in recent years, mariculture stakeholders provide a better understanding of the impact have noted that organisms in lagoon of global warming on the Magdalen Islands breeding sites are showing signs of and will be used to study potential scenarios weakening. These changes appear to for producers. coincide with increased exposure time to The research results will suggest potential temperatures above 20°C and higher than concrete solutions to help Magdalen Islands normal summer temperatures. To answer shellfish producers adapt to global warming. industry’s questions about the effects of warmer water temperatures on production DATE: JUN. 2014–JUL. 2017 and to help industry deal with this new FUNDED BY: Fonds de recherche du Québec problem, it is important to consider scenarios en Nature et technologies (FRQNT); Merinov and that will ensure sustainable aquaculture UQAR–Fonds d’Amorçage de Partenariat (FAP) management in the context of global Lisandre Gilmore-Solomon warming. PROJECT LEAD: (Merinov) The main objective of the project is to assess the ability of Magdalen Islands PROJECT TEAM: Madeleine Nadeau, mariculture production to adapt to global François Gallien, Francine Aucoin, Jules Arseneau, Michèle Langford, Chantal Vigneau, warming by studying the three species of Claude Poirier, Denis Boudreau, Yvon Chevarie, bivalves produced at two experimental Francis Poirier, Pascale Chevarie, Mickael Cyr (Merinov) sites. During the three-year project, the COLLABORATORS: Réjean Tremblay environmental conditions of the breeding (UQAR-ISMER) sites were measured, and aquaculture production yields were assessed for survival, CONTACT: [email protected] Respirometry system for measuring the physiological status of bivalves. Photo: Lisandre Gilmore-Solomon growth, and condition index. Physical, WEBSITE: www.merinov.ca (Merinov; CÉGEP de la Gaspésie et des Îles) biochemical, and genomic measurements CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 61

Study of the Effects on Adult Study on the Sublethal Effects of the Sea Lice Pesticide Salmosan® American Lobsters (Homarus (Azamethiphos) on Adult Male Lobsters (Homarus americanus) americanus) Consuming Clams Exposed to Atlantic Salmon Sea Lice Therapeutants

common approach to control infestations of sea lice on farmed A Atlantic Salmon involves the use of in-feed pharmaceutical products, such as emamectin benzoate and ivermectin, both of which persist in marine sediments. The effects of these treatments on non-target species such as the American Lobster have been studied in the past but focussed primarily on lethality tests conducted over short time frames. New research is needed to determine chronic lethal and sublethal effects under realistic exposures. The present study will be completed in 2017 to provide further essential non-target ecotoxicology data associated Sampling for hemolymph on adult male lobsters (Homarus americanus) exposed to sublethal levels of Salmosan® with the response of adult American Lobsters (azamethiphos). Photo: Dounia Daoud (EcoNov Inc.) following voluntary consumption of exposed clams. Marine clams will be exposed to almosan® (active ingredient: This study provides new information on sediment with varying concentrations of azamethiphos) is one of two pesticides the sublethal effects of current use anti-sea the commercial formulations of emamectin currently permitted for use as a bath lice pesticide on adult American Lobsters. benzoate and ivermectin, individually and in S treatment to control sea lice in farmed salmon combination. In addition to providing in Atlantic Canada. The release of pesticides toxicological data on native species exposed DATE: JAN. 2014–JUN. 2015 from fish farms has raised concern regarding to two relevant chemotherapeutants, this FUNDED BY: DFO–National Contaminants the potential for indigenous, non-target species approach will initiate the study of food Advisory Group (DFO–NCAG) to be exposed. In particular, there are growing chain effects on American Lobsters concerns regarding the potential for effects on PROJECT LEAD: Dounia Daoud (UPEI; providing insight into effects within a more Homarus Inc.; EcoNov Inc.) American Lobsters, a commercially important environmentally relevant scenario where sea species in Atlantic Canada that is found in the PROJECT TEAM: Jason Bernier (CBCL Limited); lice treatment compounds are found in the near-shore environment where fish farms are Jordana Lynne Van Geest (Golder Associates Ltd.); benthic environment. Michael Van Den Heuvel (UPEI); Andrea Battison located. Lobsters have been found to be the This study provides new information (CrustiPath Inc.); Nathalie Lefort, Marc Surette most sensitive species tested in laboratory on uptake and effects of presently used (U Moncton) assays examining the acute lethality of anti-sea lice treatments in marine clams azamethiphos in the Salmosan® formulation. COLLABORATORS: Homarus Inc. and the American Lobster. In this study, adult male lobsters were exposed CONTACT: [email protected] to 0.06, 0.5, and 5 µg L−1 azamethiphos for one DATE: DEC. 2016–MAR. 2017 hour, repeated five times, over 48 h. Lobsters FUNDED BY: DFO–National Contaminants were assessed immediately after exposure Advisory Group (DFO–NCAG) and over six days of recovery. PROJECT LEAD: Dounia Daoud (UPEI; Highlights: Inhibition of muscle Homarus Inc.; EcoNov Inc.) cholinesterase activity detected in lobsters exposed to 0.5 and 5 µg L−1 azamethiphos. Jason Bernier (CBCL Limited); PROJECT TEAM: −1 Chris Bridger, Anne McCarthy, Duane Barker (HMSC); The 5 µg L dose was considered lethal Martin Mallet (EcoNov Inc.) (93% cumulative mortality). Significant changes in hemolymph plasma biochemistry CONTACT: [email protected] were most apparent in the 5 µg L−1 exposure group in the immediate post-exposure samples. Citrate synthase activity was significantly lower in muscles of the 0.5 µg L−1 exposure group compared to control lobsters. These results suggest that sublethal effects on lobster energetics may occur under laboratory exposure Adult male lobster (Homarus americanus) exposed to conditions (i.e., concentrations and duration) sublethal levels of Salmosan® (azamethiphos) placed considered environmentally relevant, in metabolic chamber for oxygen consumption which could result in impairment under measurements. Photo: Dounia Daoud (EcoNov Inc.) natural conditions. 62 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Study of the Effects of Emamectin Benzoate or Ivermectin in Validation of the Robustness of Sediments on Juvenile American Lobsters (Homarus americanus) the Ecosystem Carrying Capacity Models Being Developed for St. Peters Bay

lthough mussel aquaculture is a significant industry in Prince Edward AIsland (PEI), Canada, a moratorium on further leasing there was established in 1999–2000. Recently, a Marine Spatial Planning process was initiated in order to review the moratorium and explore the potential expansion of mussel culture in Malpeque Bay. In this study, we have focused on the effects of a projected Stage V lobsters exposed to sediment spiked with ivermectin and emamectin benzoate using commercial expansion scenario (590 ha) on current formulations in thermoregulated room. Photo: HMSC mussel lease (770 ha) productivity and availability of suspended food resources. ea lice are large ectoparasitic the response of juvenile American Lobsters The goal was to provide the most robust copepods having a pan-global when exposed to varying concentrations of scientific assessment possible using Sdistribution and are pathogenic to emamectin benzoate- and ivermectin-dosed available datasets. Towards that aim, salmonid species (e.g., Atlantic Salmon), sediment using the commercial formulations. three different modelling approaches especially populations in cage culture where This study provides new information on have been carried out: 1) a connectivity the stocking density is unnaturally high. A the effects of presently used anti-sea lice analysis among the different culture areas common approach to reduce infection of sea drugs on early post-settled life stages of of the bay; 2) a scenario analysis of organic lice to farmed Atlantic Salmon involves use of H. americanus. seston dynamics based on a simplified approved in-feed pharmaceutical products. biogeochemical model; and 3) a scenario Field studies have often measured these DATE: APR. 2016–MAR. 2017 analysis of phytoplankton dynamics based active ingredients in sediments proximal to FUNDED BY: DFO–National Contaminants on a nutrient-phytoplankton-seston-bivalve salmon farms post treatment. The effects of Advisory Group (DFO–NCAG) ecosystem model. In addition, sensitivity these products on non-target species such as tests were carried out in order to identify the American Lobster (Homarus americanus) PROJECT LEAD: Dounia Daoud (UPEI; Homarus Inc.; EcoNov Inc.) the parameters and processes for which has been studied in the past but not further research is needed to reduce model PROJECT TEAM: Jason Bernier (CBCL Limited); associated with lethal and sub-lethal effects uncertainty. The main outcomes of these from dosed sediment on which the juvenile Chris Bridger, Anne McCarthy, Duane Barker, Les Burridge (HMSC) modelling exercises suggest: 1) an 8% (± 2%) lobsters live. The goal of this study was reduction in mussel growth in the Marchwater [email protected] to assess the availability of two currently CONTACT: area due in part to direct connectivity among used sea lice treatments (active ingredients leases but also to bay-scale effects driven emamectin benzoate and ivermectin) and to by the overall increase in bivalve biomass measure acute mortality and sub-lethal effects within the bay; and 2) a 17.7% net reduction on juvenile American Lobsters following of chlorophyll a at the bay-scale compared to extended exposure to dosed sediment in a a hypothetical scenario without aquaculture. static bath with water renewal. The study will provide ecotoxicology data associated with DATE: APR. 2011–APR. 2015

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Luc Comeau (DFO)

PROJECT TEAM: Michel Starr, Liliane St-Amand, Thomas Guyondet, Rémi Sonier (DFO); Jon Grant, Ramon Filgueira (Dalhousie U)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2011-G-04-eng.html

Aerated jar with stage V lobster exposed to sediment Pill cups loaded with individual stage V lobsters spiked with emamectin benzoate using commercial before exposure to spiked sediment with ivermectin formulation. Photo: HMSC and emamectin benzoate (via commercial formulations). Photo: HMSC CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 63

Effects of Organophosphate Aquaculture Pesticide Azamethiphos on Stage I and Stage IV American Lobster (Homarus americanus) Larvae

parameters including intermoult period, specific growth rate, moult increment, and global gene expression were determined. General linear model analysis (α = 0.05) determined that intermoult period was significantly increased in the 71.11 µg L-1 azamethiphos treatment when compared to the control (<0.05 µg L-1 azamethiphos). Moult increment and specific growth rate were not significantly affected. RNA sequencing was performed using Illumina Hiseq 2500 PE125 and subsequent RT-qPCR was performed to confirm expression of genes of interest. Gene expression was used to establish effects on biological pathways of H. americanus in order to determine unique gene induction patterns. Established gene induction patterns may be used as a potential diagnostic tool for pesticide exposure in lobster. This study provides new information on the effects of a current use anti-sea lice pesticide on Stage I and IV H. americanus larvae.

DATE: APR. 2015–MAR. 2016 Holding tank for stage IV lobster larvae (Homarus americanus) exposed to sublethal levels of Salmosan® (azamethiphos). The high water bubbling tends to decrease natural cannibalism. Photo: Laura Taylor (UPEI) FUNDED BY: DFO–National Contaminants Advisory Group (DFO–NCAG)

oth the American Lobster fishery and studied but few studies have examined the PROJECT LEAD: Dounia Daoud (UPEI; Homarus Inc.; EcoNov Inc.) salmon aquaculture are important to pesticide’s effects on the health of larval the economy of Atlantic Canada. Where lobsters. Three-hour exposures using stage I PROJECT TEAM: Jason Bernier (CBCL Limited); B Spencer Greenwood, Michael Van Den Heuvel, these industries operate in close proximity, and IV H. americanus larvae were carried out research is needed to better understand using a range of azamethiphos (as Salmosan®) Laura Taylor (UPEI); Fraser Clark (Mount Allison University) any interactions and their possible effects. concentrations between 0.04–71.11 µg L-1. Salmosan® (active ingredient azamethiphos) Median lethal concentrations at three hours COLLABORATORS: Martin Mallet (Homarus Inc.) -1 is an organophosphate therapeutant used were determined to be 5.87 ± 2.01 µg L for CONTACT: [email protected] to treat Atlantic Salmon for infestations stage I and 20.45 ± 12.77 µg L-1 for stage IV of parasitic sea lice. The sensitivity of lobsters. Post-exposure, surviving stage IV crustaceans to Salmosan® has been larvae were raised to stage V and sublethal

Stage IV lobster larvae (Homarus americanus) were Stage IV lobster larvae (Homarus americanus) weighted and measured after a three hour exposure to various exposed for three hours to Salmosan® (azamethiphos) levels of Salmosan® (azamethiphos). Photo: Laura Taylor (UPEI) in 1 L jars. Photo: Laura Taylor (UPEI) 64 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Paving the Way for Salmon-Kelp Integrated Aquaculture in British Columbia: A Foundational Field Trial Assessing Sugar Kelp (Saccharina latissima) Growth and Quality at BC Salmon Farms

elp is a fast-growing marine crop that moisture) of dried kelp revealed site-specific the environmental and socio-economic requires virtually zero energy inputs, differences in nutritional parameters, with performance of salmon farm tenures. K utilizing sunlight and dissolved carbohydrates ranging from 20.4% to 47.5% of nutrients (e.g., nitrogen, phosphorus) from tissue dry weight. Metal accumulation (Al, As, DATE: OCT. 2015–DEC. 2017 the surrounding environment for growth. Ca, Cd, Cu, Fe, K, Mg, Mn, Na, P, Pb, Zn) in FUNDED BY: Natural Sciences and Engineering This study examined the feasibility of kelp tissue from the 15 salmon farms is being Research Council (NSERC)–Industrial Research growing kelp on commercial salmon farm measured using inductively coupled plasma Chairs for Colleges Grant (NSERC–IRCC) tenures where levels of dissolved nitrogen optical emission spectrometry (ICP-OES). A CO-FUNDED BY: Cermaq Canada Ltd.; Creative and phosphorus may be locally-enriched. follow-up, more intensive kelp production trial Salmon Co. Ltd.; Grieg Seafood BC Ltd.; North Island In January 2016, Sugar Kelp (Saccharina at select sites will commence in 2017 using College (NIC) latissima) seed was deployed on 5 m vertical horizontal kelp lines deployed from polyethylene lines at 15 salmon farms and customized floating rafts. PROJECT LEAD: Stephen Cross (NIC) two oyster farms around Vancouver Island. The siting of many salmon farm operations PROJECT TEAM: Allison Byrne (NIC) Kelp was harvested in the summer after in British Columbia would support excellent COLLABORATORS: NIC-CARTI; Cermaq Canada approximately 150 days; frond length, width, Sugar Kelp production, a sustainable crop with Ltd.; Creative Salmon Company Ltd.; Grieg Seafood wet/dry weight, proximate analysis, and metal diverse commercial applications. Through field BC Ltd.; Mac’s Oysters Ltd.; Odyssey Shellfish Ltd. accumulation were measured. Maximum frond studies such as this we hope to demonstrate CONTACT: [email protected] length ranged from <20 cm to >330 cm, the feasibility of salmon-kelp integrated depending on the site. Proximate analysis (KJ, aquaculture in BC with the goal of improving WEBSITE: https://www.nic.bc.ca/research protein, ash, fat, calories, carbohydrates,

Stephen Cross examining a Sugar Kelp, Saccharina latissima, frond. Photo: Allison Byrne (NIC) CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 65

The Effects of Sublethal Aquaculture Chemotherapeutant Exposure and several species of Pacific shrimp on Pink Salmon including the Coonstripe (Pandalus hypsinotus), Dock (Pandalus danae), and Pink Shrimp (Pandalus jordani), Spot Prawn (Pandalus platyceros), Ghost Shrimp (Neotrypaea spp.), and an unidentified sand shrimp. Shrimp were exposed to at least five concentrations of either SLICE®, Salmosan®, or Paramove 50® for 1 to 96 h. Juvenile Pacific coast shrimp were equally as sensitive to all three chemicals as their east coast counterparts. Spot Prawn (Pandalus platyceros) exposed to water containing the Swim tunnel used for assessing fish swimming performance (critical swimming speed [Ucrit]) following exposure active ingredients of SLICE®, Salmosan®, to chemotherapeutants. Photo: Feng Lin (SFU) and Paramove 50® (emamectin benzoate, azimethiphos, and hydrogen peroxide) n improved understanding of resulted in concentration-dependent chemical impacts on near-shore DATE: SEP. 2014–MAR. 2017 increases in oxygen consumption. In a choice/ ecosystems is essential to FUNDED BY: DFO–National Contaminants avoidance assay, unexposed Spot Prawns, A Advisory Group (DFO–NCAG) acclimated in a shuttle box apparatus, showed responsible stewardship of Canada’s coastal areas. In order to accurately assess CO-FUNDED BY: Simon Fraser University (SFU) conflicting results to hydrogen peroxide, the risk to non-target marine fish species emamectin benzoate, and azamethiphos at PROJECT LEAD: Chris Kennedy (SFU) posed by the use of the chemotherapeutants several concentrations. Prawns were actively emamectin benzoate, azamethiphos, PROJECT TEAM: Katerina Vasilenko (SFU) attracted and actively avoided all chemicals at low concentrations. This research will deltamethrin, cypermethrin, or hydrogen CONTACT: [email protected] peroxide in the receiving environment, ensure the appropriate regulation of information regarding their sublethal toxicity chemotherapeutant use in Canadian is essential. Pink Salmon (Oncorhynchus aquaculture and maintain the goal of gorbuscha) embryos were hatched in the protecting non-target organisms in The Lethal, Physiological, the marine environment. laboratory, transferred to seawater, and and Behavioural Effects of raised until they were the appropriate New data will support assessments size for swimming and behavioural assays Anti-Sea Lice Therapeutants in of risk from current-use chemotherapeutants following exposure (pulse: 1 h, 3 h, 6 h; and Non-Target Crustacean Species posed to a range of non-target benthic longer term: 96 h) to several concentrations crustaceans found in proximity to Pacific of each aquaculture chemical. Fish were nvironmental contamination and effects salmon aquaculture facilities. tested for swimming performance using a on non-target organisms associated measure of critical swimming speed (Ucrit), Ewith the chemotherapeutic control of DATE: OCT. 2015–MAR. 2017 sea lice infestations in salmonid aquaculture avoidance/attraction behaviour, and the FUNDED BY: DFO–National Contaminants ability to detect food. All aquaculture has emerged as a significant concern. This Advisory Group (DFO–NCAG) pesticides (except hydrogen peroxide) research specifically addresses information CO-FUNDED BY: Simon Fraser University (SFU) reduced Ucrit values at concentrations gaps that need to be filled to properly manage any risks associated with the use Chris Kennedy (SFU) below 96 h-LC50 values determined for PROJECT LEAD: of three chemicals currently used in Canada. this species in preliminary toxicity tests. PROJECT TEAM: Jill Bennett (SFU) For azamethiphos, cypermethrin, Several shrimp species were tested for the CONTACT: [email protected] deltamethrin, and emamectin benzoate, acute lethal effects of current-use chemicals: concentration-dependent reductions in the reference species Mysid shrimp swim performance were seen. Fish actively (Mysidopsis bahia East coast species), avoided all chemicals except deltamethrin at similar concentrations and avoidance to hydrogen peroxide only occurred at the highest concentration. Following exposure to each chemical at various concentrations for longer exposures (6 and 96 h), a loss of attraction to food was noted in olfactory response tests. The data obtained from this research will allow regulators to assess the risks posed to the environment adjacent to salmon aquaculture facilities and the risks posed to non-target fish species from chemotherapeutant use. New data will support assessments of risks posed to the environment adjacent to salmon aquaculture facilities and the risks posed to non-target fish species Tanks holding Spot Prawn (Pandalus platyceros) for lethal and sublethal toxicity experiments. Photo: Kate Mill (SFU) from chemotherapeutant use. 66 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

The Effects of Anti-Sea Lice Chemotherapeutants on Sensitive Life Stages of Non-Target Crustacean Species in Combination with Environmental Stressors

here is specific concern regarding the use of the anti-sea lice therapeutants TSalmosan®, SLICE®, and Paramove 50® in the aquaculture industry specifically in regard to their toxicity to Pacific coast region organisms. In real world scenarios, organisms are often challenged with multiple environmental stressors simultaneously, including those of a physical nature (e.g., oxygen, temperature, and salinity fluctuations). In these studies, the range of oxygen, temperature, and salinity tolerances in Spot Prawn, Pandalus platyceros, were determined in order to design experiments to measure the acute toxicity of these chemicals under varying physical conditions. In acute lethality studies, Spot Prawn juveniles and adults were exposed to five concentrations of each individual chemical formulation in glass 40-L glass aquaria for up Exposure tanks for Spot Prawn (Pandalus platyceros) for toxicity experiments under multiple stressor conditions. to 96 h under varying oxygen, temperature, Photo: Feng Lin (SFU) and salinity conditions. Juvenile Spot Prawns were much more sensitive to all chemicals than adults, and acute toxicity research provided information on the toxicity DATE: SEP. 2014–MAR. 2017 of these chemicals under environmentally was exacerbated by exposure to physical FUNDED BY: DFO–National Contaminants conditions approaching tolerable limits. In realistic conditions to a representative and Advisory Group (DFO–NCAG) particular, oxygen concentrations, followed sensitive Pacific coast marine organism. Simon Fraser University (SFU) by temperature, and then salinity had the New data will support assessments CO-FUNDED BY: most pronounced effects on increasing of risk from chemotherapeutant use in PROJECT LEAD: Chris Kennedy (SFU) chemical toxicity. This research specifically combination with environmental stressors PROJECT TEAM: Kate Mill, Jill Bennett (SFU) addresses information gaps that need to be posed to a non-target benthic crustacean [email protected] filled in order for proper assessments of the found in proximity to Pacific coast salmon CONTACT: environmental consequences of sea lice aquaculture facilities. pesticide use in Canada to be made. This

The Environmental Fate and Non-Target Effects of Sea Lice Drugs and Pesticides Used in Salmon Aquaculture

ive chemotherapeutants used globally chemicals was cypermethrin > deltamethrin > these important aquaculture chemicals to to control sea lice in salmon farming emamectin benzoate > azimethiphos > protect the environment. Foperations of particular interest hydrogen peroxide. In standardized acute New information on the environmental with regard to their fate and toxicity are: toxicity tests, the susceptibility to each fate and non-target toxicity of five deltamethrin, cypermethrin, azamethiphos, chemical was species-specific and chemotherapeutants will inform decisions hydrogen peroxide, and emamectin no general trends were evident. Kelp on the responsible use and management benzoate; the latter three of which are Macrocystis pyrifera germination and of these products for the control of sea lice. currently used in Canada. Predictions of the growth were only affected by hydrogen persistence and toxicity of these chemicals peroxide. Echinoderm Strongylocentrotus DATE: SEP. 2014–MAR. 2017 to non-target organisms has been difficult, purpuratus fertilization was affected by FUNDED BY: DFO–National Contaminants and data gaps make estimations of risk cypermethrin > deltamethrin > emamectin Advisory Group (DFO–NCAG) highly inaccurate. The main objectives benzoate > hydrogen peroxide. Bivalve of this research were to assess: 1) the Mytilus edulis development was affected by CO-FUNDED BY: Simon Fraser University (SFU) environmental persistence and partitioning hydrogen peroxide > emamectin benzoate > PROJECT LEAD: Chris Kennedy (SFU) of these compounds, and 2) their acute azamethiphos. For the mysid Americamysis PROJECT TEAM: Fauve Strachan (SFU) and sublethal toxicity to non-target marine bahia, all chemicals tested were highly toxic organisms. In micrososm experiments, at concentrations far below those used in COLLABORATORS: Frank Gobas, Victoria Otton (SFU; Nautilus Environmental) the partitioning behaviour, and water aquaculture (deltamethrin > cypermethrin > and sediment half-lives were determined. emamectin bezoate > azimethiphos > CONTACT: [email protected] Emamectin benzoate, cypermethrin, hydrogen peroxide). This research yields and deltamethrin partitioned mainly important information required to ensure into sediments, while azimethiphos and the proper and safe use of aquaculture hydrogen peroxide remained in the aqueous pesticides, and to appropriately regulate phase. Generally, the persistence of these CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 67

Structure and Function of the Salmon Farm “Reef” Identifying Critical Ecological Thresholds for Tunicate he presence of fish farm infrastructure Understanding the community of native provides habitat for native marine flora species inhabiting fish farm infrastructure Infestations on Mussel Farms Tand fauna from the surrounding over time and in different locations will help ussel farmers in PEI have developed environment, in many ways acting as an identify key relationships between salmon treatment regimens to control artificial “reef”. This project is documenting farms and the surrounding environment, invasive tunicates (Ciona intestinalis the reef community structure at four salmon providing insight into the function of these M and Styela clava). To study the ecological farms in different environments around dynamic communities. thresholds of these treatments on the benthic Vancouver Island. Scraped samples and environment and the water column, we set up high-resolution photos of the community at DATE: APR. 2016–MAR. 2018 field and laboratory experiments and used each site are being collected seasonally FUNDED BY: BCSFA–Marine Environmental modelling to predict farm-scale effects. Firstly, from billets on all sides of the farm. The Research Program (BCSFA–MERP) we studied high pressure water treatment for abundance (biomass per unit area) and C. intestinalis in St. Mary’s Bay. Treatments composition (biodiversity) of the communities CO-FUNDED BY: Cermaq Canada Ltd.; Creative Salmon Co. Ltd.; Grieg Seafood BC Ltd.; Marine effectively removed 54% and 78% of will be compared within and between sites Harvest Canada Limited; North Island College (NIC) C. intestinalis from infested socks in July and over time. In addition to seasonal billet September, respectively. During treatment, PROJECT LEAD: Stephen Cross (NIC) sampling, five hard plastic panels were drifting tunicates were observed in narrow deployed at 1 m depth at each site and will PROJECT TEAM: Chris McKindsey (DFO); patches, but most of the sinking biomass fell Allison Byrne (NIC) remain in the water undisturbed (with the directly below the pressure-washed line. We exception of being photographed) for COLLABORATORS: NIC–CARTI; found no significant difference in organic 18 months. These will be used to document Cermaq Canada Ltd.; Creative Salmon Company Ltd.; enrichment in sediments below the treated and compare the settlement rate and Grieg Seafood BC Ltd.; SEA Vision Group Inc.; line and those below the untreated line. composition in different farming CONTACT: [email protected] These results could be due to heavy environments. WEBSITE: https://www.nic.bc.ca/research predation by crabs during treatment activities. For most stations, mean redox fell within the anoxic category. A synoptic survey of the Bay of St. Mary’s found hypoxic sediment conditions in July and oxic conditions in November, regardless of whether sediments were within or outside of the mussel farm. A preliminary modelling assessment indicated that C. intestinalis fouling is best controlled by applying early treatments (combination July and August) to limit impacts in terms of food reduction and total organic sedimentation under the lines. Secondly, we studied water pH variation during hydrated lime treatment for S. clava in Malpeque Bay. Overall the treatment produced a negligible pH signal in the water column and on the benthic substrate with a short-term increase followed by a quick return to baseline values.

DATE: APR. 2011–APR. 2015

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Thomas Landry (DFO)

PROJECT TEAM: Andrea Locke, Chris McKindsey, Monique Niles, Daniel Bourque, Thomas Guyondet, Luc Comeau (DFO); Aaron Ramsay (DFARD); Jeff Davidson, Thitiwan Patanastienkul (UPEI–AVC)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2011-G-05-eng.html Examples of different reef communities observed on fish farm billets. Photo: NIC 68 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Co-Culture of Blue Mussel (Mytilus edulis) and Sugar Kelp (Saccharina latissima): Exploring the Potential Effect of Seaweeds in Deterring the Effect of Duck Predation on Mussels, Cascapedia Bay (Quebec)

n Europe and Canada, the economic losses in Blue Mussel (Mytilus edulis) farms Idue to duck predation represent a major problem. In this proof of concept experiment, an alternative approach will be presented that aims to reduce duck predation in Canadian mussel farms where traditional techniques are not effective. These methods generally either focus on protecting mussels by isolating them in nets or cages, or use active repelling techniques (sound, light, etc.). Such techniques are often expensive, stressful to duck populations, only effective for a short time, and do not take into consideration drifting ice. To solve the problem, Sugar Kelp (Saccharina latissima) will be cultivated above the mussel culture line, to visually shield the mussels. The hypothesis is that by hiding the mussels from ducks’ field of vision, they could get some protection without imposing further stress on the ducks. Additionally, it is suggested that Sugar Kelp and Blue Mussels could benefit from each other’s proximity in terms of production yields, consumption, and The twine carrying the Sugar Kelp (Saccharina latissima) plantlets is wound around the culture line on the mussel excretion. The Sugar Kelp plantlets were farm. Photo: Pierre-Olivier Fontaine (UW; CEGEP-EPAQ) outplanted at sea in November 2016. Their biomass and overall aspect will be recorded simultaneously with the mussels’ yield (wet kg / m), survival rate (# indiv. / m), and overall quality (Body Condition Index) during the summer of 2017. This proof of concept is being carried out in the Cascapedia Bay (Québec) in partnership with the mussel industry. This work will contribute to provide alternative solutions to prevent the predation of culture mussel by sea ducks. It will also document the potential benefits of polyculture in a mussel farm.

DATE: AUG. 2016–JUL. 2017

FUNDED BY: Ministère de l’éducation et de l’enseignement supérieur du Québec (MÉES) [Québec Ministry of Higher Education and Training]

CO-FUNDED BY: Merinov

PROJECT LEAD: Pierre-Olivier Fontaine (UW; CEGEP–EPAQ)

PROJECT TEAM: Estelle Pedneault, Éric Tamigneaux, Quentin Cometti (CEGEP–EPAQ)

COLLABORATORS: Éric Bujold (La Ferme Maricole du Grand Large)

CONTACT: [email protected] Setting artificial kelp made of fabric (control treatment) on the mussel farm. Photo: Pierre-Olivier Fontaine (UW; CEGEP-EPAQ) CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 69

Tracking in Situ Real-Time Responses of Ocean Acidification Effects on Biological Organisms and Influence on Plankton Diversity

oastal margins are under increasing human-induced pressures including Ceutrophication and ocean acidification, which interact with natural environmental fluctuations in ways that can exacerbate calcium carbonate (CaCO3) mineral corrosivity. Ocean acidification negatively impacts a range of species, especially those dependent on

CaCO3 saturation states for shell formation, including socio-economically important species like marine shellfish. The capacity for marine populations to adapt to these changes is unknown, and the loss of dominant coastal and estuarine organisms such as shellfish may significantly alter marine ecosystem structure and function, as well as threaten food security. This research combines lower trophic level monitoring (plankton analysis), physiological responses (functional genomics of multiple species of shellfish) and high speed (0.5Hz) near real-time oceanographic monitoring at a field site in the northern Salish Sea in British Columbia (BC). This initial project is a novel pairing of these technologies in situ, and provides information on coastal variability and impacts on ecosystem productivity in Quadra Island field-site. Photo: Kayla Mohns (VIU) a poorly sampled portion of the BC coastal margin. This work is currently ongoing, but preliminary results of gene expression studies of multiple commercial shellfish species and accompanying plankton work are underway. Recent equipment updates have allowed direct sampling of biological responses to ocean acidification conditions in a real world environment, to enable the examination of the impact of ocean acidification on the long-term health and productivity of coastal ecosystems in BC and elsewhere.

DATE: FEB. 2015–ONGOING One of the test species and life stages – adult Pacific Oyster (Crassostrea gigas). Photo: Kayla Mohns (VIU) FUNDED BY: Hakai Institute

CO-FUNDED BY: Pacific Salmon Foundation (PSF); Vancouver Island University (VIU)

PROJECT LEADS: Helen Gurney-Smith (DFO); Wiley Evans (Hakai Institute)

PROJECT TEAM: Kayla Mohns, Caitlin Smith (VIU); Tamara Russell (VIU; Microthalassia Inc.)

COLLABORATORS: Léo Pontier, Katie Pocock, Alex Hare (Hakai Institute)

CONTACT: [email protected]

WEBSITE: http://seaomics.wixsite.com/research/ research-blog From left to right, Caitlin Smith, Helen Gurney-Smith (DFO), and Léo Pontier (Hakai Institute) at a shellfish Molecular laboratory analysis (Kayla Mohns). raft monitoring station. Photo: Kayla Mohns (VIU) Photo: Caitlin Smith (VIU) 70 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Building an Understanding of the Mobile Wild-Farmed Interactions Occurring around Aquaculture Farms in the Bay of Fundy

an-made structures in the ocean are often attractive to a multitude Mof different species. Not only do these three-dimensional structures provide habitat and shelter from predation for various organisms, structures such as fish farms, where food is added on a daily basis, often provides nourishment for the food webs that become established on these structures. The biological interactions that occur on aquaculture farms are easily apparent in the form of naturally occurring biofouling organisms. They coat the lines and nets, causing increased physical drag on the system from currents as well as a reduction in water flow through the nets. This can sometimes affect oxygen levels in the water within the cage. These organisms are often sessile and many studies have been done on their development and possible methods for control. However, there is also a mobile suite of species, both benthic and pelagic, Utilization of a mussel farm by wild fish and biofouling species at an aquaculture farm site in Spain. Similar that are attracted to the energy and habitats situations occur in the Bay of Fundy around aquaculture farms, however, poor water visibility prevents a clear photo representation. Photo: Shawn Robinson (DFO) associated with aquaculture farms. These organisms are much more transitory and difficult to sample and as a result, very little is known of their ecological interactions and Understanding the scale at which wild DATE: APR. 2016–MAR. 2019 their relative presence on the site. This study species are utilizing intensively cultured FUNDED BY: DFO is starting to document the mobile fauna aquaculture sites will provide a basis for the PROJECT LEAD: Shawn Robinson (DFO) that are using the site on a seasonal basis determination of the likelihood of negative through a combination of acoustic and interactions happening. These interactions PROJECT TEAM: Chris McKindsey, Gregor Reid, Steve Neil, Craig Smith, Jonathan Day (DFO) photographic technologies to assess can go both ways from either farm to wild or the potential interactions that they may vice versa and can be either detrimental or COLLABORATORS: Eva Enders (DFO) have with the cultured species. These beneficial. It has implications on fish health CONTACT: [email protected] observations will form the basis of an (parasites and disease) and the zone of WEBSITE: http://www.mar.dfo-mpo.gc.ca/SABS/ understanding on the scale of benefits influence from farming activities. Home that these species may accrue and also the potential risks they represent.

Meta-Analysis of Freshwater Aquaculture Provincial Water Quality Monitoring Data

ecent increases in production capacity conducted. One of the primary environmental as they demonstrate to the public that the in Ontario, Saskatchewan, and British concerns restricting the expansion of the industry is being carefully monitored by the RColumbia have prompted regulators freshwater finfish cage industry is the ability provincial regulator and that there has been to consider strategies for managing of the environment to assimilate waste, in no trend of decreasing water quality at active freshwater finfish aquaculture, in particular, particular phosphorus. Phosphorus is the aquaculture sites. ecosystem carrying capacity which is tightly nutrient that limits the biomass of primary coupled with the phosphorus released in producers; excessive amounts of phosphorus DATE: APR. 2014–MAR. 2015 aquaculture waste. Currently in Ontario, a released from aquaculture cages pose a risk FUNDED BY: DFO–Program for Aquaculture water quality monitoring program is imposed of eutrophication in freshwater ecosystems. Regulatory Research (DFO–PARR) as a condition to aquaculture licenses to A decade of water monitoring data collected ensure that the release of phosphorus from through the historic Ontario monitoring program PROJECT LEAD: Cheryl Podemski (DFO) finfish farms does not exceed regulatory was analyzed to determine if there is evidence CONTACT: [email protected] thresholds. The program, however, does that freshwater finfish cages are contributing to WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ not address phosphorus levels near or elevated phosphorus concentrations and to the parr-prra/projects-projets/2014-CA-09-eng.html downstream from freshwater finfish farms, or eutrophication in the environment. The results if phosphorus concentrations have increased from this work have a high probability of being over the decade that sampling has been used to improve social license for the industry CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 71

Evaluation of Benthic Far-Field and Site Recovery Effects from Aquaculture within the Letang Inlet, New Brunswick

ne of the primary environmental effects of coastal marine aquaculture Ois related to the deposition of organic material (uneaten fish food and feces) to the seabed and the associated change in benthic organisms inhabiting the affected area. While the obvious effects of organic deposition are limited to close proximity of an aquaculture site, there exists concern that there may be impacts in the far-field from the cumulative effect of multiple commercial operations within a limited area. In the restricted area of the Bay of Fundy’s Letang Inlet in New Brunswick, there is some concern about these types of effects where changes in the macrofauna species Gerhard Pohle taking a water sample during field work on board the CCGS Viola M. Davidson. composition have been previously observed. Photo: Andrew Cooper (DFO) The industry has attempted to remediate this situation using various management strategies such as reduction of operational Freshwater Finfish Cage Aquaculture: Development sites, and employment of fallowing periods according to Bay Management Areas of Sediment Biogeochemical Indicators for Regulation designation. However, the effectiveness of Freshwater Cage Aquaculture of these changes has not yet been assessed. This project assesses the far-field enthic macroinvertebrates play a major 2) Describe the gradient of effects of environmental effects of marine aquaculture role in waste assimilation (recycling organic carbon deposition on the on the benthic community structure within Bwaste) and in the transfer of carbon biology and geochemistry of the the Letang Inlet over a four-year period. It and energy from aquaculture wastes to freshwater benthic environment; higher trophic levels within lake ecosystems will also compare these far-field effects to 3) Identify thresholds of geochemical (i.e., they eat the waste and grow larger, thus a previous baseline study to determine changes in freshwater sediments becoming a bigger source of food for species whether the management approaches within associated with major changes in the higher up in the food chain). Letang Inlet have stabilized or improved structure of the invertebrate community; conditions. This will provide valuable Waste from freshwater finfish cage farms 4) Support the development of regulatory information to aquaculture regulators and directly impacts nearby benthic invertebrate thresholds for managing the deposition the industry on the effectiveness of current abundance and diversity. Preserving the of aquaculture wastes at levels that management measures. function of benthic invertebrate communities would maintain an acceptable degree This project supports the DFO priority is necessary given their role in organic carbon of benthic alteration; of environmental performance. cycling near freshwater aquaculture farms. Benthic invertebrates are typically used 5) Support the assessment of risk associated as indicators of benthic condition; however, DATE: JUN. 2013–JUN. 2016 with the deposits of wastes; and sample collection and taxonomic identification FUNDED BY: DFO–Aquaculture Collaborative of the various species within a monitoring 6) Contribute to the development of Research and Development Program (DFO–ACRDP) program framework are time consuming and regulatory standards and monitoring protocols for aquaculture-affected CO-FUNDED BY: Northern Harvest Sea Farms Ltd. costly. The development of a reliable, readily measurable proxy for benthic invertebrate sediments, including fallowing PROJECT LEADS: Andrew Cooper (DFO); practices for freshwater aquaculture, Gerhard Pohle (Huntsman Marine Science Centre) indicators would expedite the process of sediment monitoring. Such a proxy is by identifying potential sediment PROJECT TEAM: Rebecca Milne, contingent on a well-established relationship recovery targets. Lou Van Guelpen (Huntsman Marine Science Centre); Marc Blanchard (DFO); Robert Findlay to the invertebrate community structure and (U Alabama); Robert Clarke (Plymouth Marine requires testing across a range of locations DATE: APR. 2014–MAR. 2017 Laboratory); Karl Whelan (Eastern Charlotte to ensure cross-region applicability. Waterways Inc.) This project will: FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR) COLLABORATORS: Larry Ingalls (Northern 1) Study the biogeochemistry of Harvest Sea Farms Ltd.) sediments receiving a gradient PROJECT LEAD: Cheryl Podemski (DFO) of aquaculture wastes; CONTACT: [email protected] PROJECT TEAM: Megan Otu, Cyndi Wlasichuk, Jian Zhang, Doug Geiling (DFO) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/M-13-01-003-eng.html CONTACT: [email protected] WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2014-CA-08-eng.html 72 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Effect of Wind Forcing on the Oceanographic Conditions of Fortune Bay–Belle Bay: Identification of Changes in Water Physical Conditions and Ocean Currents, and Development of a Forecasting Tool

esults of recent research have indicated that while the tide accounts for less than R10% of the ocean current variability in most of Fortune Bay–Belle Bay (Newfoundland and Labrador), wind forcing and water physical structure have a significant, if not dominant, influence. Present findings also suggest that large-scale (e.g., at scale of Fortune Bay and/or the Newfoundland shelf) mechanisms affecting the water physical conditions and ocean currents are taking place as a response to wind forcing. This project aims to identify and describe some of the dominant mechanisms responsible for short-term upwelling and downwelling events as well as surface and sub-surface oceanic circulation induced by wind forcing. This project will also develop a high resolution numerical (computer) model able to reproduce and forecast the consequences of wind events on oceanographic features which will be applied to aquaculture related issues. For instance, results from this project will help inform the aquaculture industry as they conduct aquaculture operations such as when best to apply pesticides, choose appropriate Location of field activities conducted in November 2016. Photo: Pierre Goulet (DFO) sites and design the infrastructure to prevent failure. Results from this project will also help inform the regulators in matters such as fish pest and pathogen management, release of organic matter into the environment as well as cumulative effects and ecosystem management.

DATE: APR. 2015–JUN. 2018

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: Newfoundland Aquaculture Industry Association; Cold Ocean Salmon Inc.; Northern Harvest Sea Farms Ltd.; IFREMER

PROJECT LEADS: Sebastien Donnet, Andry Ratsimandresy (DFO)

PROJECT TEAM: Dwight Drover, Pierre Goulet, Shannon Cross, Guoqi Han (DFO); Pascal Lazure (IFREMER)

COLLABORATORS: Mark Lane (NAIA); Julia Bungay (Cold Ocean Salmon Inc.); Jennifer Caines (Northern Harvest Sea Farms Ltd.)

CONTACT: [email protected], [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/15-1-N-02-eng.html

Project lead Sebastien Donnet (DFO) preparing an oceanographic mooring to be deployed in Fortune Bay. Photo: Pierre Goulet (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 73

Robustness of Alternative Benthic Impact Indicators: Quantification of Spatial and Temporal Variability of Alternative Methods, and Application at Aquaculture Sites Across Different Farm and Environmental Conditions

Casey O’Laughlin and Emma Poirier (DFO) bringing a sediment core on board the CCGS Viola M. Davidson at a salmon aquaculture study site near Southwest Nova Scotia. Photo: Peter Cranford (DFO).

enthic effects associated with concentrations have been developed that DATE: APR. 2016–MAR. 2019 biochemical oxygen demanding may address some of the weakness of the (BOD) matter effluents at aquaculture methods traditionally used. This project FUNDED BY: DFO–Program for Aquaculture B Regulatory Research (DFO–PARR) sites are currently assessed by monitoring will test these new methodologies and the oxic state of surficial sediment. The technologies across a range of aquaculture PROJECT LEAD: Lindsay Brager (DFO) Aquaculture Activity Regulations (AAR) (shellfish and finfish) and seabed conditions PROJECT TEAM: Peter Cranford, Fred Page, require measurements of sulfide (mud, sand, and mixed) in Canada to David Wong, Brent Law (DFO) concentrations around finfish aquaculture determine the general applicability of CONTACT: [email protected] sites as a proxy for benthic biodiversity these methods for reaching conclusions impacts. However, it has been widely on sediment oxic state and related benthic WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2016-M-08-eng.html recognized that there are some problems impacts, and to measure the temporal and with current protocols used for monitoring spatial variability in oxic state indicators the oxic state of sediments. Alternative among these different methods. methods for measuring sulfide and oxygen 74 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

The Development of a Robust Methodology for Sulfide Probe between offshore culture sites and Calibration and Sediment Sampling commercially important wild species (lobster, rock crab, and winter flounder) are he results of this project can contribute DATE: JUL. 2014–JUN. 2016 largely unknown, remaining a concern for local fisheries and industry stakeholders. to the development of a reliable, FUNDED BY: DFO–Aquaculture Collaborative accurate, consistent, and robust Research and Development Program (DFO–ACRDP) This study investigates both concerns, T along with the use of standard geochemical methodology for sediment sampling, which CO-FUNDED BY: Atlantic Canada Fish Farmers measures for monitoring the organic loading could be adopted by provincial regulators. Association (ACFFA); SIMCorp In various provinces, sulfide concentrations in the proposed offshore site. in sediment are measured as the fundamental PROJECT LEAD: Monica Lyons (DFO) This project supports the DFO objective indicator of environmental impacts from PROJECT TEAM: Blythe Chang, David Wong, of environmental performance. It found that aquaculture. Because each provincial Kenneth MacKeigan, Fred Page, Ed Parker, modelling combined with in situ measurements government has established its own SOPs Nathan Blasco (DFO); Bob Sweeney, showed that a stocking density of 2.5 times that Leah Lewis-McCrea, Tara Daggett, Amanda Smith, for interpreting sulfide concentrations, the of densities used in the existing farm site could Janelle Arsenault (SIMCorp); Jessica Whitehead be deployed in the entire proposed bivalve evaluation of environmental impacts could (NSDFA); Troy Lyons (NB–DELG); Betty House (ACFFA) differ among provinces. culture zone without going over the carrying Betty House (ACFFA); Previous research has revealed that COLLABORATORS: capacity of Baie de Plaisance. The abundance Bob Sweeney (SIMCorp) the standard solutions (“standards”) used of most animals (e.g., lobster, seastars, crabs, in sediment sulfide monitoring and probe CONTACT: [email protected] and flounder) was much greater in the farm accuracy (post-calibration) degrade WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ than the areas around it. Lobster movement significantly over time. These findings suggest acrdp-pcrda/projects-projets/M-13-01-001-eng.html was followed throughout the spring/summer the need for standardized sediment sulfide using telemetry. Lobster movements did not methodologies. This study examines potential differ greatly between farm and surrounding sources of error related to the methods used areas other than the animals concentrating their in the collection, storage, transportation, and movements in smaller areas within the farms. handling of sediment samples. Although the communities living in sediments This project supports the DFO objective within the farm boundary differed slightly from of environmental performance. Specifically, those in sediments outside of the farm, the following results were found: geochemical measures showed no patterns. • Sample collection: No one sampler DATE: JUN. 2013–JUN. 2016 worked well in all sediment types investigated. In all sediment types, FUNDED BY: DFO–Aquaculture Collaborative multiple samples may need to be taken Research and Development Program (DFO–ACRDP) before an acceptable one is collected. Sulfide probe, temperature probe, meter (left to right). CO-FUNDED BY: Merinov; Société de Photo: Fred Page (DFO) Video footage of deployment and retrieval Développement de l’Industrie Maricole Inc. (SODIM); of gear was useful in assessing gear University of Quebec– Rimouski (UQAR); University performance and confidence in the of Quebec–Chicoutimi (UQAC); Ressources Aquatiques Québec (RAQ) integrity of collected samples. PROJECT LEAD: Chris McKindsey (DFO) • Sample storage: During storage, Sustainable Development of sediment sulfide concentration changed Offshore Bivalve Culture in the PROJECT TEAM: Philippe Archambault, Céline Audet (UQAR–ISMER); François Bourque, over time, depending on sediment type, Magdalen Islands: Production Madeleine Nadeau (Merinov); Pascal Sirois (UQAC); level of sulfide present, and storage Capacity and Interactions with Luc Comeau, Andrea Weise (DFO) temperature. To reduce variability due to Commercial Fisheries storage, all samples should be treated COLLABORATORS: Madeleine Nadeau (Merinov); Gilbert Scantland (SODIM); Philippe uniformly until analyzed. o expand the shellfish industry in Archambault (UQAR); Pascal Sirois (UQAC) Québec, MAPAQ wishes to establish an • Sample analysis: Sulfide measurements CONTACT: [email protected] should be made as soon as possible after offshore bivalve (mussel) culture site T WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ collection, with a standardized time of (15 to 25 m depth) in the Magdalen Islands. acrdp-pcrda/projects-projets/Q-13-01-001-eng.html analysis established. The differing ages There are concerns that the production of probes used in analyses were not a carrying capacity (maximum harvest) will concern in readings. exceed the ecological carrying capacity (when ecological impacts become unacceptable), depleting plankton (food source for mussels) and producing excessive organic waste (feces). The interactions CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 75

Developing the Benthic Component of Integrated Multi-Trophic Aquaculture to Reduce the Impact of Organic Nutrients from Fish Farms and Evolving Standard Operating Procedures

Photograph of Northern Sea Cucumbers in the lab feeding actively on particles in the water. The feathery orange structures are the feeding tentacles that capture the food and put it into the mouth of the sea cucumber. Photo: Terralynn Lander (DFO)

here is a desire and requirement footprint for open water, marine aquaculture This project supports the DFO objectives for aquaculture sites to control sites practicing IMTA. Specifically, this of environmental performance and optimal Tthe amount of organic loading project will develop protocols for juvenile fish health. that comes from commercial fish farms. production, assess the organic particle capture Integrated Multi-Trophic Aquaculture (IMTA) efficiencies, scan for pathogens, and explore DATE: APR. 2014–JUN. 2017 is an advanced ecological engineering potential wild-farmed interactions. Three target DFO–Aquaculture Collaborative technique that has been developing in species are being studied: Northern Sea FUNDED BY: Research and Development Program (DFO–ACRDP) Canada for over a decade on both the East Cucumber (Cucumaria frondosa), Green Sea and West Coasts. IMTA mimics a natural Urchin (Strongylocentrotus droebachiensis), CO-FUNDED BY: Kelly Cove Salmon Ltd. ecosystem by combining the farming of and Sea Scallop (Placopecten magellanicus). PROJECT LEAD: Shawn Robinson (DFO) multiple, complementary species from Results are showing the species can take up PROJECT TEAM: Terralynn Lander, different levels of the food chain in a way fish farm nutrients and experience significantly Craig Smith (DFO) that allows a portion of the uneaten feed, increased growth rates compared to their wild wastes, nutrients, and by-products of one conspecifics. COLLABORATORS: Keng Pee Ang (KCS) species to be recaptured and converted The results of this project will provide CONTACT: [email protected] into fertilizer, feed, and energy for the some of the information required by the WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ growth of the other species. aquaculture industry to create effective acrdp-pcrda/projects-projets/M-14-01-002-eng.html Different trophic levels have different Standard Operating Procedures to farm extraction efficiencies. The third extractive these species in a way that reduces the level of the IMTA food chain (benthic portion) environmental impact of the site. It will needs further research to develop the suite also identify research areas that may of species and the structures for industry to be profitable for further biological or adopt to viably reduce the environmental technological development. 76 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Impact of Finfish Farms in Eastern Canada on Lobster Distribution and Condition

rganic waste from coastal net-pen fish farming may settle to the sea Obottom close to farms, becoming a novel and attractive food source for wild animals. In addition, the physical structures associated with net-pens may act as artificial reefs and attract a variety of mobile predatory and scavenging species. Little work has addressed how such changes may have bottom-up effects that impact fisheries species. Impacts may not be restricted to aggregating animals around farm sites, but may also include impacts to wild fisheries due to altered productivity, distribution, or catchability of target species. Indeed, some fishers believe that lobsters congregate in aquaculture sites and thus deploy their traps immediately outside of farm sites whereas others avoid farms areas and do not consider these areas as high quality fishing A lobster fitted with an acoustic transmitter to follow their movements within and around salmon farms in grounds. Lobster is one of the most widely southwest New Brunswick. Photo: Chris McKindsey (DFO) and intensively fished species in Eastern Canada and landings are at historically high levels. Concurrently, the production and the number of fish farms have also increased. Concerns about the influence of finfish aquaculture sites on lobster distribution and condition may create challenges for managers, especially if the lobster fishery faces challenges, such as shell disease or decreases in landings, in the coming years as scientific information on the subject is largely absent. This project examines the spatial distribution and movement of lobster within and around finfish aquaculture sites to Deployment of hydrophones around a salmon farm in Doctor’s Cove, southwest New Brunswick, to triangulate evaluate their association with fish farms signals from acoustic transmitters to follow lobster movements. Photo: Émilie Simard (DFO) areas. We will also evaluate how bottom-up effects induced by farm-related organic loading influences lobster condition. Influence of Eastern Oyster environmental conditions (i.e., different types of sediments) and also operations of other (Crassostrea virginica) DATE: APR. 2016–MAR. 2019 culturists. We hypothesize that light limitation Aquaculture Overwintering may not impact mature eelgrass during the FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR) on Eelgrass (Zostera marina) autumn and winter months because the oyster bags are placed on the bottom as PROJECT LEAD: Chris McKindsey (DFO) hade produced by floating and the plants undergo a period of low/no PROJECT TEAM: Rénald Belley, Andrew Cooper, off-bottom oyster bag culture has photosynthetic activity. Annick Drouin, Julien Gaudette, Frédéric Hartog, been shown to significantly impact Peter Lawton, Shawn Robinson, Paul Robichaud, S the localized structure and productivity of DATE: APR. 2012–APR. 2015 François Roy, Anne-Sara Sean, Émilie Simard (DFO) eelgrass beds. Considering these results, FUNDED BY: DFO–Program for Aquaculture COLLABORATORS: Ocean Tracking Network the objective of the present study was to Regulatory Research (DFO–PARR) (OTN); Rémy Rochette (UNB); Pierre Blier (UQAR); determine if the overwintering of oyster gear Keng Pee Ang (Cooke Aquaculture Inc.) directly on eelgrass beds could produce PROJECT LEAD: Simon Courtenay (DFO; U Waterloo) CONTACT: [email protected] results similar to those observed during the growing season. To test this hypothesis, we PROJECT TEAM: Monica Boudreau (DFO); WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Marc Skinner (Stantec Consulting Ltd.; parr-prra/projects-projets/2016-P-01-eng.html assessed impacts of overwintering practices in an experimental overwintering area and a Canadian Rivers Institute) 13-year-old active overwintering site. Overall, COLLABORATORS: André Mallet (L’Étang the results of our study suggest no apparent Ruisseau Bar Ltd.) impacts of oyster overwintering practices on CONTACT: [email protected] eelgrass beds. We recommend additional www.dfo-mpo.gc.ca/aquaculture/rp-pr/ studies in other bays to assess potential WEBSITE: parr-prra/projects-projets/2012-G-01-eng.html impacts of this practice under different CANADIAN AQUACULTURE R&D REVIEW 2017 ENVIRONMENTAL INTERACTIONS 77

Evaluating the Effectiveness of Fallowing as a Mitigation Tool at Effects of Cage Aquaculture Predominantly Hard-Bottom Aquaculture Sites in Newfoundland on Freshwater Benthic Communities tlantic Salmon aquaculture sites basis for changes in the distribution of in Newfoundland are located bacterial mats and OPC during fallowing will age aquaculture results in the release A predominantly over hard ocean be examined to improve our understanding of organic matter to the lake with substrates where sediment samples are of the processes of benthic recovery in the the greatest deposition under the consistently difficult to obtain and require the Newfoundland and Labrador Region. The C cages. Organic matter deposition can lead use of visual imaging to monitor aquaculture results will shed light on the degree of to alterations of the benthic invertebrate impacts. Fallowing (leaving the site without benthic recovery associated with various populations exposed. Total abundance, fish) at the end of a production cycle is lengths of fallowing, the biological processes richness, and biomass are classical proxies the primary mitigation measure to manage underlying OPC dynamics in association for benthic community succession during impacts from uneaten food and faeces. with organic matter degradation, and the exposure to organic matter enrichment. Optimal fallowing times and the factors that effectiveness of fallowing as a mitigation Measures of total abundance, richness, and can influence the rate of benthic community strategy. biomass of benthos from three commercial recovery remain key knowledge gaps in the freshwater finfish aquaculture farms in Lake environmental management of the industry. DATE: APR. 2014–MAR. 2017 Huron were presented spatially to measure This project seeks to examine the FUNDED BY: DFO–Program for Aquaculture the net effect of aquaculture waste. In recovery processes at predominantly Regulatory Research (DFO–PARR) 2009 and 2012, sediment cores were hard-bottom aquaculture sites undergoing collected from under the cages to 110 m PROJECT LEAD: Dounia Hamoutene (DFO) fallowing by evaluating how the fallowing distance away, as well as at six distant duration influences the distribution of visual PROJECT TEAM: Kimberley Burt, reference sites. Our data showed that total bioindicators of organic disposition such as Flora Salvo (DFO) abundance, richness and biomass of bacterial mats and Opportunistic Polychaete COLLABORATORS: Suzanne Dufour (MUN); benthos were suppressed under and in Complexes (OPC). This study will also Robert Sweeney (SIMCorp) close proximity to the farm, while further examine changes in the presence of CONTACT: [email protected] afield invertebrate abundance and biomass flocculent matter and non-indicator species of some taxa were elevated above reference www.dfo-mpo.gc.ca/aquaculture/rp-pr/ (epifauna) during fallowing. The biological WEBSITE: values. We quantified the total biomass per parr-prra/projects-projets/2014-NL-07-eng.html m2 and initial results found that total biomass loss was comparable amongst all three farms. However, reference sites are the determinant for calculating the net gain or Characterization of Pesticide Post-Deposit Exposure Zones loss of benthic invertebrates at a farm and net biomass results differed among farms. he finfish aquaculture industry within conducted in relation to salmon farming in Farm three measured a net gain as Canada can make use of pesticide the Bay of Fundy and will contribute to a compared to the other two farms that bath treatments to manage sea lice foundation of knowledge that can be used to T experienced a smaller net loss. Net infestations on netpen farmed salmon. Once design a post-deposit pesticide monitoring biomass is a simplistic metric and does each treatment is completed, the pesticide approach. The work also complements other not completely present the dynamic bath water is released into the ambient projects focused on biochemical oxygen change in diversity or functional groups by water where the pesticide is transported demanding (BOD) matter dispersal from benthic invertebrates. Rather, net biomass and diluted by the ambient hydrographic fish farms. represents the recycling of energy from conditions. Non-target organisms and aquaculture farm waste into invertebrates habitats within the spatial and temporal DATE: APR. 2016–MAR. 2019 and potentially to higher trophic levels domain occupied by the pesticide may FUNDED BY: DFO–Program for Aquaculture like wild fish. experience exposure to the pesticide. Regulatory Research (DFO–PARR) The deposition activities are authorized and guided by the Aquaculture Activity PROJECT LEAD: Fred Page (DFO) DATE: APR. 2011–APR. 2015 Regulations under the Fisheries Act. This PROJECT TEAM: Susan Haigh, Yongshen Wu, FUNDED BY: DFO–Program for Aquaculture project builds on earlier modelling and field Brent Law, Stacey Paul, Mitchell O’Flerhaty-Sproul, Regulatory Research (DFO–PARR) Sean Corrigan, Sarah Scouten, Monica Lyons, work aimed at defining the exposure zones PROJECT LEAD: Cheryl Podemski (DFO) by refining vertical dispersion estimates and David Wong (DFO) PROJECT TEAM: Jian Zhang, Megan Otu (DFO) incorporating baroclinicity in the circulation COLLABORATORS: Michael Beattie (NBDAAF); models, and by exploring how model Kevin Wickens (Health Canada) CONTACT: [email protected] exposure zones vary with fish production CONTACT: [email protected] WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ husbandry factors such as treatment parr-prra/projects-projets/2011-CA-07-eng.html WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ method, net pen size, and frequency of bath parr-prra/projects-projets/2016-M-12-eng.html treatment. This project will also explore to what extent the zones include exposure of benthic environments. The work will be 78 ENVIRONMENTAL INTERACTIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Comparing the Impact of Bottom and Suspended Oyster Culture on Bay-Scale Food Resources (Foxley/ Trout River, PEI)

Bottom cultured oyster (Foxley, PEI). Photo: Luc Comeau (DFO)

ivalve aquaculture is extractive available food resources. The 2013-2014 rather than fed and there is results on quantitative comparison of Binherent sustainability assuming suspended and bottom oyster culture in one can manage the limiting resource, PEI suggested that a transition from bottom i.e., phytoplankton. Oyster aquaculture is to suspended culture results in an actual gradually evolving from a traditional use of reduction in oyster stock densities and the benthic environment (bottom culture) grazing rates. to a novel use of the three-dimensional water column (suspended culture). Both DATE: APR. 2012–APR. 2015 industry and regulators recognize the need FUNDED BY: DFO–Program for Aquaculture to evaluate the ecological impact of growing Regulatory Research (DFO–PARR) oysters in the water column. Specifically, the project addressed three objectives: PROJECT LEADS: Luc Comeau, Rémi Sonier (DFO) 1) assessing the bottom vs. suspended oysters diet overlap; 2) determining filtration PROJECT TEAM: Réjean Tremblay (UQAR-ISMER) rates of oysters from the two culture CONTACT: [email protected], types (bottom and suspended); and [email protected] 3) incorporating the latter results into a WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Floating cages for suspended oyster culture simple bay-scale model and quantify the parr-prra/projects-projets/2012-G-05-eng.html (Foxley, PEI). Photo: Luc Comeau (DFO) impact of different culture scenarios on CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 79 CIMTAN

2010–2017: Seven Productive Years for the Can Filter-Feeding Bivalves Ingest Planktonic A Variation on the IMTA Theme for Land-Based, Canadian Integrated Multi-Trophic Aquaculture Sea Lice, Leading to Reduced Sea Lice Numbers Freshwater Aquaculture Operations: The Network (CIMTAN) on Cultivated Salmon? Development of Freshwater IMTA (FIMTA) for Salmon and Aquaponic Plants Quantifying the Capture and Conversion Presence, Effect, and Bioaccumulation of Efficiencies of Species Being Considered for Therapeutants in Polychaetes Spatial and Temporal Particulate Dynamics and Organic Extraction in Open-Water IMTA Systems Their Influence on Update Species Placement Mathematical Modelling for Open-Water IMTA: at an IMTA Site Cultivation of Complementary Inorganic Extractive Developing Tools to Support System Design and Species for Increased System Performance Measures of Sustainability Design and Demonstration of a Renewable Energy System Powering an IMTA Site Quantifying the Role of Microbes in the Nutrient Evaluating the Performance of Proposed and Recycling of Organic Material from IMTA Sites Existing IMTA Sites Using an Ecosystem Optimizing IMTA Species Components Stocking Modelling Approach Densities and Infrastructure Orientation to Quantifying Energy and Nutrient Dispersal Maximize Overall System Efficiency and Scales of Influence on Wild Species from Extensive Versus Intensive IMTA Systems – Open-Water IMTA Sites Hydrographic Influences and the Implications to Economic Implications of IMTA Infrastructure Design and Operational Efficiency Loma salmonae: A Microsporidian Model to Help Social Implications of IMTA: Coastal Communities Assess Transmission Dynamics to Pathogens and the Appetite for Aquaculture within an IMTA Setting 80 CIMTAN CANADIAN AQUACULTURE R&D REVIEW 2017

2010–2017: Seven Productive Years for the Canadian Integrated Multi-Trophic Aquaculture Network (CIMTAN)

fter seven years of intense activities, between 2010 and 2017, the NSERC A strategic network, the Canadian Integrated Multi-Trophic Aquaculture Network (CIMTAN), is finished. The aim of CIMTAN’s research was to ecologically engineer systems for increased environmental sustainability (ecosystem services and green technologies for improved ecosystem health), economic stability (improved output, lower costs, product diversification, risk reduction, and job creation in coastal and rural communities), and societal acceptability (better management practices, improved regulatory governance, nutrient trading credit incentives, and appreciation of differentiated and safe products). The Network was organized into three linked Domains: 1) environmental system performance and species interactions; 2) system design and engineering; and 3) economic analyses and social implications. An IMTA site in the Bay of Fundy, New Brunswick, Canada: two salmon cages on the left, one mussel raft on the Each Domain was co-led by one scientist at right and two seaweed rafts in the background. Photo: Thierry Chopin (UNBSJ) an academic institution and one at a Fisheries and Oceans Canada (DFO) laboratory. The transfer in several sectors, to the extent that 842 subscribers, some of whom are known entire Network was comprised of it is no longer necessary to re-explain what to have redistributed CIMTAN Snippets 28 scientists from 8 universities, 6 DFO IMTA is about at each meeting. to others. YouTube has been a very efficient laboratories, 1 provincial government CIMTAN was always interested in dissemination platform for the IMTA concept laboratory (New Brunswick Research and disseminating and translating its scientific and the principles on which it is based. Productivity Council), and 4 industrial partners. research, results, and perspectives. CIMTAN By December 31, 2016, the IMTA YouTube The Network was hosted by the University produced a substantial number of publications channel (https://www.youtube.com/user/ of New Brunswick in Saint John (UNBSJ), (617), testifying to the accomplishments and imtacanada/videos) had reached 85,334 total where the Scientific Director of the Network vitality of the Network. More than 1150 contacts views of its 15 videos. was located. were made with 232 media outlets across The following research articles in this The budget for CIMTAN was nearly $12.8 M 42 countries, through interviews or citations. section describe each of the 16 projects over the 7 years of its existence. This was The deliberate choice to use a diverse array of CIMTAN. consequential as it enabled the Network to of documents and media platforms (scientific papers, papers and abstracts in conference obtain far-reaching achievements along the DATE: JAN. 2010–JAN. 2017 continuum R&D&C (commercialization). Of proceedings, book chapters, theses, reports, this, over $5 M was received from NSERC professional magazines articles, newspapers/ FUNDED BY: Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic with the rest leveraged through both cash radio/TV interviews and documentaries, Network Program and in-kind contributions from government, public school activities, Google Scholar, academic, and industrial partners. ResearchGate, LinkedIn, YouTube videos, CO-FUNDED BY: Fisheries and Oceans Canada Training of highly qualified personnel (HQP) CIMTAN Snippets newsletter, Wikipedia, etc.) (DFO); University of New Brunswick (UNB); New Brunswick Research Productivity Council (NBRPC); was a very high priority for CIMTAN and has enabled the Network to reach varied Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; 137 HQP (120% of the initial target) were targeted fields and audiences in Canada and Marine Harvest Canada Limited; Grieg Seafood trained: 76 undergraduate students, 35 Masters beyond, and to spread the IMTA message BC Ltd. students, 6 PhD students, 7 postdoctoral widely with researchers, federal and provincial PROJECT LEAD: Thierry Chopin (UNBSJ) fellows, 12 technicians, and 1 research scientist. agencies, the industry, professional CIMTAN enabled the priming of young talents associations, coastal and rural communities, PROJECT TEAM: Bruce MacDonald, Adrian Hamer (UNBSJ); Gregor Reid (UNBSJ; DFO); so they could enter a highly skilled labour force First Nations, national and international Shawn Robinson, Chris Pearce, Saleem Rahman well-prepared, capable of thinking critically environmental non-governmental organizations (DFO); Maycira Costa (UVic); Duncan Knowler (SFU) and independently, and well-versed in the (ENGOs), and the general and school public. interdisciplinary approach to problem solving. Two media were very successful at COLLABORATORS: DFO; NBRPC; Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; Marine Our CIMTAN HQP have either pursued higher reaching audiences beyond those associated Harvest Canada Limited; Grieg Seafood BC Ltd. academic degrees or found jobs in a variety with the traditional scientific dissemination of sectors (academic, industrial, regulatory or tools: the Network newsletter CIMTAN CONTACT: [email protected] non-governmental). It is interesting to see Snippets and 15 videos posted on YouTube. WEBSITE: http://www.cimtan.ca/ how these HQP have become respected There were 40 issues of CIMTAN Snippets professionals and remarkable agents of over 6 years, totaling 331 pages of information knowledge dissemination and technology about the activities of the Network, sent to CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 81

Quantifying the Capture and Conversion Efficiencies of Species Being Considered for Organic Extraction in Open-Water IMTA Systems

his project assessed the capability of different invertebrate species to T capture, absorb, and convert particulate fish-farm waste into new production. On the east coast, Blue Mussels (Mytilus edulis) were capable of ingesting and efficiently absorbing small organic material from both fish food and faeces. After a variety of feeding trials using artificial diets in the laboratory and natural particles at IMTA sites, we determined that the Orange-Footed Sea California Sea Cucumber, Parastichopus californicus. Photo: Dominique Bureau (DFO) Cucumber (Cucumaria frondosa) could also efficiently extract larger organic material from farm waste. Biodeposition techniques and Cultivation of Complementary Inorganic Extractive Species for flume feeding trials revealed that C. frondosa Increased System Performance fed equally among all particle sizes monitored (200-1200 µm) but rates of clearance in his project investigates the red alga aquaculture operations. It has highlighted -1 the field (7.2 L day ) were relatively low Palmaria palmata (Dulse) for increased the ecosystem functions and services provided compared to other species being inorganic biomitigation of IMTA systems by the inorganic extractive component of considered for mitigation. T when kelps are not present at the sites. IMTA. It has brought understanding to the On the west coast, species assessed for Large-scale cultivation of this species has been need to consider IMTA within the context extractive capabilities include filter feeders hampered by a complex life history, in which of an integrated coastal area management such as Basket Cockles (Clinocardium nuttallii) P. palmata alternates between sexual (with strategy. Integration should be understood and Blue Mussels (M. edulis), as well as macroscopic male and microscopic female as cultivation in proximity, not considering deposit feeders such as Green Sea Urchins gametophytes) and asexual (with macroscopic absolute distances but connectivity in terms (Strongylocentrotus droebachiensis), California tetrasporophytes) reproduction. One of the of ecosystemic functionalities, which means Sea Cucumbers (Parastichopus californicus), current challenges is that male gametophytes that entire bays/coastal areas/regions could and Pacific Prawns (Pandalus platyceros). are indistinguishable from tetrasporophytes be the units of IMTA management. Green Sea Urchins and California Sea by conventional microscopy when they are Cucumbers ingest and absorb Sablefish not reproductive. DATE: JAN. 2010–JAN. 2017 (Anoplopoma fimbria) faeces at rates We took two approaches (molecular and FUNDED BY: Natural Sciences and Engineering comparable to or higher than those for spectroscopic) to make identification easier. traditional diets such as kelps and natural Research Council of Canada (NSERC) Strategic We designed and tested primers to target Network Program sediment, respectively. DNA in an intron region in an actin gene that Fisheries and Oceans Canada This research has enabled the assessment is expressed in tetrasporophytes, but not in CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New of nutritional responses for a variety of males, in an attempt to identify a sex-linked shellfish and deposit-feeder species on Brunswick Research Productivity Council (NBRPC); molecular marker, however, the intron region Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; diets of fish-farm organics, thereby providing showed no difference. Individual ratios, or Marine Harvest Canada Limited; Grieg Seafood crucial insight into co-cultured species combinations of ratios, of spectral bands BC Ltd. selection and IMTA system efficiency. obtained by Raman and near infrared (NIR) PROJECT LEAD: Thierry Chopin (UNBSJ) spectroscopy allowed for classification Constanza Chianale, DATE: JAN. 2010–JAN. 2017 PROJECT TEAM: between male gametophytes and Caroline Longtin, Ellen Belyea, Adrian Hamer, FUNDED BY: Natural Sciences and Engineering tetrasporophytes. Samuel Backman (UNBSJ) Research Council of Canada (NSERC) Strategic The cultivation of P. palmata in the laboratory Cooke Aquaculture Inc. Network Program has progressed (design and testing of new COLLABORATORS: [email protected] CO-FUNDED BY: Fisheries and Oceans Canada substrates/panels; increased light irradiance CONTACT: (DFO); University of New Brunswick (UNB); New and photoperiod). The best timing of transfer WEBSITE: http://www.cimtan.ca/ Brunswick Research Productivity Council (NBRPC); to the sites remains to be better understood Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; to reduce biofouling. Marine Harvest Canada Limited.; Grieg Seafood The cultivation, harvesting, and processing BC Ltd. of the two kelps (Saccharina latissima and PROJECT LEAD: Bruce MacDonald (UNBSJ) Alaria esculenta) continue to be improved. PROJECT TEAM: Shawn Robinson, Chris Pearce, They have continuously been organically Dan Curtis (DFO); Gregor Reid, Emily Nelson, certified since 2014. Kurt Simmons (UNBSJ); Stephen Cross, Lindsay Orr, The project is also looking at the Sarah Sprague (UVic); Helen Gurney-Smith (VIU); development of appropriate and efficient Shannon Balfry (UBC); Vancouver Aquarium); regulations for seaweeds and the Steve Pace (UBC) management of inorganic nutrient COLLABORATORS: Cooke Aquaculture Inc.; loading, within an integrated coastal Kyuquot SEAfoods Ltd. area management strategy and scale. CONTACT: [email protected] This research has developed a better Line of Sugar Kelp (Saccharina latissima) at an IMTA site in the Bay of Fundy, New Brunswick, Canada. WEBSITE: http://www.cimtan.ca/ understanding of the issues related to the management of the inorganic load from Photo: Thierry Chopin (UNBSJ) 82 CIMTAN CANADIAN AQUACULTURE R&D REVIEW 2017

Quantifying the Role of Microbes in the Nutrient Recycling of Organic Material from IMTA Sites

lowest where the bacteria and other to convert organic carbon which will have microbes reside. direct implications on feeding rates of the The objective of this project was to evaluate fish and time required for fallowing the site and quantify the role that bacteria play in after a production cycle. The research may nutrient recycling at a salmon aquaculture site also provide insights on what proactive and to evaluate the relative scale of their ability measures might be taken before fish to convert organic particles into inorganic production starts. components. Specifically, we enumerated bacteria and their respiration rates on and away DATE: JAN. 2010–JAN. 2017 from finfish aquaculture farms in both the water FUNDED BY: Natural Sciences and Engineering column and the benthos on a seasonal basis at Research Council of Canada (NSERC) Strategic Miniature respiration chamber holding a filter (0.2 μm IMTA sites in the Bay of Fundy. Additionally, we Network Program pore size) coated with bacteria and seston from a identified prominent members of the benthic sample. The pink dot is an oxygen optode that reads Fisheries and Oceans Canada and pelagic bacterial communities associated CO-FUNDED BY: oxygen levels over time inside the vial when pulsed (DFO); University of New Brunswick (UNB); New with blue light from outside the vial with the black with the aquaculture sites and how they varied Brunswick Research Productivity Council (NBRPC); fibre optic probe. Photo: Shawn Robinson (DFO) with depth, distance, and time. Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; The results are demonstrating that these Marine Harvest Canada Limited; Grieg Seafood nderstanding the various paths and non-pathogenic bacteria are playing a very BC Ltd. processes by which energy flows large role in carbon conversion on a farm PROJECT LEAD: Shawn Robinson (DFO) through an IMTA site is one of the lease and should be considered in the U PROJECT TEAM: Bruce MacDonald, main objectives in the creation of sustainable design of aquaculture sites in the future. This Thierry Chopin, David Thumbi, Hannah Bradford, aquaculture systems using ecosystem-based information is also contributing to a model Kelli Mitchell, Leslie-Marie MacArthur-Britt, approaches. As food from one trophic level being prepared on energy flow through an Eric Manuel (UNBSJ); Ben Forward (NBRPC); is recycled through another, the energy IMTA site. Terralynn Lander, Craig Smith (DFO) associated with the organic particles is This research provided insight into the role COLLABORATORS: Cooke Aquaculture Inc. stripped out and is converted to inorganic heterotrophic bacteria are playing in the waste products such as ammonia, carbon recycling of organic wastes near salmon CONTACT: [email protected] dioxide, or heat. This transfer process occurs aquaculture farms. This will provide much WEBSITE: http://www.cimtan.ca/ between all trophic levels right down to the needed guidance on what the carrying capacity is for benthic and pelagic microbes

Quantifying Energy and Nutrient Dispersal and Scales of Influence on Wild Species from Open-Water IMTA Sites

his research, on methods to quantify This is key information to support the the effect of mid-water nutrients in design of IMTA sites using nutrient extracting Twild species, revealed that site-specific species, as well as to understand IMTA hydrographic conditions are critical performance measures for those species components for colonization, growth, and integrated for the purpose of extracting quality of many nutrient extracting wild aquaculture-related nutrients. species that inhabit the coastal zone near aquaculture farms. DATE: JAN. 2010–JAN. 2017 One approach has been to sample wild FUNDED BY: Natural Sciences and Engineering species biocolonization to measure changes Research Council of Canada (NSERC) Strategic in diversity and growth in the “near-field” Network Program and “far-field”. This revealed that introduced Fisheries and Oceans Canada habitats placed near and far from CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New aquaculture sites attract very different Brunswick Research Productivity Council (NBRPC); species rather than altered growth of any Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; one dominant organism. Differences in Marine Harvest Canada Limited; Grieg Seafood BC Ltd. mid-water physical environment and the Biocollector plates used to measure natural biocolonization of wild species at an IMTA PROJECT LEAD: Andrew Cooper (DFO) presence of appropriate habitat substrates, aquaculture site. Photo: Andrew Cooper (DFO) from cage structure or coastal topography, PROJECT TEAM: Thierry Chopin, Jonathan Day (UNBSJ) are as important to wild species colonization changes in colour characteristics throughout as the availability of nutrients alone. their growing season. Within a relatively COLLABORATORS: Cooke Aquaculture Inc. Another approach has sought to measure confined geographic location and season, CONTACT: [email protected] changing colour characteristics of wild algal the relationship between colour and tissue species as a proxy to current analytical nutrient content (% nitrogen) is small. However, WEBSITE: http://www.cimtan.ca/ laboratory techniques to measure nitrogen differences in colour and the relationship concentrations in the water column or nitrogen with % nitrogen is more pronounced among content in algal tissues. Several species of different locations and time periods and naturally occurring algae (some of which may could be a potential tool to monitor changes also be commercially important) exhibited in nutrient availability on a larger scale. CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 83

Loma salmonae: A Microsporidian Model to Help Assess Transmission Dynamics to Pathogens within an IMTA Setting

ur goal has been to modify an infection of them stored for several weeks within mussel The introduction of a bivalve component model for the microsporidian pathogen viscera. Spores are not rendered defective alongside a salmon growing operation may OLoma salmonae, and use this model to whether they are retained, or passed within provide beneficial disease reduction services. evaluate the role that Blue Mussels may have egesta; in vitro tests of spore viability have A greater understanding of disease dynamics in extracting environmentally released spores been evaluated against the gold standard between trophic levels is a key part of health within an IMTA setting. Specifically, asking the in vivo measures of infectivity. management within integrated settings. question of whether Blue Mussels may serve to mitigate disease transmission by deactivating DATE: JAN. 2010–JAN. 2017 spores that they encounter during feeding. The FUNDED BY: Natural Sciences and Engineering model has been successfully developed and Research Council of Canada (NSERC) Strategic now allows us to modify various environmental Network Program and temporal parameters. A very useful and Fisheries and Oceans Canada unexpected outcome was the establishment CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New of L. salmonae within cell culture. This advance Brunswick Research Productivity Council (NBRPC); will allow far greater flexibility in our studies, Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; both as a tool for producing spores, but also Marine Harvest Canada Limited; Grieg Seafood for detecting them within environmental niches BC Ltd. under study. To date, we have determined that PROJECT LEAD: Dave Speare (UPEI–AVC ) Blue Mussels are very effective in extracting PROJECT TEAM: Sarah McConnachie, microsporidial spores from the environment; Nicole Guselle (UPEI–AVC) spores are subsequently released in CONTACT: [email protected] pseudofeces, or feces, and small proportion Microsporidial spores developing within a cell-cultured xenoma. Photo: Sarah McConnachie (UPEI–AVC) WEBSITE: http://www.cimtan.ca/

Can Filter-Feeding Bivalves Ingest Planktonic Sea Lice, Leading to Reduced Sea Lice Numbers on Cultivated Salmon?

sea lice densities inside of the cages were low (typically < 1 m-3), and sea louse mitigation by bivalves may, therefore, require the larvae be concentrated using light or other means and/or the strategic placement of a higher density of bivalves. The development of non-chemical sea lice mitigation techniques, such as IMTA filter-feeding bivalves, may help improve the environmental, social, and economic performance of salmon farms.

DATE: JAN. 2010–JAN. 2017

Cleaning biofouling from Pacific Oyster trays at a salmon farm in the Broughton Archipelago, British Columbia. FUNDED BY: Natural Sciences and Engineering Photo: Allison Byrne (UVic; DFO) Research Council of Canada (NSERC) Strategic Network Program

CO-FUNDED BY: Fisheries and Oceans Canada he close proximity of salmon farms and 13 months. The 30,000 experimental oysters (DFO); University of New Brunswick (UNB); New wild Pacific salmon stocks in British were deployed in trays at 1, 3, and 6 m around Brunswick Research Productivity Council (NBRPC); TColumbia (BC) is an important incentive one end of the farm’s 2x7 square-cage array, Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; for precautionary, environmentally-friendly and at a nearby reference site. Marine Harvest Canada Limited; Grieg Seafood BC Ltd. sea lice management strategies. Bivalve growth (both shell size and tissue PROJECT LEAD: Chris Pearce (DFO) A field trial was conducted to determine biomass) was significantly affected by depth whether IMTA filter-feeding bivalves can and side of the fish cage. Oysters from select PROJECT TEAM: Allison Byrne, Janis Webb (UVic; DFO); Stephen Cross (UVic); Simon Jones, provide preventative, natural sea louse control sides were consistently, significantly larger Shawn Robinson (DFO); Matt Miller, Devan Johnson, by ingesting sea lice larvae (nauplii and than those from other sides and from the Colleen Haddad (VIU; DFO) copepodids) from the water column; a system reference site. Sea lice mitigation by oysters Grieg Seafood BC Ltd.; that exploits the sea louse life cycle and was assessed by comparing monthly sea lice COLLABORATORS: Marine Harvest Canada Limited the natural filtration capabilities of bivalves. larval densities inside bivalve and non-bivalve Pacific Oysters, one of several bivalve species fish cages, and by analyzing preserved oyster CONTACT: [email protected] that consumed sea lice larvae in previous digestive tracts for presence of sea lice DNA. WEBSITE: http://www.cimtan.ca/ laboratory experiments, were grown at a Using these methods, no significant evidence commercial Atlantic Salmon farm in BC for of sea lice mitigation was detected. Planktonic 84 CIMTAN CANADIAN AQUACULTURE R&D REVIEW 2017

Presence, Effect, and Bioaccumulation of Therapeutants in Polychaetes

cto-parasites are common on Atlantic and results indicate that anti-sea louse Salmon under cage culture conditions. treatments have the potential to negatively ESevere infestations require treatment affect this species. These negative effects with drugs and pesticides. Considerable could affect the suitability of this species to research has been conducted to assess the be co-cultured in IMTA. risk of these compounds to non-target species, mostly focusing on indigenous species of DATE: JAN. 2010–JAN. 2017 known commercial or ecological value. FUNDED BY: Natural Sciences and Engineering In this project, the non-target species Research Council of Canada (NSERC) Strategic of interest is one being considered as a Network Program co-cultured species in an IMTA setting, the CO-FUNDED BY: Fisheries and Oceans Canada Sand Worm Nereis virens. As a co-cultured Preparing Nereis virens worms for a 30-day sublethal (DFO); University of New Brunswick (UNB); New species, the worms would be exposed to exposure. Photo: Geoffrey McBriarty (UNBSJ) Brunswick Research Productivity Council (NBRPC); compounds during routine anti-parasitic Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; treatments. Worms were exposed, in treated Marine Harvest Canada Limited; Grieg Seafood water, sediment, or sand, to one drug (Slice®, well above the recommended dose, but BC Ltd. active ingredient emamectin benzoate (EB)) survived exposures in sediment. Worms PROJECT LEAD: Karen Kidd (UNBSJ) and one pesticide (AlphaMax®, active exposed to as little as 11 µg/g of wet sediment PROJECT TEAM: Les Burridge (DFO); ingredient deltamethrin). Survival was in 30-day trials stopped burrowing and Jordana van Geest (DFO; UNBSJ); monitored, as well as sublethal indicators showed poor condition, including loss of Geoffrey McBriarty (UNBSJ) of “wellness”. weight. Anti-sea louse treatment could be Cooke Aquaculture Inc. Worms exposed to Slice® survived exposure hazardous to N. virens; however, in the COLLABORATORS: to environmentally-relevant concentrations absence of data regarding concentrations of CONTACT: [email protected] (~360 µg/kg dry sand) of the product; however, EB or deltamethrin near cage sites, it is difficult WEBSITE: http://www.cimtan.ca/ in 30-day studies worms stopped burrowing to assess the potential risk to cultured worms. in the treated substrate and showed signs of While the two anti-sea louse products are poor condition including loss of weight. Worms not particularly lethal to N. virens, worms exposed to AlphaMax® died at concentrations were affected by exposure to these products

Mathematical Modelling for Open-Water IMTA: Developing Tools to Support System Design and Measures of Sustainability

his project aimed to quantify efficiency of nutrient recovery and augmented Tgrowth in open-water IMTA systems. One study explored the seaweed biomass required to remove soluble nutrients from salmon culture. The mean weight ratios of the seaweeds Alaria esculenta and Saccharina latissima required to sequester all soluble nutrients excreted per unit weight of salmon range from 4:1 to 13:1, depending Schematic representation of model elements to estimate weight ratios of seaweeds needed to sequester on the nutrient. Another study reported nutrients from salmon. the proportion of fish farm solids ingested by mussels needed to reduce site-wide discrepancies between annual peak loading DATE: JAN. 2010–JAN. 2017 organic loading at an IMTA site, which periods, enabling better matches of co-cultured FUNDED BY: Natural Sciences and Engineering ranged between 10% and 20%. A third species biomass with nutrient supply compared Research Council of Canada (NSERC) Strategic study suggested the biomitigation potential to more rapidly growing fish. Network Program of mussels will be greatest where seston Some field data were recently combined CO-FUNDED BY: Fisheries and Oceans Canada abundance is low, organic dietary content with Norwegian field data to publish a (DFO); University of New Brunswick (UNB); New high, and that achieving maximal waste report on discrete water quality sampling at Brunswick Research Productivity Council (NBRPC); extraction by mussel co-culture entails open-water aquaculture sites, their limitations Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; food particle depletion that may limit and recommended strategies. Finally, project Marine Harvest Canada Limited; Grieg Seafood BC Ltd. mussel production. results are providing valuable inputs for an Commercial Sablefish growth and nutrient IMTA bio-economic model under development. PROJECT LEAD: Gregor Reid (UNBSJ; DFO) loading were also modelled. Results suggested This work has led to a better understanding PROJECT TEAM: Bruce MacDonald, that the predicted peak nutrient loading in year of overall system efficiencies and has guided Thierry Chopin (UNBSJ); Shawn Robinson, two of production was only 1.7 times greater the effective development of open-water Peter Cranford (DFO); Margaret Quinton (U Guelph) than the peak loading in year one, less than IMTA farms, through such mechanisms as the COLLABORATORS: Cooke Aquaculture Inc. half the annual loading difference reported for Canadian Science Advisory Secretariat review cultured Atlantic Salmon. The slower relative process to support policy development and CONTACT: [email protected] growth rate of large Sablefish reduces the management for Fisheries and Oceans Canada. WEBSITE: http://www.cimtan.ca/ CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 85

Evaluating the Performance of Proposed and Existing IMTA Sites Using an Ecosystem Modelling Approach

obtaining maximal mitigation under oligotrophic conditions that stimulate shellfish filtration activity; (2) the dominance of vertical fluxes of particulate matter triggered by the high settling velocity of finfish aquaculture wastes suggests that suspended shellfish aquaculture cannot significantly reduce organic loading of the seabed; and consequently, (3) waste mitigation at IMTA sites should be best achieved by placing organic extractive species (e.g., deposit feeders) on the seabed directly beneath finfish cages rather than in suspension in the water column.

Plan view and vertical profile trajectories after 12 hours of a subset of particles with different settling velocities DATE: SEP. 2012–JAN. 2017 released at random positions in three finfish cages (light grey). Mussel longlines are represented in light blue. Note that the vertical and horizontal scales in the vertical profile are different for visualization purposes. FUNDED BY: Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Network Program aximizing the mitigation potential of different components of the seston, including CO-FUNDED BY: Fisheries and Oceans Canada open-water finfish-shellfish IMTA farms feed wastes, fish faeces, shellfish faeces, (DFO); University of New Brunswick (UNB); New Mis complex in terms of co-locating the natural detritus, and phytoplankton. Based Brunswick Research Productivity Council (NBRPC); trophic components. Both the dispersal of on the specific characterization of these fluxes Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; finfish aquaculture wastes and biological to local conditions, the model can be used Marine Harvest Canada Limited; Grieg Seafood processes are highly influenced by water to explore different spatial arrangements of BC Ltd. circulation. Consequently, the evaluation of IMTA farms for evaluating finfish-shellfish farm PROJECT LEAD: Jonathan Grant (Dalhousie U) shellfish-finfish synergy requires a combined mitigation efficiency. A hypothetical IMTA site PROJECT TEAM: Ramón Filgueira (Dalhousie U); study of biological and physical processes, was used as a testing ground of the model Peter Cranford, Thomas Guyondet (DFO); which can be achieved by the implementation to explore mitigation efficiency under a Gregor Reid (UNBSJ; DFO) and coupling of mathematical models. broad range of environmental conditions Cooke Aquaculture Inc. In the context of this project, a highly and farm arrangements. COLLABORATORS: configurable mathematical model that can be The model predicts that: (1) mitigation CONTACT: [email protected] applied at the apparent spatial scale of IMTA efficiency is highly dependent on the WEBSITE: http://www.cimtan.ca/ sites has been developed. The model tracks background environmental conditions,

Extensive Versus Intensive IMTA Systems – Hydrographic Influences and the Implications to Infrastructure Design and Operational Efficiency

This was followed by the development of DATE: JAN. 2010–JAN. 2017 1:15 scale model cage-arrays, which were FUNDED BY: Natural Sciences and Engineering deployed in the Flume Tank facility at Research Council of Canada (NSERC) Strategic Memorial University of Newfoundland. Network Program Current meters measured wake, velocity, CO-FUNDED BY: Fisheries and Oceans Canada and turbulence around circular and square (DFO); University of New Brunswick (UNB); New aquaculture cage-arrays, deployed in common Brunswick Research Productivity Council (NBRPC); configurations used on the west and east Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; coasts. Dye release studies showed how flow Marine Harvest Canada Limited; Grieg Seafood BC Ltd. fields in and around cages behaved within and down-stream from the array. Results PROJECT LEAD: Gregor Reid (UNBSJ; DFO) Dye release study with 1:15 scale model cage-array, at the Flume Tank facility of Memorial University of quantified large velocity deficits in cages PROJECT TEAM: Tiger Jeans, Adam Turner Newfoundland. Photo: Adam Turner (UNBF) wakes, flow forcing around and below cages, (UNBF); Mike Foreman (DFO); Stephen Cross, and unsteadiness of large scale turbulence in Di Wan (UVic) his project helped to quantify near array wakes. The dye release data agree well COLLABORATORS: SEA Vision Group Ltd.; GMG and far-field hydrodynamics of square with wake velocity measurements. Fish Services Ltd.; Marine Harvest Canada Limited and circular cage arrays to guide in This work has led to a better understanding T CONTACT: [email protected] the placement of co-cultured species. Initial of overall system efficiencies and has guided project work utilized the Finite-Volume the effective development of open-water WEBSITE: http://www.cimtan.ca/ primitive equation Community Ocean Model IMTA farms, through such mechanisms as the (FVCOM) to model localized currents around Canadian Science Advisory Secretariat review an IMTA site in Kyuquot Sound, Vancouver process to support policy development and Island, to explore influences at the bay-scale. management for Fisheries and Oceans Canada. 86 CIMTAN CANADIAN AQUACULTURE R&D REVIEW 2017

A Variation on the IMTA Theme for Land-Based, Freshwater Aquaculture Operations: The Development of Freshwater IMTA (FIMTA) for Salmon and Aquaponic Plants

reshwater IMTA (FIMTA) applies the was to identify a suitable freshwater salmon temperature and light controlled pilot-scale same principles as those used in hatchery. This was done with routine water FIMTA/aquaponic system to test potential Fmarine IMTA, but in a freshwater testing at a number of sampling locations plant species in terms of growth and nutrient setting. Aquaponics is a form of FIMTA that within eight hatcheries (4 flow-through and removal capabilities. Biochar produced from combines animal aquaculture and plant 4 recirculating). The data were used to select IMTA grown kelps was used as a substrate. culture, through a microbial link and in a a hatchery for further development and to A total of 13 plant species were tested at symbiotic relationship. Wastes produced also create a software program that can be temperatures of 10-15°C, as this is the optimal from the fish are either absorbed directly used by hatchery managers to quickly identify water temperature range for growing salmon by the plants or converted by microbes inadequacies in their water treatment systems in freshwater hatcheries. The ability of the and then consumed by the plants. and effluent discharge. The second part of system to remove nutrients from the collected The development of our FIMTA system the investigation was to collect effluent water salmon effluent varied depending on the involved a two-part investigation. The first part from the selected hatchery and use it in a species selected and the biomass they produced, as well as the variability of nutrient levels in the collected effluent. The analyses indicated that recirculating hatcheries are more valuable candidates for FIMTA systems than conventional flow-through hatcheries. The development of FIMTA for commercial salmon hatcheries will aid in the completion of IMTA from egg to plate. Not only can this be useful for branding purposes, but it can also aid farmers in waste reduction, increased water reuse, increased product diversification, and improvement of societal acceptance of the industry. In particular, reducing phosphorus levels in effluents can help farmers meet water quality guidelines and prevent eutrophication in the environment. IMTA and FIMTA are included in the Canadian Organic Aquaculture Standard.

DATE: SEP. 2012–JAN. 2017

FUNDED BY: Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Network Program

CO-FUNDED BY: Fisheries and Oceans Canada (DFO); University of New Brunswick (UNB); New Brunswick Research Productivity Council (NBRPC); Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; Marine Harvest Canada Limited; Grieg Seafood BC Ltd.

PROJECT LEAD: Thierry Chopin (UNBSJ)

PROJECT TEAM: Stacy Murray, Hamid Khoda Bakhsh, Ellen Belyea, Adrian Hamer (UNBSJ)

COLLABORATORS: Cooke Aquaculture Inc.

CONTACT: [email protected]

WEBSITE: http://www.cimtan.ca/

The principles of marine IMTA can also be applied to land-based, freshwater systems, also called aquaponics. Yarrow, mint, lettuce, chamomile, and nasturtium after six weeks of growth at 13-15°C in effluent collected at a commercial salmon hatchery. Photo: Thierry Chopin (UNBSJ) CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 87

Spatial and Temporal Particulate Dynamics and Their Influence on Update Species Placement at an IMTA Site

nvironmental concerns about the location of open-water aquaculture Esites are based on issues such as organic wastes, primarily made up of uneaten feed and fecal material. IMTA can potentially minimize this issue by placing species that capture the produced organic matter. The main goal of this project was to investigate the open-water daily temporal and vertical dispersal of waste particles for better defining the placement of extractive species and the required background environmental conditions at an IMTA site on the west coast of Vancouver Island. We conducted in situ measurements, before and after fish feeding, of bio-optical properties, such as particle light scattering and backscattering as proxies for organic particle concentrations, and particulate backscattering ratio and estimated particle index of refraction as indicators of particle compositions, along with discrete measurements of high performance liquid chromatography (HPLC) derived pigments and particulate organic carbon, within and beside a finfish cage in the autumn, spring, and summer. During autumn, lower-cage post feeding optical measurements suggest the dominance of large particles with high indices of refraction, possibly due to the influence of fish fecal particles. Optical variability in spring was driven by diatom bloom conditions (Chaetoceros and Skeletonema) with the optical proxies suggesting dominance by large particles with low indices of refraction. Summer conditions displayed noticeably high and persistent particulate backscattering in surface waters, suggesting the presence of an Emiliania huxleyi bloom. Optical characterization of particulate waste dispersal is constrained ̃ to low ambient seston conditions, and 2011 conditions colour map time series of a) density (sigma-t) and b) backscattering ratio, bbp (660nm) (%). Times are normalized to feeding starting at before-feeding (BF), followed by after-feeding (AF) and then one would be beneficial for environmental hour intervals through the day from the AF time-step. After-feeding times are shown by the vertical solid line monitoring of ambient particles moving and high tide (HT) times are shown by the dashed-dotted vertical line. The horizontal lines represent the central through aquaculture systems. depths, 9 m and 13 m, of the averaged time series data presented in c) and d), respectively. In order to reduce the influence of spikes in the data at a single depth, data were averaged from 8–10 m and 12–14 m, with one standard Tracking and quantifying particulate deviation shown as shaded colours. On these plots bbp̃ (660 nm) (%) (primary y-axis) and ξ (right y-axis) are plotted wastes in these sites generally relies on time at the same time scales as the colour maps, with the grey shading representing feeding duration. consuming, expensive, and low temporal and spatial resolution discrete sampling methods. We utilized in situ bio-optical sensors to DATE: JAN. 2010–JAN. 2017 collect data at high temporal and vertical FUNDED BY: Natural Sciences and Engineering Research Council of Canada (NSERC) Strategic Network Program resolutions to track particulates within and Fisheries and Oceans Canada (DFO); University of New Brunswick (UNB); New Brunswick beside a finfish aquaculture cage. CO-FUNDED BY: Research Productivity Council (NBRPC); Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; Marine Harvest Canada Limited; Grieg Seafood BC Ltd.

PROJECT LEAD: Maycira Costa (UVic)

PROJECT TEAM: Stephen Cross, Justin Del Bel Belluz (UVic); Gregor Reid (UNBSJ; DFO)

COLLABORATORS: Kyuquot SEAfoods Ltd.

CONTACT: [email protected]

WEBSITE: http://www.cimtan.ca/ 88 CIMTAN CANADIAN AQUACULTURE R&D REVIEW 2017

Design and Demonstration of a Renewable Energy System Powering an IMTA Site

Renewable energy provision on site is both viable and critical to achieving truly sustainable operations by avoiding the burning of fossil fuel, as well as associated environmental contamination risks of spills. This project developed a tool for designing such systems and implemented a field Installed renewable energy system components at Kyuquot SEAFoods Ltd. site: modular solar panels on dock demonstration of the system components. (left and middle) with battery storage and power electronics in locker (right). Photo: Stephen Cross (UVic) DATE: JAN. 2010–JAN. 2017

FUNDED BY: Natural Sciences and Engineering MTA aims to reduce the environmental the peak loads, as well as average energy, Research Council of Canada (NSERC) Strategic impacts of seafood production. However, as were satisfied throughout the year. Diesel Network Program most sites are quite remote, diesel fuel is the genset back-up was also considered alongside I CO-FUNDED BY: Fisheries and Oceans Canada primary fuel but is clearly non-sustainable from full battery systems. Mounting of the solar (DFO); University of New Brunswick (UNB); New climate change and fuel spill risk perspectives. panels and battery bank was also investigated Brunswick Research Productivity Council (NBRPC); This project demonstrated a renewable energy on-board the dockside tram and in stationary Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; system starting with a detailed assessment of locations on the docks. In the end, a system Marine Harvest Canada Limited; Grieg Seafood BC Ltd. the solar, wind, tidal, and wave resources with genset backup was found to be most cost PROJECT LEAD: Curran Crawford (UVic) on-site along with the loads associated with effective to meet extreme power loads in case dockside operations (primarily for extractive of protracted low solar irradiation during winter. PROJECT TEAM: Stephen Cross, Adam Gray, Nima Tehrani, Pouya Amid (UVic) species hoists). The site is purposely sheltered The system has been installed on site for long from the open sea, and therefore only solar term in situ testing and validation of the design, COLLABORATORS: Kyuquot SEAfoods Ltd. was found to be viable, although this is likely and the modeling tool is available for optimizing CONTACT: [email protected] different at other IMTA sites. A solar-battery such renewable energy systems at other WEBSITE: http://www.cimtan.ca/ system was optimized with particular emphasis IMTA sites. on fine-grained temporal resolution to ensure

Optimizing IMTA Species Components Stocking Densities and Infrastructure Orientation to Maximize Overall System Efficiency

o improve the sustainability of aquaculture farms. These studies will also IMTA systems, extractive species contribute to the understanding of the risk of Tstocking densities and infrastructure various materials advecting away from the farm orientations need to be optimised such that point-source in relation to the dilution rates. they maximise the interception of excess Expanding our knowledge of P. californicus fish-farm nutrients and IMTA efficiency. as a benthic extractive species within IMTA In order to achieve this objective, the systems and addressing issues such as dynamics of nutrient transfer within the site containment of this species will be mutually needs to be understood to choose the best beneficial to resource managers and configuration and species mix. On the east industry partners. coast, empirical studies were done on flow patterns and organic particle dilution rates Taryn Minch (UNBSJ) and Adena Peters (UNBSJ) DATE: JAN. 2013–JAN. 2017 and their potential utilization by farmed and monitoring an acoustic Doppler current profiler (ADCP) FUNDED BY: Natural Sciences and Engineering wild species was studied on conventional while it measures the current speed and direction of the water in the water column around an aquaculture farm Research Council of Canada (NSERC) Strategic and IMTA salmon sites to provide input on in the Bay of Fundy. Photo: Shawn Robinson (DFO) Network Program a model for site efficiency. Results indicated Fisheries and Oceans Canada substantial spatial and temporal variation in CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New flows around the farm. On the west coast, availability and higher containment success Brunswick Research Productivity Council (NBRPC); the project was focused on optimizing the compared to a control site 320 m away. In Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; benthic extraction of nutrients within an IMTA examining different suspended tray designs, Marine Harvest Canada Limited; Grieg Seafood system using the detritus-feeding California we determined that reduced food availability BC Ltd. Sea Cucumber, Parastichopus californicus. increases the occurrence of visceral atrophy, PROJECT LEAD: Shawn Robinson (DFO) The California Sea Cucumber has been reduces sea cucumber growth, and decreases PROJECT TEAM: Bruce MacDonald, Taryn Minch, established as a promising candidate for overall IMTA system nutrient recycling Thierry Chopin (UNBSJ); Gregor Reid (UNBSJ; DFO); IMTA due to its ability to extract benthic efficiency. A trade-off between containment Chris Pearce (DFO); Stephen Cross, Angela Fortune, nutrients and its high market value. This and food availability was found for the Hailey Davies (UVic); Colleen Haddad (VIU) study confirmed the potential for cultivation co-cultured sea cucumbers. COLLABORATORS: Cooke Aquaculture Inc.; of juvenile P. californicus within suspended Expanding our knowledge of nutrient Effingham Oysters Ltd.; Kyuquot SEAfoods Ltd. trays of an IMTA system. The results of a transfer within current IMTA site designs will six-month field trial indicated a positive effect help the industry develop their infrastructure CONTACT: [email protected] of co-culture with oysters with greater food and also provide inputs into future designs of WEBSITE: http://www.cimtan.ca/ CANADIAN AQUACULTURE R&D REVIEW 2017 CIMTAN 89

Economic Implications of IMTA

ur research has addressed key Our main impact will be on how policymakers economic aspects of the aquaculture respond to the problems associated with Ocommercialization process in monoculture salmon farming and on how Canada, namely benefits for consumers of to help assess the role IMTA should play in aquaculture products and society at large, as the process. This can influence the design of well as potential producer benefits. In the first programs and incentives to help the industry case, extensive household surveying in the better align its activities to benefit society. major consuming region (west coast, USA) Support for IMTA as expressed in survey responses by demonstrated a clear willingness to pay (a) salmon consumers in USA west coast markets, and DATE: JAN. 2010–JAN. 2017 more for IMTA products (e.g., salmon, (b) the general public in British Columbia, Canada. FUNDED BY: Natural Sciences and Engineering shellfish)–averaging 9% more for IMTA Research Council of Canada (NSERC) Strategic versus conventional farmed salmon. Salmon On the producer side, the results are only just Network Program consumers were also willing to pay more for emerging. Earlier economic studies suggested Fisheries and Oceans Canada IMTA products versus those from closed IMTA is more profitable than conventional CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New containment aquaculture (CCA). The reverse salmon farming. But if this is true, why has it not Brunswick Research Productivity Council (NBRPC); was true in the producing region (British been adopted more extensively? Earlier studies Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; Columbia, Canada) when the general likely underestimated the added costs of IMTA Marine Harvest Canada Limited; Grieg Seafood public was asked about their willingness to production, such as the extra management BC Ltd. pay to support the development of IMTA costs and risk associated with a more complex PROJECT LEAD: Duncan Knowler (SFU) versus CCA: CCA attracted greater levels production system. We are carrying out more PROJECT TEAM: Patrick Kitchen, Winnie Yip, of support. In general, preferences for IMTA rigorous modelling to factor in real world Kim Irwin, Stefan Crampton, Hossein Ayouqi, were stronger in the USA than in Canada constraints, such as effluent standards and Mark Carras (SFU) (see figure attached), while preferences for site licensing limits, and to investigate policy [email protected] CCA were stronger in Canada than in the tools to promote IMTA. CONTACT: USA, where a small segment of consumers WEBSITE: http://www.cimtan.ca/ actually see CCA negatively.

Social Implications of IMTA: Coastal Communities and the Appetite for Aquaculture

ur work has continued along the west and east coasts of Canada, and to Our research indicates that the adaptability tenets of social license and situate these perceptions amongst finfish, of the IMTA system is its greatest asset in its Operceptions of IMTA in Canada. In shellfish, and seaweed aquaculture, as future development. Different interest groups 2015, we co-hosted information workshops well as seafood consumption and purchase will express different values in the design, where an exchange of dialogue and preferences. Survey teams were dispatched scale and operations of a system amidst a knowledge explored the particular and to the small coastal communities variegated geographic and often contentious nuanced interests of British Columbia First (populations < 5,000 inhabitants) of political landscape that has characterized Nations communities. Building on this work Vancouver Island in British Columbia, and to much of Canada’s aquaculture development. we sought to further explore perceptions of the Maritime communities along the coast of In the new era of participatory governance, IMTA amongst coastal communities of the Prince Edward Island, New Brunswick, and the undermining or absence of including Nova Scotia. Together, the teams collected significant interest groups may pre-emptively 657 survey interviews. determine the future of IMTA development. Preliminary findings indicate significant differences in awareness of aquaculture and DATE: JAN. 2010–JAN. 2017 in perceptions, and between the two coasts. FUNDED BY: Natural Sciences and Engineering The overall response to IMTA was favourable. Research Council of Canada (NSERC) Strategic In British Columbia and the Maritimes, the Network Program majority of respondents thought the Fisheries and Oceans Canada government should encourage the present CO-FUNDED BY: (DFO); University of New Brunswick (UNB); New finfish aquaculture industry to adopt IMTA Brunswick Research Productivity Council (NBRPC); methods (54% and 71%, respectively), and Cooke Aquaculture Inc.; Kyuquot SEAfoods Ltd.; over 65% of respondents from both coasts Marine Harvest Canada Limited; Grieg Seafood would support the development of new BC Ltd. aquaculture farms based on the IMTA PROJECT LEAD: Mark Flaherty (UVic) production system. Notably, 44% of British PROJECT TEAM: Stephen Cross, Erin Latham, Columbia respondents and 35% of east coast Katie Tebutt (UVic); Grant Murray (VIU) respondents said they would pay more for products certified as IMTA; however, almost CONTACT: [email protected] half of all respondents also identified that WEBSITE: http://www.cimtan.ca/ they do not purchase farmed seafood, citing Erin Latham (UVic) helping with scallop lantern nets. their ability to access and obtain wild seafood Photo: David Schmidt (Gwa’sala-’Nakwaxda’xw through personal means or social networks. First Nation) 90 SHELLFISH: MUSSELS CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS

Effects of Husbandry Practices and Mitigation Mussel Stock Structure and Density in Characterization of Lobster Habitat and Fishery’s Treatments on the Long-Term Control of Longline Culture Spatial Use in Relation to Shellfish Aquaculture Tunicate Infestation in PEI Mussel Farms Leases in Malpeque Bay, PEI Serial Knots in Mussel Culture Ropes Assessing the Effect of Climate-Change-Related Increase Spat Collection and Reduce Develop Diagnostic Markers to Assess Summer Heat Wave on the Condition and Duck-Related Mortality Mussel Population Health in Response to Physiology of the Cultured Blue Mussel Environmental Stress Comparison of the Health and Condition of (Mytilus edulis) and Monitoring of the Carbonate Cultured Mussels from Deep and Shallow Sub-Lethal Biological Effects on the Blue Mussel System within Prince Edward Island Bays Water Sites in Newfoundland with Reference (Mytilus edulis) from Chronic Exposure to Three Identification of Mussel Spat Supply Strategies to Environmental Conditions, Condition Index, Types of Conventional and Unconventional Oil in the Magdalen Islands Physiological Stress, and Lipid Biochemistry under Ice Cover in Winter A Study of the Reproductive Patterns of Blue Passive Protection of Mussel Production Characterization of Interactions Between Mussel Mussel, Mytilus edulis, Grown in Deep and Through Use of Exclusion Cages to Prevent Aquaculture and Adult American Lobsters Shallow Water Sites in Notre Dame Bay, Duck Predation in the Gaspé, Quebec Impact of Mussel Culture on Infauna and Newfoundland and Labrador Monitoring Variability of Environmental Factors Sediment Biogeochemistry Assessment of Strategies to Prevent Farmed Impacting Tunicate Infestation on Coastal Mussel Predation by Sea Ducks Shellfish Farms in Nova Scotia CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS 91

Assessing the Effect of Climate-Change-Related Summer Heat Wave Effects of Husbandry Practices on the Condition and Physiology of the Cultured Blue Mussel (Mytilus and Mitigation Treatments on the edulis) and Monitoring of the Carbonate System within Prince Edward Long-Term Control of Tunicate Island Bays Infestation in PEI Mussel Farms limate change is an issue that will START DATE: APR. 2015–JUN. 2018 unicate infestations have severely impact the shellfish aquaculture FUNDED BY: DFO–Aquaculture Collaborative impacted the shellfish aquaculture industry in Atlantic Canada. There are Research and Development Program (DFO–ACRDP) industry in Atlantic Canada, particularly C a number of questions related to the impact T CO-FUNDED BY: Prince Edward Island the mussel aquaculture industry in PEI. of the physical effects of climate change on Aquaculture Alliance Floating or submerged substrates such as the environment (such as ocean acidification) shellfish aquaculture structures, gear, and in which the shellfish aquaculture industry PROJECT LEAD: Carla Hicks (DFO) mussel lines provide ideal surfaces for the operates, which would consequently affect PROJECT TEAM: Luc Comeau, colonization of invasive tunicates. While the health and health management of Kumiko Azetsu-Scott (DFO); Aaron Ramsay current mitigation practices (e.g., pressure farmed animals. [PEI–Department of Fisheries, Aquaculture washing) address the immediate removal of This project will quantify the physiological and Rural Development (PEI-DFARD)]; Sarah Stewart-Clark (Dalhousie U) tunicates from mussel lines and substrate, stress (shellfish health impact) associated with they do not prevent re-infestation. Past increased water temperature for extended COLLABORATORS: Peter Warris (PEIAA) research has focused primarily on the timing, periods of time. In relation to ocean CONTACT: [email protected] frequency, and ecological sustainability of acidification, parameters of the carbonate www.dfo-mpo.gc.ca/aquaculture/rp-pr/ these practices; however, there have been no system will be measured within the shellfish WEBSITE: acrdp-pcrda/projects-projets/15-1-G-02-eng.html long-term assessments of these treatments or aquaculture environment to assess current of alternative measures. Examining the role levels. Results from this project will offer of bay-wide mussel stocking densities and guidance on maintaining healthy mussel related effects on tunicate recruitment could populations in the face of climate change and provide insights into alternative options for sustainable management of shellfish managing tunicates on shellfish farms. aquaculture in the present and future. In the case of tunicates, it is recognized that unused space or substrate availability facilitates the settling of these invasive species in a new environment. This project investigates the relationship between available recruitment space and levels of infestation by the invasive Vase Tunicate, Ciona intestinalis, on PEI mussel culture sites. The study will be conducted at the scale of a typical mussel aquaculture site, and will entail multi-year simulations to assess the overwintering potential of tunicates. The effect of different mussel stocking densities on infestation levels will be assessed, and numerical models developed to simulate the effects of fallowing of culture leases. The results from this study are intended to inform long-term tunicate management strategies at both farm and bay-scale levels.

DATE: APR. 2014–MAR. 2017

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEADS: Thomas Landry, Thomas Guyondet (DFO)

COLLABORATORS: Aaron Ramsay (DFARD); Jeffrey Davidson, Thitiwan Patanasatienkul (UPEI–AVC)

CONTACT: [email protected], [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2014-G-03-eng.html

Blue Mussels. Photo: DFO 92 SHELLFISH: MUSSELS CANADIAN AQUACULTURE R&D REVIEW 2017

Identification of Mussel Spat Supply Strategies in the A Study of the Reproductive Magdalen Islands Patterns of Blue Mussel, Mytilus or more than 20 years, Magdalen with environmental parameters to identify edulis, Grown in Deep and Islands mussel farmers have collected the most important parameters. Shallow Water Sites in Notre Fmost of their mussel spat in Bassin du The outcome of the project will profile Dame Bay, Newfoundland Havre Aubert (BHA), where the stock is more alternative collection scenarios, enabling and Labrador resistant to episodes of summer mortality current and future companies to meet than stocks in other water bodies. However, their production and profitability targets. otre Dame Bay, Newfoundland and the space available for collecting spat is The proposed strategies will support the Labrador, traditionally uses shallow limited in BHA, and it is essential that the proposals made at the end of the marine water sites for mussel aquaculture, potential supply in other Magdalen Island aquaculture fisheries project (Merinov) and N but changing spawning patterns have had water bodies be assessed to ensure active mariculture development approaches in a direct effect on sustainability. Offshore and and future supply. The main objective of this the Magdalen Islands. deeper sites may provide a more stable project is to identify the various strategies for deep water environment that might help to Blue Mussel (Mytilus edulis) spat supply in DATE: APR. 2014–DEC. 2017 reduce physical and environmental stresses. the Magdalen Islands. The project contains This can include mitigating temperature FUNDED BY: Ministère de l’Agriculture, des two specific components and sub-objectives: Pêcheries et de l’Alimentation du Québec (MAPAQ) and salinity changes, less mechanical 1) collection yield at three other sites; and disturbance due to wave action, or different MITACS; Merinov 2) performance (survival and growth) of CO-FUNDED BY: concentrations of phytoplankton, all of stocks from these sites (stock site design). PROJECT LEAD: Nicolas Toupoint (Merinov) which are thought to influence the frequency Preliminary results indicate that, although PROJECT TEAM: Carole Cyr, of spawning events. Offshore sites would alternative stocks appear to be more resilient Jean-François Laplante (Merinov); François Bourque also have lesser impacts on the benthic than in the 1990s, the BHA stock is still (MAPAQ); Réjean Tremblay (ISMER) environment, enabling enhanced the most resilient. Genetic analyses will COLLABORATORS: UQAR; Moules de Cultures environmental sustainability. be performed to study the basis of this des Îles inc.; Grande-Entrée Aquaculture inc. Preliminary results have suggested that: adaptation. Stock performance (survival 1) Blue Mussels from deep water sites can CONTACT: [email protected] and growth) differs among grow-out sites, show improved conditions versus shallow reflecting a variation in local conditions. WEBSITE: www.merinov.ca water sites; 2) spawning events are more Correlation analyses will be performed infrequent and predictable; and 3) meat yield is maintained. This project will document, characterize, and compare the gonadal development in mussels cultured in deep vs. shallow water sites to determine differences in spawning frequency. The project will also monitor environmental factors that might affect gonadal development in Blue Mussels. Results from this project will assist the mussel industry to enhance environmentally responsible operations by optimizing the utilization of resources on leases. Industry will be provided with important information on the reproductive condition and patterns of farmed mussels, leading to better overall management. The success of this project would also help reduce the impact of mussel farming in the near-shore environment. Collection yield–collector analysis. Photo: Nicolas Toupoint (Merinov)

DATE: SEP. 2015–JUN. 2018

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: Norlantic Processors Ltd.

PROJECT LEAD: Harry Murray (DFO)

PROJECT TEAM: Sharon Kenny, Dwight Drover (DFO)

COLLABORATORS: Terry Mills (Norlantic Processors Ltd.)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/15-1-N-03-eng.html

Stock performance–in situ measurement process. Photo: Nicolas Toupoint (Merinov) CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS 93

Assessment of Strategies to Prevent Farmed Mussel Predation by Mussel Stock Structure and Sea Ducks Density in Longline Culture

ith the proposed increase in mussel production in Malpeque WBay, PEI, there is a need to determine the amount of aquaculture production that can be supported by the aquatic environment without causing permanent changes in ecosystem function, species populations, communities, or habitats; this is also known as the Ecological Carrying Capacity (ECC). ECC is typically estimated using mathematical models which combine and describe complex interactions among Buoy system, installed around the mussel lines, to keep protective netting out of the water. Photo: Lise Chevarie (Merinov) shellfish aquaculture, natural shellfish populations, and the environment (e.g., currents, water exchange, nutrient dynamics, etc.). For example, the size and density of cultured mussels will determine the amount of phytoplankton being removed from the water column which, in turn, influences the overall ability of the system to sustainably support both cultured and natural shellfish populations. In PEI, leaseholders provide stock information to DFO on an annual basis, which is useful for assessing whether or not leases are used, but has little value in informing the estimate of ECC. To address this gap, a survey of the PEI Blue Mussel (Mytilus edulis) longline system will be carried out to generate information on mussel lease use. Specifically, the survey will focus on seasonal trends in stock composition, densities, and High-density mussel sock when transferred to a wild duck-free environment. Photo: Lise Chevarie (Merinov) the degree of fouling by invasive tunicates. Characteristics such as size and weight will redation by wild ducks has affected mussels reached a size less favoured by also be recorded and used to calculate rates the mussel industry for several years eiders and scoter ducks, they were returned of filtration and waste production (i.e., Pand causes considerable damage at to the producer’s site to continue growing biodeposition). This new information will some production sites. The various scaring to commercial size. The inter-site transfers contribute to improving the accuracy of model techniques tested to date (e.g., chasing by worked well. The results demonstrate that simulations and predictions of the overall boat, sound recordings, etc.) have been high-density socking is an option under capacity of an area to support changes in unsuccessful because they require a lot of certain conditions. Analysis of the economic shellfish aquaculture production. energy and sometimes become ineffective data will be completed in the winter of in harsh weather conditions or when the 2016–2017 and will help determine the real DATE: APR. 2015–MAR. 2017 birds become habituated. effectiveness of these transfer scenarios. In the Magdalen Islands, Grande-Entrée The purpose of this research project is to FUNDED BY: DFO–Program for Aquaculture lagoon is a Quebec mussel site that is prevent predation of mussels by sea ducks Regulatory Research (DFO–PARR) greatly affected by this problem. In order and protect mussel farmers’ production. PROJECT LEAD: Luc Comeau (DFO) to protect mussels from predation, Merinov PROJECT TEAM: Peter Warris (PEIAA); installed vertical nets that surround DATE: OCT. 2013–DEC. 2016 André Nadeau, John Davidson (DFO); production lines and cover the entire water Jonathan Hill (UPEI) CO-FUNDED BY: Merinov; Grande-Entrée column to keep ducks from landing near the Aquaculture Inc.; Culti-mer Inc.; Biomer COLLABORATORS: Jeffrey Davidson (UPEI) lines. Unfortunately, some environmental conditions prevented the netting from PROJECT LEAD: Lise Chevarie (Merinov) CONTACT: [email protected] staying in its optimal position. COLLABORATORS: Grande-Entrée Aquaculture WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Other Merinov initiatives included transferring Inc.; Culti-mer Inc.; Biomer parr-prra/projects-projets/2015-G-06-eng.html young mussel socks at different high densities CONTACT: [email protected] to two sites currently not visited by ducks: a www.merinov.ca lagoon and an open environment. When the WEBSITE: 94 SHELLFISH: MUSSELS CANADIAN AQUACULTURE R&D REVIEW 2017

Serial Knots in Mussel Culture Ropes Increase Spat Collection and Reduce Duck-Related Mortality redation by sea ducks is a threat to In the 2015 experiment, control ropes per 30.5 cm, respectively, with slight mussel culture in many sites. In many collected about 2700 individual spat per differences between variants. This is a two to Pnatural situations, however, mussel 30.5 cm (October 2015; mussels smaller four-fold increase as compared to controls. survivorship is enhanced by crevices and than 0.5 cm not included). Knotted ropes Adding serial knots in spat collectors substrate features because predators have collected roughly 4000 individual spat ropes increases spat collection, which is reduced access to their prey. We mimicked per 30.5 cm. This is a 1.5-fold increase useful wherever spat are in short supply. the effect of crevices by using loosely as compared to controls. Survivorship in Survivorship also increases, thus providing a knotted spat collector ropes. The knots used June 2016 was roughly 10-15% in knotted potential method for reducing duck predation. were the chain sinnet and variants thereof. ropes but was less than 5% on control These are serial knots which can be knotted ropes. Survivors and spat smaller than START DATE: JUN. 2013–DEC. 2017 easily for spat collection and socking, and 0.5 cm in spring provided a residual FUNDED BY: R-D Mytis Ltée undone easily at harvest. population which grew during the summer The knots were tested against regular and reached about 1500 individuals per CO-FUNDED BY: La Ferme Maricole unknotted ropes for their efficiency at 30.5 cm in Oct. 2016 (versus roughly 400 du Grand Large collecting spat and providing anti-duck on control ropes). Size-related effects on PROJECT LEAD: Marcel Fréchette refuges in Cascapédia Bay, Quebec. Two survivorship will be examined in June 2017. (R-D Mytis Ltée) suspended culture variants were used, the In the 2016 experiment, control ropes COLLABORATORS: Éric Bujold (La Ferme standard autocollector method used in collected about 1300 individual spat per Maricole du Grand Large) Cascapédia Bay in 2015 and U-shaped 30.5 cm. The chain sinnet and its variants [email protected] collectors hanging from long lines in 2016. collected 2900 and roughly 5900 individuals CONTACT:

Comparison of the Health and Condition of Cultured Mussels from Deep and Shallow Water Sites in Newfoundland with Reference to Environmental Conditions, Condition Index, Physiological Stress, and Lipid Biochemistry condition after 12 months when compared to shallow sites. • Under temperate conditions, mussels grown in shallow sites do as well or slightly better than those grown in deep water sites. However, under extreme environmental and surface weather conditions (i.e., abnormally cold water, wind, and ice), mussels have better overall condition over long term in deeper water, which offers more stable environmental conditions compared to shallow sites. It is recommended that farmers in the Notre Dame Bay region take advantage of the benefits of growing in both deep and shallow water sites within a bay or Deep water mussel site near Pleasantview, Notre Dame Bay, NL. Photo: Harry Murray (DFO) lease to maintain consistent accessibility to high quality product regardless of the ussels are typically cultured in between shallow versus deep sites, and weather conditions. sheltered nearshore areas. investigates potential correlations between Traditional shallow water coastal environment and mussel condition, M DATE: JUL. 2012–JUN. 2015 areas (estuaries, harbours, and shallow physiological stress, and lipid biochemistry. bays) can be affected by land runoff and This information will help industry make FUNDED BY: DFO–Aquaculture Collaborative contaminants, especially during precipitation. decisions regarding whether expanding Research and Development Program (DFO–ACRDP) Increased pressure for lease space in production to deep water sites will add CO-FUNDED BY: Norlantic Processors Ltd. these areas has raised concerns regarding increased sustainability for Newfoundland PROJECT LEAD: Harry Murray (DFO) carrying capacity (maximum population mussel culture. without affecting the environment) and Specifically, the following results PROJECT TEAM: Kim Hobbs, Sharon Kenny (DFO) thus sustainability. were found: COLLABORATORS: Terry Mills (Norlantic Industry has recently begun to develop • Mussels grown in deep sites demonstrate Processors Ltd.) offshore and deep water bivalve culture in higher Omega-3 and essential fatty acids, CONTACT: [email protected] Newfoundland’s Notre Dame Bay region. which are key factors contributing to food However, little is understood about how quality in mussels and seafood. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ deep water environments affect mussel acrdp-pcrda/projects-projets/N-12-01-001-eng.html • Deep water sites in Notre Dame Bay health and condition. This project generally demonstrated increased overall characterizes and compares seasonal changes in environmental conditions CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS 95

Passive Protection of Mussel Production Through Use of Exclusion Cages to Prevent Duck Predation in the Gaspé, Quebec

igrating ducks that feed on farmed predation compared to the traditional DATE: MAY 2015–DEC. 2016 mussels cause significant economic methods used for self-regulating mussel FUNDED BY: DFO–Aquaculture Collaborative Mlosses for the mussel aquaculture collectors. Research and Development Program (DFO–ACRDP) industry and current deterrent systems are The results of this project will increase CO-FUNDED BY: La Ferme Maricole du Grand becoming increasingly ineffective at keeping the knowledge surrounding diving duck Large; Moules Tracadigash Inc. the ducks away. The aquaculture industry predation on mussel farms in Québec (and in Chaleur Bay, Québec, normally uses elsewhere) and how this impact may be PROJECT LEAD: Chris McKindsey (DFO) self-regulating mussel collector techniques. responsibly mitigated while adhering to PROJECT TEAM: Annick Drouin, It is believed that mussels grown in this way the Migratory Birds Convention Act (1994). Marie-France Lavoie, Paul Robichaud, would be best protected from diving ducks The results will also improve the economic François Roy, Anne-Sara Sean, Émilie Simard, Andréa Weise (DFO); Élisabeth Varennes (UQAR) by deploying a passive, physical deterrent situation of the Québec mussel industry system of underwater duck exclusion cages and provide the industry and authorized COLLABORATORS: Éric Bujold (La Ferme around the mussels. management bodies with effective and Maricole du Grand Large); Manon Deslauriers The project aims to develop protective conservation-oriented mitigation tools. (Moules Tracadigash Inc.) cage prototypes made with common and This will benefit the mussel aquaculture CONTACT: [email protected] locally-available materials to keep costs as industry as a whole by allowing it to WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ low as possible. It will determine the optimal better understand and mitigate potential acrdp-pcrda/projects-projets/15-1-Q-01-eng.html type of netting to prevent duck bycatch and wild-farmed interactions concerning duck biofouling, while measuring the effectiveness predation to improve the sustainability of the exclusion cages in preventing duck of the shellfish culture industry.

Deployment of a cage structure to protect the Retrieval of mussel lines that had been deployed to mussels on the lines within it from diving ducks. collect mussel spat (juvenile mussels) for grow-out for Photo: Paul Robichaud (DFO) aquaculture. Photo: Paul Robichaud (DFO) 96 SHELLFISH: MUSSELS CANADIAN AQUACULTURE R&D REVIEW 2017

Monitoring Variability of Environmental Factors Impacting Tunicate Develop Diagnostic Markers Infestation on Coastal Shellfish Farms in Nova Scotia to Assess Mussel Population Health in Response to ase Tunicate (Ciona intestinalis) movement), temperature and salinity Environmental Stress is an invasive species negatively have the most influence on Vase Tunicate Vimpacting mussel farm productivity in population dynamics. This suggests his project is focused on generating Nova Scotia and Prince Edward Island. They that coastal sites with generally cooler better tools to enable industry to grow in dense groups on mussel ropes, nets, water or with greater or more frequent determine and analyse the stressors and the mussels themselves, competing for freshwater inputs may be less susceptible T that impact cultured Blue Mussels and what resources and resulting in crop losses. They to heavy tunicate fouling. At cooler sites, effects these can have on their condition are difficult to remove and remain persistent initial tunicate settlement may be delayed and health. This project aims to be proactive even after pressure washing, brine dips, and growth may be slower throughout the in managing health issues that may arise liming, UV treatment, and electric shocks. season, resulting in smaller populations, for cultured shellfish species in relation to The spatial distribution of tunicates is while their abundance can be reduced climate change (water temperature and pH), highly heterogeneous and could be the further if salinity is lower. tunicate treatment (high pressure water result of variation in environmental factors • Predictive NMLE (non-linear mixed spray and hydrated lime) and other among sites. This study examines the effect effects) model is under development environmental stressors (food availability, of variability of environmental factors (salinity, to aid in future aquaculture siting and hypoxia and salinity). temperature, pH, and water movement) management decisions. This project will identify genetic markers on the establishment and proliferation of that can be used: 1) to investigate the causes tunicates. Research results may suggest of stress within underperforming mussel an environmental factor as an indicator to DATE: JUN. 2013–JUN. 2015 populations; and 2) to develop mitigating assess aquaculture sites (either current FUNDED BY: DFO–Aquaculture Collaborative strategies to minimize the impacts of the or future proposed sites) for their risk of Research and Development Program (DFO–ACRDP) underlying environmental/mechanical tunicate infestation and inform siting stressors on the long term viability of Aquaculture Association of decisions by the government. This study CO-FUNDED BY: Nova Scotia (AANS) the mussel aquaculture industry in PEI. may also help reduce further spread of The stress response (heartbeat, lysosomal tunicates and the need for control treatments PROJECT LEAD: Dawn Sephton (DFO) destabilization) in mussel populations through the identification of sites less PROJECT TEAM: Danielle Goodfellow, after an event challenge (food availability, vulnerable to infestation. Bruce Hancock (AANS); Benedikte Vercaemer (DFO); hypoxia, salinity, thermal, pH, tunicate This project supports the DFO objective Cory Bishop, Russell Wyeth (StFX) (Ciona intestinalis) recruitment/removal) of environmental performance. Specifically, COLLABORATORS: Danielle Goodfellow (AANS) will be evaluated. At the same time, the following results were found: CONTACT: [email protected] transcriptomic data will be collected to • Of the four environmental factors considered develop molecular markers related to a (i.e., salinity, temperature, pH, and water WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ specific stressor. We plan on using RT-qPCR acrdp-pcrda/projects-projets/M-13-01-002-eng.html markers identified via RNA-Seq to evaluate stress responses.

Characterization of Lobster Habitat and Fishery’s Spatial Use in START DATE: OCT. 2016–MAR. 2020

Relation to Shellfish Aquaculture Leases in Malpeque Bay, PEI FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP) hellfish aquaculture is an important This project addresses management economic activity for coastal questions related to the interactions CO-FUNDED BY: Prince Edward Island Scommunities in Atlantic Canada. The between lobster and cultured mussels by Aquaculture Alliance (PEIAA) Blue Mussel industry emerged on the east investigating the potential overlap between PROJECT LEAD: Denise Méthé (DFO) coast during the 1970s and expanded rapidly proposed mussel aquaculture sites with PROJECT TEAM: Sarah Stewart-Clark, in PEI during the 1990s. Today, Blue Mussels lobster rearing grounds and fishing activities Stephanie Hall (Dalhousie U); Carla Hicks (DFO); are the nation’s leading cultured shellfish in Malpeque Bay. The outcomes of this study Fraser Clark (Mount Allison U) species by weight and value. In 2013, will inform departmental and provincial COLLABORATORS: PEIAA Fisheries and Oceans Canada (DFO) decision-makers in their marine spatial identified the need to develop a detailed planning processes and contribute to a CONTACT: [email protected] spatial plan to accommodate a possible sustainable aquaculture industry. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ increase in leases for mussel aquaculture in acrdp-pcrda/projects-projets/16-1-G-04-eng.html Malpeque Bay, PEI. In addition to considering DATE: APR. 2015–MAR. 2017 the scale of shellfish aquaculture that can be FUNDED BY: DFO–Program for Aquaculture sustainably cultured in Malpeque Bay, there Regulatory Research (DFO–PARR) also remain questions related to interactions between lobster and cultured mussels. In PROJECT LEAD: Marc Ouellette (DFO) making decisions or proposing potential PROJECT TEAM: Michel Comeau, increases in the number of leases in Denis Gagnon, Angeline LeBlanc, Malpeque Bay, aquaculture managers Bruno Comeau, Deryck Mills (DFO) have to consider complex coastal zone CONTACT: [email protected] management issues, including the potential for habitat overlap between lobsters and WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2015-G-02-eng.html aquaculture mussel leases. Left to right: Sarah Stewart-Clark (Dalhousie U), Denise Méthé (DFO), and Stephanie Hall (Dalhousie U). Photo: Scott Jeffrey (Dalhousie U) CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS 97

Sub-Lethal Biological Effects on the Blue Mussel (Mytilus edulis) from Chronic Exposure to Three Types of Conventional and Unconventional Oil under Ice Cover in Winter estern Canada has huge bitumen deposits, a source Wof unconventional oil. Once diluted, it is easily exported, which suggests it will be a leading component of future Canadian exports. The Estuary and Gulf of St. Lawrence are highly coveted shipping points given their adequate port infrastructure and strategic access to foreign markets. In addition to its extreme winter weather conditions, the St. Lawrence supports vital economic operations such as shellfish farming in outlying areas. Dilbit’s (diluted bitumen) behaviour and biological effects are still unknown in the event of a spill occurring in winter under ice cover in the marine environment, not to mention the adverse economic repercussions if a spill were to occur near aquaculture facilities. We quantified the immediate and delayed Photograph of larval production (day two) in adults exposed to the control treatment. biological effects by reproducing such Photo: Anthony Schmutz (UQAR-ISMER) a scenario and exposing commercial size mussels Mytilus edulis to dilbit and conventional crude oil for seven days. After a 72-hour exposure, bioaccumulation of the hydrocarbons as well as cellular and physiological stress were observed. A depuration period was observed after exposure during which the mussels eliminated the accumulated hydrocarbons. Several months after winter exposure and despite the depuration period, negative effects on spring spawning were evident mainly in larval survival and development. Our experiments revealed immediate toxicity (bioaccumulation, cellular and physiological stress) in addition to delayed toxicity (reproductive success). A more pronounced biological response to exposure to unconventional crude oil was also demonstrated. Photograph of larval production (day two) in adults exposed to unconventional oil treatment. This study investigated the consequences Photo: Anthony Schmutz (UQAR-ISMER) of an oil spill in the cold northern marine environment on the Mytilus edulis farmed mussel.

DATE: AUG. 2015–AUG. 2017

FUNDED BY: DFO–National Contaminants Advisory Group (NCAG)

CO-FUNDED BY: Fonds de Recherche du Québec en Nature et Technologies (FRQNT)

PROJECT LEAD: Anthony Schmutz (UQAR-ISMER)

PROJECT TEAM: Richard St-Louis (UQAR); Réjean Tremblay, Céline Audet, Jean-Pierre Gagné; Émilien Pelletier, Mickaël Barthe (UQAR-ISMER)

COLLABORATORS: Richard St-Louis (UQAR), Réjean Tremblay, Céline Audet, Jean-Pierre Gagné, Émilien Pelletier, Mickaël Barthe (UQAR-ISMER)

CONTACT: [email protected]

Photograph of larval production (day two) in adults exposed to conventional oil treatment. Photo: Anthony Schmutz (UQAR-ISMER) 98 SHELLFISH: MUSSELS CANADIAN AQUACULTURE R&D REVIEW 2017

Characterization of Interactions Between Mussel Aquaculture and Adult American Lobsters

nderstanding the influence of mussel the organisms that grow on them) that fall and Oceans Canada (DFO) aquaculture culture sites on the distribution and from the suspended culture structures as managers make scientifically sound Ucondition of lobsters is an important the mussels grow. The physical structures decisions in support of ecologically and question for managers who evaluate of aquaculture equipment also provide economically sustainable aquaculture. requests for new mussel farms as there is potential habitat for organisms that need limited scientific information on the subject. solid substrate to grow, which may attract DATE: APR. 2015–MAR. 2018 Additionally, it is widely perceived by lobster a variety of predatory and scavenging FUNDED BY: DFO–Program for Aquaculture fishers that lobsters that congregate around species. As a result, there may be Regulatory Research (DFO–PARR) aquaculture sites may become sedentary ecological effects because of changes and are therefore less available to the in the productivity, distribution, or PROJECT LEAD: Chris McKindsey (DFO) lobster fishery. Known environmental catchability of target (fishery) species. PROJECT TEAM: Rénald Belley, Luc Comeau, interactions between mussel (and other The goal of this project is to describe the Catherine Couillard, John Davidson, Annick Drouin, shellfish) aquaculture include water extent and effect of interactions between Jonathan Hill, Marie-France Lavoie, column-related effects on plankton and mussel aquaculture activities and adult Domynick Maltais, François Roy, Paul Robichaud, nutrients due to mussel filter-feeding, as American Lobsters, including the spatial Émilie Simard, Anne-Sara Sean (DFO) well as localized effects on infaunal (benthic) distribution and movement of lobsters within COLLABORATORS: Ocean Tracking Network communities from increased organic loading and around mussel aquaculture sites, and (OTN); Philippe Archambault (ISMER); on the seafloor. In the case of suspended their availability to the fishery. The influence Jeffrey Davidson (UPEI) mussel culture, organic loading comes from of mussel aquaculture on the condition of CONTACT: [email protected] faeces, pseudofaeces (biodeposits), and lobsters and their diet will also be evaluated. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ from large quantities of farmed mussels (and The results of the study will help Fisheries parr-prra/projects-projets/2015-QC-01-eng.html

Mussel socks with a hydro-acoustic receiver used to detect ultrasonic signals emitted by acoustic transmitters affixed to lobsters and crabs in Malpeque Bay. Photo: Chris McKindsey (DFO)

Annick Drouin and Marie-France Lavoie (DFO) take tissue samples of a lobster to determine its condition in a study on the influence of mussel farms on lobster condition and movement. Photo: Chris McKindsey (DFO)

Map of arrays of acoustic receivers (blue points) deployed around mussel farms in Richmond Bay (left, 0.9 km2 coverage) and Marchwater (right, 2.0 km2 coverage) to detect lobster movements inside and outside of mussel farms (orange polygons) in Malpeque Bay, Prince Edward Island. CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: MUSSELS 99

Impact of Mussel Culture on Infauna and Sediment Biogeochemistry

nteractions between bivalve aquaculture and the environment are complex. I In suspended mussel culture, great quantities of waste (digested and undigested planktonic food, or biodeposists) may fall from culture structures and this may impact benthic communities, particularly those living in bottom sediments. Different biogeochemical methods have been developed as proxies to monitor the health of benthic communities. While some work has examined dose (biodeposition) – response (benthic conditions) relationships, these studies often suffer from procedural issues or have been done over limited levels of biodeposition and mechanisms have not been evaluated, making the determination of benthic ecological carrying capacity difficult. This study evaluates the dose-response relationship between mussel biodeposition and benthic conditions over a wide range of deposition levels and over more than one year. Measurements will be taken to A diver examines a benthic mesocosm to evaluate benthic respiration and nutrient fluxes around mussel lines in determine the processes by which bottom Havre-aux-Maisons Lagoon, îles-de-la-Madeleine. Photo: Anne-Sara Sean (DFO) sediments and communities are impacted with the aim of determining the ecological carrying capacity of the benthic environment of Malpeque Bay, PEI, for mussel aquaculture. Combining the results of this study with ongoing organic loading models for bivalve aquaculture will inform managers on how many mussels may be farmed in an area while protecting the benthic environment.

DATE: APR. 2016–MAR. 2019

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Chris McKindsey (DFO)

PROJECT TEAM: Luc Comeau, Annick Drouin, Nathalie Forget, Frédéric Hartog, Élise Lacoste, Marie-France Lavoie, François Roy, Émilie Simard, Anne-Sara Sean, Andrea Weise (DFO)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2016-Q-01-eng.html

Marie-France Lavoie and François Roy (DFO) prepare sediment traps and sample jars to evaluate sedimentation around mussel lines in îles-de-la-Madeleine. Photo: Andrea Weise (DFO) 100 SHELLFISH: OYSTERS CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OYSTERS

Investigating Polydora Outbreak in New Impacts of Aquaculture Operations on the Genetic Improving Physiological Health of Oysters by Brunswick Off-Bottom Cultured Oysters Health of Natural Populations of the Eastern Selecting Seed for Stress Resilience Oyster, Crassostrea virginica Assessment of Oyster Spat Collection Eastern Oyster, Crassostrea virginica, Potential in Bouctouche Bay, New Brunswick Quantifying the Effect of Winter Siltation and Response to Environmental, Physiological, Burial on Crassostrea virginica’s Health and Mechanical Stressors CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OYSTERS 101

Investigating Polydora Outbreak in New Brunswick Off-Bottom Cultured Oysters

Some reports have indicated that heavy infestations can result in low meat quality, abscesses, alteration of growth patterns, and weakened shells (increasing predator susceptibility). This unusual increase could ultimately lead to serious impacts on oyster populations and result in economic losses for the aquaculture industry. To help identify the current impact of Polydora on New Brunswick oyster growing areas, this project aims to: 1) document the presentation and level of the infestation of Polydora; 2) document the impact of Polydora on overall oyster health; and 3) document distribution and infestation level of Polydora in relation to environmental conditions.

DATE: APR. 2014–MAR. 2017

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP) Crassostrea virginica shells with varying degrees of mud blister impact from Polydora websteri. (A) shells not impacted, (B) shells mildly impacted , and (C) shells severely impacted. Mud blisters are outlined in red. CO-FUNDED BY: Huîtres Aquador Oysters Inc. Photo: Jeffery Clements (DFO) PROJECT LEAD: Daniel Bourque, Mary Stephenson (DFO)

better understanding of the increased dead shellfish. Commonly found in intertidal PROJECT TEAM: Daniel Bourque, intensity and prevalence of Polydora and subtidal areas in Atlantic Canada, its Mary Stephenson, Janelle McLaughlin, Arelated to environmental conditions presence among New Brunswick oyster Jeff Clements (DFO) and their impact on oyster health would populations has normally been minor COLLABORATORS: Serge Gaudet (Huîtres assist industry in developing management and usually of low intensity with burrows Aquador Oysters Inc.) and mitigation strategies. containing little or no mud. However, there CONTACT: [email protected], Known simply as a “mudworm” or have been sporadic increases of infestation [email protected] “blisterworm”, Polydora websteri has the rates observed in off-bottom (or suspension) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ ability to bore into the shells of live and oyster growing sites in New Brunswick. acrdp-pcrda/projects-projets/G-14-01-002-eng.html

Assessment of Oyster Spat Collection Potential in Bouctouche Bay, New Brunswick

he oyster culture industry in New possible repercussions of one (or more) spat to this pattern in the context of a scenario Brunswick depends on the oyster spat evolution scenarios on the hydrodynamics where a storm would result in breaching Tcollected at four sites–Bouctouche (examining the erosion effects on the flow of the sand dune in front of the seed Bay, Cocagne Bay, Caraquet Bay, and of water and nutrients) and overall spat collection area. Miramichi Bay. In 2009, lower than average collection potential within the bay. oyster spat collection rates were a source The results from this experiment showed DATE MAY 2013–JUN. 2015 of concern for producers. To properly that the seed collection area is located in FUNDED BY: DFO–Aquaculture Collaborative manage these fluctuations, an in-depth a retention zone of the bay where renewal Research and Development Program (DFO–ACRDP) understanding of the various factors by Northumberland Strait waters is slowest influencing collection rates and recruitment and indicated that water circulation within CO-FUNDED BY: Entreprise Baie Acadienne Inc. numbers within the system is needed. Bouctouche Bay is sensitive to meteorological PROJECT LEAD: Thomas Guyondet (DFO) This project studied the factors influencing forcing (wind and atmospheric pressure). PROJECT TEAM: Marie-Josée Maillet (DAAF); oyster spat collection in Bouctouche Bay, A particle tracking module was coupled Serge Jolicoeur (U Moncton); Dominique Bérubé New Brunswick by using modelling with the hydrodynamic model in order to (New Brunswick Department of Energy and Resource techniques to reproduce the oyster larval investigate in more detail the transport of Development) transport from spawning to recruitment for oyster larvae within Bouctouche Bay. Further COLLABORATORS: Entreprise Baie Acadienne Inc. environmental conditions observed in situ analysis of the particle tracking results is (in the field) and assessing the relative underway to provide the relative contribution CONTACT: [email protected] contribution of the various larval sources of each area of the bay, the effects of WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ (wild versus cultured stock). This modelling meteorological and river forcing on these acrdp-pcrda/projects-projets/G-13-01-002-eng.html will also help researchers evaluate the contributions, and potential modifications 102 SHELLFISH: OYSTERS CANADIAN AQUACULTURE R&D REVIEW 2017

Impacts of Aquaculture Quantifying the Effect of Winter Siltation and Burial on Crassostrea Operations on the Genetic virginica’s Health Health of Natural Populations n commercial shellfish aquaculture regardless of whether they were buried in of the Eastern Oyster, operations located within the Gulf of the sediment or lying on top of it. Crassostrea virginica St. Lawrence estuaries, mesh bags I • Buried oysters were likely physiologically containing cultivated Eastern Oysters stressed during quiescence. Early “rescue” his information will allow for both (Crassostrea virginica) are lowered onto unburying of quiescent oysters did not a better assessment of the genetic soft seabeds in the autumn and recovered improve survival rates; instead, unearthing health of Crassostrea virginica in the spring. Occasional mortalities suggest T provoked stress and accelerated the populations in the Maritimes, and for that oysters are vulnerable to sedimentation depletion of energy reserves, suspected the establishment of hatchery-based and burial during winter. to be the result of oysters burning energy breeding programs. This study explored the cause-effect to remove excess silt clogging their gills. Oyster farmers currently rely on relationship of winter siltation and burial Because resuspending mesh bags in wild-caught seed (also known as spat) on oyster health and productivity. It provides early spring would have minimal mitigation to stock their aquaculture sites. The number the first complete assessment of winter effect on survival rates, avoiding soft bottoms and quality of seed, however, is highly quiescence (extended period of valve altogether (to avoid burial) remains best for variable from year-to-year and juvenile closure) in oysters. Specifically, this project oyster health and survival. oysters must often be sold and transported found the following results: from regions with a high seed set • The autumnal burial of Eastern Oysters (abundance) to regions with a poor seed set. into the sediment disrupts their quiescent DATE: JUL. 2014–JUN. 2016 To address this issue, a commercial-scale behaviour and leads to irreversible and hatchery in New Brunswick is currently FUNDED BY: DFO–Aquaculture Collaborative potentially lethal consequences, occurring Research and Development Program (DFO– ACRDP) being developed to provide adequate oyster approximately five months following burial. L’Étang Ruisseau Bar Ltd. seed to oyster farms within the Maritimes. The risk of winter death from burial is real, CO-FUNDED BY: The potential impact of hatchery-spawned and, consequently, overwintering oysters PROJECT LEAD: Luc Comeau (DFO) oysters, as well as transplanted wild-caught in deeper channel waters (soft-bottom PROJECT TEAM: Claire Carver (Carver Marine spat, on the genetic integrity of neighbouring sediments) is not recommended. Consulting); Jeffrey Davidson (UPEI); wild oyster beds greatly depends on the Jean-Bruno Nadalini, Réjean Tremblay (UQAR) factors underlying the genetic structure of • Burial had no effect on the tissue André Mallet (L’Étang natural populations. Conversely, the health concentration of lipids, proteins, and COLLABORATORS: Ruisseau Bar Ltd.) and vigour of cultured oysters depends on glycogen, nor did it impact the energy the quality of available spat, whether from content index that was developed from CONTACT: [email protected] these biochemical constituents. Oysters wild-caught sources or hatchery production. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ This project will examine genetic diversity had their valves completely closed most acrdp-pcrda/projects-projets/G-14-02-001-eng.html between populations of the Eastern Oyster, of the time, operating anaerobically, identify functional diversity in terms of health indicators such as condition index, growth, survival, and reproduction, as well as evaluate the potential impacts of gene flow between wild and cultivated oyster populations. The goal of this project is to evaluate the genetic sequence of natural oyster populations through the creation of a high-density linkage map for the molecular markers associated with functional diversity in the Eastern Oyster.

DATE: APR. 2013–JUN. 2017

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: L’Étang Ruisseau Bar Ltd.

PROJECT LEAD: Mark LaFlamme (DFO)

PROJECT TEAM: Jean-René Arseneau, Royce Steeves (DFO); Martin Mallet (L’Étang Ruisseau Bar Ltd.)

COLLABORATORS: André Mallet (L’Étang Ruisseau Bar Ltd.)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Oysters on the sea floor in an eelgrass bed. Photo: Luc Comeau (DFO) acrdp-pcrda/projects-projets/G-13-01-001-eng.html CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OYSTERS 103

Improving Physiological Health of Oysters by Selecting Seed for Stress Resilience

effort) and have increased resistance to deal with stressful events (lower stress response) will ultimately be healthier and thus have greater resilience to pathogens and environmental changes. This project identified genetic markers in the Eastern Oyster associated with metabolic and feed absorption efficiency (10 SNPs and 14 SNPs. respectively) and produced a first generation crop of oysters. In 2017, the progeny will be monitored (and genotyped) to verify if they display these particular traits. This project is focused on generating efficient and resilient oysters to ensure that if faced with a pathogen or environmental stressor, they will have an increased capacity to launch an immune response.

DATE: JAN. 2015–JUN. 2017

FUNDED BY: DFO–Aquaculture Collaborative Research and Development Program (DFO–ACRDP)

CO-FUNDED BY: L’Écloserie Acadienne Ltd.

Gillian Huxley-Tobin (DFO) sieving oyster larvae Oyster larvae ready to set. Photo: Denise Méthé (DFO) PROJECT LEAD: Denise Méthé (DFO) produced from selected broodstock. Photo: Denise Méthé (DFO) PROJECT TEAM: Sarah Stewart-Clark, Stephanie Hall (Dalhousie U); Gillian Tobin-Huxley (DFO); Fraser Clark (Mount Allison U) ccess to a consistent supply of high change) has been identified as a key quality and resilient seed stocks constraint for the continued viability and COLLABORATORS: Maurice Daigle (L’Écloserie A (i.e., those with the capacity to expansion of the Eastern Oyster industry in Acadienne Ltd.) launch an immune response when faced with Atlantic Canada. Selecting oysters that are CONTACT: [email protected] pathogens or withstand fluctuations in salinity more efficient (lower metabolic need, better WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ and temperature associated with climate feed conversion, and lower reproductive acrdp-pcrda/projects-projets/G-14-03-001-eng.html

Eastern Oyster, Crassostrea virginica, Response to Environmental, Physiological, and Mechanical Stressors

n New Brunswick, oyster mortalities Hemocyte mortality (8.4%) and lysosomal destabilization. Lysosomal destabilization appear to be closely related to destabilization (40%) remained slightly remains a sensitive biomarker of stress Ienvironmental factors (e.g., temperature, above that reported in literature (5% and response in oysters. salinity, etc.) and husbandry (rearing) 30%, respectively). Phagocytic activity Field monitoring established seasonal practices. The physiological health of the was normal, hovering around 20% with baseline levels for a number of physiological animal can determine how well it adapts to, greater fluctuations at the Indian Island biomarkers of stress for oysters. and recovers from, exposure to potential site. Oxidative stress was most apparent stressors. This study investigated the during summer months (June-Sept), as DATE: OCT. 2012–JUN. 2015 relationship between oyster health and expected. Likewise, tubule atrophy indices FUNDED BY: DFO–Aquaculture Collaborative environmental changes to identify critical were 5X higher during winter months Research and Development Program (DFO–ACRDP) periods of physiological stress. (December–April) compared to the In 2013, the physiological health of oysters growing season (May–November). CO-FUNDED BY: La Maison BeauSoleil Inc. (phagocytosis, hemocyte viability, oxidative Condition index remained above 30%, PROJECT LEAD: Daniel Bourque (DFO) stress, lysosomal destabilization, condition except in July–August (25%), due to PROJECT TEAM: Denise Méthé, index, tubule atrophy) from two culture sites spawning event—as confirmed through Janelle McLaughlin (DFO) in Richibucto estuary (Aldouane River, Indian histology. Likewise, tubule atrophy was Amédée Savoie (La Maison Island) were evaluated monthly (10 oysters/ noticeably higher in pre-spawned individuals, COLLABORATORS: BeauSoleil Inc.) site). Additional samples were taken during indicative of no feeding activity. Interestingly, periods of expected stress (i.e., pre- and the other biomarkers showed no stress CONTACT: [email protected] post-spawning, air drying). Air drying is a response to spawning. Finally, air drying WEBSITE: http://www.dfo-mpo.gc.ca/aquaculture/ technique used by oyster growers to control was identified as a stressful event for rp-pr/acrdp-pcrda/index-eng.html fouling on culture gear and oysters. oysters, but based solely on lysosomal 104 SHELLFISH: OTHER CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OTHER

Developing an Ecological Carrying Capacity The Effects of a Hydraulic Dredge and Adding Microplastics and Shellfish Aquaculture: for Shellfish Aquaculture in Baynes Sound, Shells on the Environment and Soft-Shell Clam Investigating Presence, Extent, and Potential British Columbia Population Dynamics Impacts and Mitigation Measures Understanding the Distribution of a Nemertean Bay Characterization for Nova Scotia The Effect of Cultured Shellfish on Eelgrass Predator, Cerebratulus lacteus, in Clam Flats: Shellfish Aquaculture Productivity in Estuaries of New Brunswick Implications for Control Measures The Ecological Effects of Clam Harvesting by Improving Ecological Models for a Sustainable Mechanical Means in St. Mary’s Bay, Nova Scotia Development of Bivalve Culture in Eutrophic Estuarine Complexes CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OTHER 105

Developing an Ecological Understanding the Distribution of a Nemertean Predator, Carrying Capacity for Shellfish Cerebratulus lacteus, in Clam Flats: Implications for Control Measures Aquaculture in Baynes Sound, he results of this project will provide correlated to high field mortality in Soft-shell British Columbia information to better understand Clams. Very little, however, is known about the factors involved in the patchy the factors regulating the patchy distribution n British Columbia (BC), shellfish culture T distribution and abundance of Cerebratulus of this predator. The present study will is located primarily on the west coast lacteus. This information will aid in the examine the factors regulating the patchy Iof Vancouver Island and the Strait of development of efficient management distribution and abundance of C. lacteus Georgia, with the most prolific production sites strategies to minimize the effect of this to allow for the development of predator associated with Baynes Sound, Cortez Island, predator on clam populations. management strategies. and Okeover Inlet. Although the culture of Clams have been identified as an shellfish was developed over 100 years ago important alternate species for the future DATE: APR. 2014–JUN. 2017 in BC, little research exists pertaining to the development of aquaculture in Atlantic ecological capacity of shellfish production FUNDED BY: DFO–Aquaculture Collaborative Canada. One of the major obstacles in Research and Development Program (DFO–ACRDP) in these prolific, sheltered bays. Shellfish the development of clam culture has been production is influenced by a balance of controlling predators on culture sites, CO-FUNDED BY: Innovation Fisheries Products Inc.; Mills Seafood Ltd. water quality, hydrodynamics (bay flushing), particularly endobenthic species (those and food supply (plankton). A carrying that live in the sediment). In recent years, PROJECT LEADS: Daniel Bourque, capacity assessment is required to assess commercial size Quahaug and Soft-shell Angeline LeBlanc (DFO) this balance and identify any bay-wide Clam densities have reportedly been lower. PROJECT TEAM: Jeffery Clements (DFO) limitations due to a potential competition While the cause for these declines has not for resources or shift in ecosystem COLLABORATORS: Doug Bertram (Innovative yet been documented, harvesters have Fisheries Products Inc.); Tim Williston (Mills Seafood Ltd.) functioning. A high-resolution, spatially-explicit noted the important presence of predatory hydrodynamic-biogeochemical coupled worms at clam harvesting sites. The Milky CONTACT: [email protected], [email protected] model [e.g., Finite Volume Community Ocean Ribbon Worm, C. lacteus, is an important Model (FVCOM)–Bivalve Culture Ecosystem predator of many endobenthic bivalve WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Model] is being developed to assess the species and its presence has been acrdp-pcrda/projects-projets/G-14-01-001-eng.html ecological carrying capacity of shellfish aquaculture in Baynes Sound. These mathematical models, groundtruthed with local data, will integrate the complex Improving Ecological Models for a Sustainable Development of interactions among aquaculture activities, Bivalve Culture in Eutrophic Estuarine Complexes shellfish physiology, and the ecosystem. arrying capacity of coastal systems allowing future applications to other coastal DATE: OCT. 2011–MAR. 2018 for bivalve culture has typically been embayments. Adding these new modules FUNDED BY: DFO–Program for Aquaculture Cinvestigated using mathematical will increase model veracity and provide new Regulatory Research (DFO–PARR) models restricted to a Nutrient-Phytoplankton- insights into aquaculture-coastal ecosystem PROJECT LEAD: Terri Sutherland (DFO) Zooplankton-Detritus-Cultured Bivalve interactions, especially in quantifying the representation. The present project aims influence on species with commercial, PROJECT TEAM: Peter Cranford, Chris Pearce, to generate a more detailed understanding recreational, and aboriginal fishery value. Hannah Stewart (DFO) of nutrient dynamics in order to accurately Results of this project should further our COLLABORATORS: BC Shellfish Growers Association; gauge the influence exerted by cultured understanding of interactions between Mac’s Oysters Ltd.; Hollie Wood Oysters Ltd. bivalves. Specifically, macroalgae, a primary bivalve aquaculture and coastal ecosystems. CONTACT: [email protected] producer whose contribution can be The model developed will provide relevant significant, especially in eutrophic systems information and a generic tool to improve the WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2011-P-21-eng.html and wild bivalve population modules, management of bivalve culture activities. will be coupled to an existing ecosystem carrying capacity model. These new DATE: NOV. 2015–APR. 2018 ecophysiological modules will be built FUNDED BY: DFO–Program for Aquaculture using the Dynamic Energy Budget theory Regulatory Research (DFO–PARR) to account for the use of resources by bivalves and macroalgae and also reproduce PROJECT LEAD: Thomas Guyondet (DFO) the effects of various aquaculture scenarios PROJECT TEAM: Luc Comeau, Romain Lavaud, in terms of wild bivalve productivity. Model Marc Ouellette (DFO) development will be supported by field COLLABORATORS: Ramón Filgueira (Dalhousie U); and experimental work to characterize Cindy Crane (PEI Department of Communities, distribution, abundance, and growth for Land and Environment); Jeff Davidson (UPEI–AVC); both macroalgae and wild bivalves. Model Réjean Tremblay (UQAR–ISMER) application will be performed for Malpeque CONTACT: [email protected] Bay (Prince Edward Island); however, the model will be given a generic structure

Juvenile oyster seed in culture trays in Baynes Sound, British Columbia. Photo: Terri Sutherland (DFO) 106 SHELLFISH: OTHER CANADIAN AQUACULTURE R&D REVIEW 2017

The Effects of a Hydraulic Dredge and Adding Shells on the The Ecological Effects of Clam Environment and Soft-Shell Clam Population Dynamics Harvesting by Mechanical Means in St. Mary’s Bay, Nova Scotia o improve the profitability of Soft-shell states, and has been shown to increase Clam farms in Atlantic Canada, growers Quahog and Soft-shell Clam recruitment. he clam aquaculture industry has Twant to use hydraulic dredging as Results from this project (i.e., the addition of experienced major challenges a means of harvesting clams. The effects shells) may mitigate the potential negative recruiting and retaining clam of dredging, however, are variable across effects of dredging. T diggers, and the disinterest from the sites. Concerns regarding mechanical clam The project seeks to compare the effects younger employable generation has resulted harvesting include shell damage, impacts of hydraulic dredging and addition of shells in an aging employee-base. Traditional hand on recruitment and survival of juveniles, to the sediment on the survival of juvenile harvesting is not considered to be socially nor impacts on biodiversity, and the release Soft-shell Clams, and on the depth profile economically sustainable due to being very of buried organic matter and reduced of physical and chemical parameters of the labour-intensive, involving the manual use of metabolites. In the presence of oxygen, this sediment (including grain size, sediment a clam hake with tines that measure 15 cm in matter oxidizes, thereby lowering the pH, compaction, pH, carbonate/aragonite length to dig up and turn over the sediment. which can reduce growth and survival saturation states, and sulphides). In addition, There is interest in using mechanical clam of bivalves. this project will provide insights related to the harvesters to complement hand harvesting Successful methods of increasing potential environmental effects from shelling of quahogs (Mercenaria mercenaria) in post-seeding survival rates, crucial to activity on surrounding areas (habitats) which St. Mary’s Bay, Nova Scotia. bivalve farming, have been demonstrated are currently not well understood. This study compared the ecological in U.S. east coast Quahog farming and effects of manual digging versus a Canadian west coast Manila Clam farming. DATE: OCT. 2015–JUN. 2018 mechanical clam harvester. It investigated Several studies show that: FUNDED BY: DFO–Aquaculture Collaborative the effects of both techniques on the 1) Hydraulic dredging enhances Research and Development Program (DFO–ACRDP) ecological health and production of the settlement and/or survival of bivalves–it area by monitoring the clam population, CO-FUNDED BY: Mills Seafood Ltd. will be important to understand the associated fauna and flora, and various effects of mechanical harvesting on PROJECT LEAD: Angeline LeBlanc (DFO) physical and chemical parameters. Methods clams and the environment. PROJECT TEAM: Jeffery Clements (DFO) for mitigating the ecological impact of harvesting, such as replanting pre-recruits 2) The presence of adults or shells increases COLLABORATORS: Marilyn Clark (Mills Seafood Ltd.) recruitment of juvenile bivalves–thus, the on size-class plots and reducing repeated addition of shells to the sediment may CONTACT: [email protected] harvesting efforts, were also investigated. increase survival of juveniles. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ Specifically, the following results were found: acrdp-pcrda/projects-projets/15-2-G-02-eng.html 1) no difference was found in physical or Adding shells to the sediment acts as a chemical characteristics of the sediment buffer by raising the pH and the saturation between non-harvested, manually, or mechanically harvested plots; 2) no differences were found before and Bay Characterization for Nova Scotia Shellfish Aquaculture after harvesting; and 3) both harvesting n the Gulf Region waters of Nova Scotia, Fisheries and Oceans Canada (DFO) has techniques either have no impact on the shellfish aquaculture remains in its early identified a number of bays in Nova Scotia sediment and on faunal assemblages, stages of development. A recent report where future aquaculture development or that recovery is rapid. I Neither harvesting technique was better based on an independent aquaculture may be likely. Key variables including regulatory review concluded, among other hydrodynamic characteristics, fisheries, or worse than the other regarding its effects things, that licencing decisions needed to and ecologically sensitive species’ habitat on sediment characteristics. While manual consider compatibility between aquaculture and distribution, as well as aquaculture- digging is possible in any sediment type, and other uses of coastal waters. Balance specific activities and mitigation options the prototype harvester used in this project between sustainable development of will be described for these bays. The results was better suited for firm sandy bottoms and shellfish aquaculture, fisheries, and other from this project will support departmental some mud, but did not perform very well in resource uses (e.g., harbours, marinas, regulatory decisions that are consistent soft mud. It will need to be improved to be cottages, etc.) can be achieved through with the ecosystem-based approach to commercially useful. marine spatial planning and the managing the shellfish aquaculture industry. implementation of a bay management DATE: APR. 2012–JUN. 2015 plan designed to protect valued species in DATE: APR. 2015–MAR. 2018 FUNDED BY: DFO–Aquaculture Collaborative fisheries and conservations areas, while Research and Development Program (DFO–ACRDP) FUNDED BY: DFO–Program for Aquaculture avoiding conflicts with other users of the Regulatory Research (DFO–PARR) CO-FUNDED BY: Innovative Fisheries Products Inc. marine resource. Although Nova Scotia has not yet developed such a plan, describing PROJECT LEAD: Monique Niles (DFO) PROJECT LEAD: Thomas Landry (DFO) and mapping of coastal areas identified PROJECT TEAM: Marc Ouellette, Thomas Guyondet, PROJECT TEAM: Angeline LeBlanc (DFO) for aquaculture would provide critical Thomas Landry (DFO); Andrew Bagnall (NSDFA); COLLABORATORS: Doug Bertram (Innovative Tim Webster, Kate Collins (AGRG–NSCC) information for planning and science-based Fisheries Products Inc.) decisions making, and could provide the CONTACT: [email protected] basis for a bay-scale management plan. CONTACT: [email protected] WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2015-G-08-eng.html acrdp-pcrda/projects-projets/G-12-01-001-eng.html CANADIAN AQUACULTURE R&D REVIEW 2017 SHELLFISH: OTHER 107

Microplastics and Shellfish Aquaculture: Investigating Presence, The Effect of Cultured Shellfish Extent, and Potential Impacts and Mitigation Measures on Eelgrass Productivity in Estuaries of New Brunswick icroplastics (i.e., plastics < 5 mm) This research will show the level of are an emerging contaminant of microplastic pollution within commercial anada’s Oceans Act promotes Mincreasing concern to industry, shellfish and their surrounding environment. an ecosystem-based approach scientists, and the general public. Microplastics It will also indicate the efficacy of depuration in managing human activities in are ubiquitous in the marine environment and to remove this contaminant, the implications C coastal and marine environments. As such, come from a wide range of sources including of microplastic ingestion on shellfish health, enhanced protection should be provided to sewage effluent and general degradation and potential microplastic sources. species, such as eelgrass (Zostera marina), of larger plastics. There are several types and community properties that are particularly of microplastics such as microbeads, fibres, DATE: JUL. 2016–MAR. 2018 significant to maintaining ecosystem and fragments which are ingested by a FUNDED BY: DFO–Aquaculture Collaborative structure and function, while allowing wide range of organisms. Ingestion of Research and Development Program (DFO–ACRDP) sustainable activities to be pursued. One microplastics can have negative physical of the human activities considered is shellfish and chemical impacts on the organisms CO-FUNDED BY: BC Shellfish Grower’s Association (BCSGA) aquaculture, an increasingly important that consume them. Because of this, the economic driver in coastal communities. aquaculture industry has the potential to be PROJECT LEADS: Sarah Dudas (VIU); Recent studies have documented some Helen Gurney-Smith, Chris Pearce (DFO) negatively affected by microplastic pollution. negative effects on eelgrass from oyster Conversely, because of the use of plastics PROJECT TEAM: Chris Pearce (DFO); Peter Ross aquaculture, in some areas and at a local in the aquaculture industry there is also (Vancouver Aquarium); Garth Covernton, scale, mostly linked with shading effects Maggie Dietterle, Matt Miller, Kayla Balmer, the potential to contribute to microplastic from aquaculture gear. However, another Monique Raap (VIU) pollution. To address these issues, we are important aspect to also consider in the conducting a collaborative study with VIU, COLLABORATORS: Darlene Winterburn (BCSGA); overall risk characterization is the potential DFO, BCSGA, Vancouver Aquarium, and Yves Perreault (Little Wing Oysters); Andre Comeau, off-setting effects from the cultured bivalve UVic. This research will: 1) determine the Chris Roberts (Okeover Organic Oysters); Dave Ritchie, Steve Pocock (Sawmill Bay Shellfish); biomass, as filter feeders, on eelgrass concentration of microplastics in clams and Brian Yip (Taylor Shellfish); Keith Reid (Stellar Bay productivity by influencing turbidity oysters cultured in coastal British Columbia; Shellfish); Andrew Dryden (Evening Cove Oysters); patterns of natural and cumulative 2) determine the concentration of Pete McLellan (Nanoose Bay Oysters) anthropogenic sources. microplastics in the surrounding environment; CONTACT: [email protected]; This study is investigating the effects of 3) characterize the type of microplastics [email protected]; cultured shellfish on eelgrass productivity at found and identify potential sources; [email protected] the bay scale. This will be achieved through 4) evaluate depuration as a potential WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ field studies that describe the seascapes of mechanism to eliminate microplastics; acrdp-pcrda/projects-projets/15-1-P-01-eng.html, study bays, with a focus on the distribution and 5) investigate the impact of microplastics http://www.ecologicalinteractions.com/ of shellfish populations (wild and cultured) on shellfish health and resilience. and eelgrass beds, using novel remote sensing tools and strategies, and turbidity patterns of the water column. A laboratory study will evaluate the resulting effects of oyster filtration on turbidity (water clarity) and light attenuation. Finally, bay scale hydrodynamic computer models will be developed for two study bays to include a turbidity module and clearing coefficients of cultured oysters, allowing for improved assessments of bay-scale effects from existing (or proposed) shellfish leases on eelgrass productivity.

DATE: APR. 2014–MAR. 2018

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

Oyster up close. Photo: Kayla Mohns (DFO) PROJECT LEAD: Marc Ouellette (DFO)

PROJECT TEAM: Monique Niles, Thomas Guyondet, Michael Coffin (DFO)

COLLABORATORS: Tim Webster, Kate Collins (AGRG–NSCC)

CONTACT: [email protected]

WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2014-G-10-eng.html

Netting. Photo: Kayla Mohns (DFO) 108 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

MISCELLANEOUS

Integrating Individual Bioenergetics into Identification of Growth Stanzas and the Benthic Culture of Sea Cucumbers: Assessing Aquaculture Management Modification of the Body Weight Exponent in the Interactions Between Cultured and Wild Thermal-Unit Growth Coefficient (TGC) Model for Populations and the Mitigation of Environmental Science-Industry Partnership Leading to a Nile Tilapia (Oreochromis niloticus) Impacts in Shellfish Co-Culture Better Understanding of Ocean Acidification in British Columbia, Canada The Feasibility of Using Bacterial Community Optimization of Fly Co-Product Processing Profiling with Next-Generation DNA Sequencing Methods for Repurposing Organic Waste Algae-Based Ingredients for Aquaculture to Assess Temporal and Spatial Environmental in Quebec Feeds in Canada Disturbances Comparative Genomics of the Salmonid Brook Development of a Brown Alga Chorda filum Metagenomic Approach to the Characterization Charr for Identifying Physiological/Expression Culture Method of Microflora in Aquaculture Effluents that Induce QTL and Conserved Gene Regulatory Networks Assessing the Efficiency of a Macroalgae Phytoprotection and Growth Promotion of Establishing Zones for Managing Risks Related Biofilter in Regulating Nitrate and Phosphate Aquaponic and Hydroponic Plants to Pathogens and/or Pollutants Originating on Concentrations in Tanks at the Montreal Biodome NSERC-Cooke Industrial Research Chair in Finfish Aquaculture Facilities in the Broughton Mimicking the Gulf of St. Lawrence Ecosystem Sustainable Aquaculture Archipelago and Discovery Islands Biotic and Abiotic Determinants Influencing Winter Evaluation of Different Biomasses for a Pilot Development of Environmental DNA Flounder Feeding Behaviour and Larval Growth Project to Breed Fly Larvae, an Alternative (eDNA)-Based Biosurveillance for Aquatic Lumpfish and Atlantic Halibut Aquaculture Source of Protein and Lipids in Animal Feed Invasive Species (AIS) to Inform Management Operations Optimization and Policy Decision-Making Associated with The Development of an FVCOM Hydrodynamic Shellfish Aquaculture Movements Physiology of Triploid Fish Model to Support Aquaculture on the West Coast of Vancouver Island Assimilation Capacity of Organic Matter from Antifouling Control: Development of Salmon Aquaculture (ACOM): Improving Model Non-Biocidal Techniques for Mariculture Fish Farm Site-to-Site Connectivity Using GPS Predictions of Benthic Impacts Tracked Surface Drifters and FVCOM-Based Engineering Project in Support of the Fishing Particle Tracking Model Evaluation of Genetic Structuring of California Sea and Aquaculture Industry Cucumber (Parastichopus californicus) Across Contribution to the Identification of a Locally Service Viviers-Conseils: Innovation Service Transfer Zones in British Columbia Available Food Source for Sustainable Tilapia in Support of the Lobster Industry (Oreochromis niloticus) Production in the Democratic Republic of Congo CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 109

Integrating Individual Bioenergetics into Aquaculture Management sites. State-of-the-art technology, such as acoustic tags and laser particle counters, will be key for the success of the program. In this program we will explore the effects of extrinsic drivers such as diseases, parasites, temperature, and food availability, as well as intrinsic factors such as the internal state of the organism. Moreover, the resulting refined and state-of-the-art individual models will be coupled to larger scale models to contextualize aquaculture at the ecosystem level with the ultimate goal of adopting an ecosystem-based management approach. This research program will generate fundamental scientific knowledge that will: 1) inform industry on key processes of individual behaviour and bioenergetics; and 2) assist policy makers and managers in dealing with current and future issues such as invasive species and aquaculture Standard Dynamic Energy Budget (DEB) model scheme (Modified from Kooijman 2010). management.

nderstanding individual bioenergetics ecosystem functioning and predict their DATE: MAR. 2016–MAR. 2021 is critical for assessing how responses to anthropogenic changes Uenvironmental drivers (e.g., and/or changes in climate. Despite the FUNDED BY: Cooke Aquaculture Inc. temperature, food availability, oxygen, individual-based approach of DEB, the CO-FUNDED BY: Dalhousie University currents, etc.) affect the performance of most recent ecosystem models rely on DEB PROJECT LEAD: Ramón Filgueira (Dalhousie U) cultured species. Dynamic Energy Budget theory to simulate individual bioenergetics and (DEB) has become the most cutting-edge extrapolate the results to the ecosystem level. COLLABORATORS: Luc Comeau, theory on the organization of metabolism of This research program focuses on Peter Cranford, Thomas Guyondet (DFO); individual organisms. The mechanistic nature individual bioenergetics of cultured species, Jon Grant (Dalhousie U); Cooke Aquaculture Inc.; Vemco of DEB allows its application to the full range ranging from Atlantic Salmon to mussels and of environmental conditions, which is vital to oysters, as well as invasive tunicates that are CONTACT: [email protected] quantify the role of cultured species in relevant to the management of aquaculture

Science-Industry Partnership Leading to a Better Understanding of Ocean Acidification in British Columbia, Canada he goal of this study is to investigate at the research station. Preliminary analyses DATE: MAY 2016–ONGOING the spatial and temporal variability of reveal two important features: 1) OA signals FUNDED BY: Hakai Institute Ocean Acidification (OA) parameters are coherent across both sites, suggesting T PROJECT LEAD: Wiley Evans (Hakai Institute) at two sites in the northern Salish Sea; one that they are influenced by similar processes being a continuous monitoring system at and that broadcast high resolution data PROJECT TEAM: Katie Pocock, Alex Hare a research station and the other being a available on a public web portal (Global (Hakai Institute) partnering local shellfish producer’s farm Ocean Acidification Observing Network COLLABORATORS: Sawmill Bay Shellfish Co. site. Increased anthropogenic carbon dioxide data portal: http://portal.goa-on.org/ CONTACT: [email protected] (CO2) uptake by the surface ocean is driving Explorer?action=oiw:fixed_platform:HAKAI_ a reduction in oceanic pH. This acidification Quadra1) is an important diagnostic for the WEBSITE: www.hakai.org alters the carbonate chemistry of the industry partner; and 2) the OA data seawater, decreasing the saturation state fluctuated across a large range between of carbonate minerals essential to shell- sampling events at the farm site indicating forming organisms. Consequently, OA will the importance of short time scale variability have major implications for the shellfish in setting conditions. aquaculture industry in the long-term. The information produced in this study Currently, key information is lacking for demonstrates the critical importance of coastal settings, hindering identification science-industry partnerships for filling of near-term effects. It is critical to monitor the extensive OA data gap present in coastal areas to determine the current status coastal settings. Ultimately the information and plan mitigation strategies for the impact garnered by studies like this will aid in of increasing OA on the shellfish industry. the development of adaptation strategies In this study, weekly OA samples were for the regional impacts of this significant collected at the farm site and compared global problem. them with the high resolution data collected Stephen Pocock (Sawmill Bay Shellfish) collects a discrete seawater sample at his aquaculture site on Read Island, BC. Photo: Wiley Evans (Hakai Institute) 110 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

Algae-Based Ingredients for Aquaculture Feeds in Canada

onventional aquaculture feed of industrial CO2 conversion. To do this, resources are becoming increasingly we use a suite of existing and emerging Ccostly and ecologically unsustainable. technologies such as, photobioreactor algal In an effort to develop more sustainable feeds cultivation and harvesting, chemical and based on ‘lower-trophic’ ingredients, certain biochemical profiling, in vitro digestibility, algae have been proposed as promising biomass processing and feed production candidates based on their perceived supply technologies, and in vivo biological of well-balanced amino acids, essential fatty performance evaluation with target species. acids, and bioactive compounds. However, In addition to valorization of the algal crop despite this encouraging trend, many of the resulting from industrial CO2 conversion, we NRC Technical Officer, Jenny MacPherson, poses nutritional claims for aquaculture feeds are expect that this applied, industrially-relevant with NRC-developed “Brite-Box” photobioreactors unsubstantiated because their required research will also help to provide essential (>10,000 L production capacity). Photo: Scott MacQuarrie (NRC) biochemical profiles, digestibility data, and nutritional data for national regulatory effects on animal performance are either approval and industry adoption of novel inadequate or non-existent. Take for dietary ingredients of algal origin in Canada. example Chlorella spp., which is one of the To date, we have generated biochemical most highly studied microalgae for industrial profiles and digestibility data (in vitro and applications. While these algae have been in vivo) for 13 microalgae species and proposed for large-scale cultivation for 9 seaweed species. bioremediation, renewable energies, health food supplements, and sustainable animal DATE: SEP. 2013–MAR. 2017 feeds, there has never been an adequate FUNDED BY: NRC–National Bioproducts Program strategic assessment of their nutritional (NBP); NRC–Algal Carbon Conversion (ACC) Program quality as feed ingredients for Atlantic Salmon; the most widely farmed fish in PROJECT LEAD: Sean Tibbetts (NRC) Canada. This is the case for virtually all PROJECT TEAM: Patrick McGinn, algal species presently considered for Stephen O’Leary (NRC) industrial mass algaculture. COLLABORATORS: André Dumas (CATC); At the National Research Council of Daniel Lemos (University of São Paulo); Example of chlorophytic microalgal biomass for Jason Mann (EWOS; Cargill Canada) Canada and in partnership with industry and nutritional evaluation as a potential novel ingredient academia, a major focus is to evaluate the CONTACT: [email protected] for aquaculture feeds. Photo: NRC potential for algal products and co-products for use in aquaculture feeds as a means to WEBSITE: http://www.nrc-cnrc.gc.ca/eng/solutions/ collaborative/algal_index.html valorize the algal crop produced as a result

Development of a Brown Alga Chorda filum Culture Method agdalen Islands mussel farming gradually reducing the water temperature companies want to diversify their to 5°C. In tanks, the average growth of the Mmarine lagoon production and are fronds was 1.3 cm/day and the largest fronds interested in growing macroalgae. Chorda reached 191 cm. Undesirable opportunistic filum, a fast growing brown alga that occurs macrophytes such as Ulva sp. were always naturally in the lagoons of the region, could present in the cultures despite the fact that be a good candidate since there are markets the fertile fronds of C. filum had been for this edible alga. The general purpose of disinfected prior to sporulation. the project was to develop an understanding The project diversified the portfolio of of the steps involved in growing C. filum, i.e., cultivable edible macroalgae species with a cultivating gametophytes in vitro, growing summer tubular species distinct from leaf kelp. sporophytes on ropes, in tanks, and growing sporophytes on a sea farm in lagoons. The DATE: SEP. 2014–OCT. 2016 project was also designed to establish the FUNDED BY: Ministère de l’éducation et de nutritional and sensory profile of this alga. l’enseignement supérieur du Québec (MÉES) Fertile fronds were harvested in September. [Québec Ministry of Higher Education and Training] Two types of lights (white and red) and three Lisandre Gilmore-Solomon temperatures (5, 10, and 15°C) were tested for PROJECT LEAD: (Merinov) growing gametophytes. Vegetative growth of in vitro gametophytes appeared to be PROJECT TEAM: Isabelle Gendron-Lemieux, optimal at 10°C in white light. Two methods Karine Berger, Éric Tamigneaux (Merinov) were used to grow sporophytes on ropes: by COLLABORATORS: Michel Fournier (Les moules directly seeding the ropes with spores and de culture des Îles inc.) by spraying gametophytes on kuralon ropes. CONTACT: [email protected] In both cases, sporophytes were produced WEBSITE: http://alguequebec.org/ by keeping cultures at 10°C in white light and A. Female Chorda filum with a developing sporophyte embryo; B. Young C. filum sporophyte; C. C. filum sporophytes on culture ropes in a tank. Photo: Isabelle Gendron-Lemieux (Merinov) CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 111

Assessing the Efficiency of a Macroalgae Biofilter in Regulating Nitrate and Phosphate Concentrations in Tanks at the Montreal Biodome Mimicking the Gulf of St. Lawrence Ecosystem o improve the quality of recycled water in the exhibition’s tanks housing the TMontreal Biodome live collections, it is necessary to search for a complementary method for controlling nitrate and phosphate build-up simultaneously. In excessive concentrations, these nutrients can become an important source of stress for aquatic organisms. Based on integrated multi-trophic aquaculture systems, we wish to design a macroalgae biofilter adapted to absorb nitrates and phosphates under conditions Anne Tremblay-Gratton in plant science room (EPAQ). Seaweed culture aquarium for the master’s project similar to those of the Montreal Biodome’s Photo: Nathalie Le François (Biodome de Montréal) in the plant science room (EPAQ). marine ecosystem. Photo: Anne Tremblay-Gratton (U Laval) The performance of native species, Ulva lactuca and Palmaria palmata, were assessed for six days at École des Pêches et de l’Aquaculture du Québec (EPAQ) in Grande-Rivière. The average daily nitrate absorption rate for P. palmata was found to be 0.65 mg∙N∙g MS-1 versus 1.76 mg∙N∙g MS-1 for U. lactuca. The average daily phosphate absorption rates for P. palmata were 0.14 mg∙P∙g MS-1 versus 0.32 mg∙P∙g MS-1 for U. lactuca. Seven to 12% of nitrates and four to 24% of phosphates were removed by P. palmata while U. lactuca removed eight to 18% of nitrates and five Ulva lactuca (EPAQ). Palmaria palmata. Biodome de Montréal. to 24% of phosphates. Photo: Anne Tremblay-Gratton (U Laval) Photo: Anne Tremblay-Gratton (U Laval) After the P. palmata culture was introduced at the Montreal Biodome, other trials led to an improvement in biofiltration performance. In addition, the excess biomass is used to fertilize the exhibition tanks. This research project has improved the water quality of the Montreal Biodome exhibition tanks, and led to the enrichment of exhibition tank by providing natural shelter and food for aquatic animals.

DATE: JAN. 2014–APR. 2017

FUNDED BY: MITACS; Société des amis du Biodôme de Montréal (SABM); Natural Sciences Palmaria palmata. Biodome de Montréal. Palmaria palmata. Biodome de Montréal. and Engineering Research Council of Canada Photo: Anne Tremblay-Gratton (U Laval) Photo: Anne Tremblay-Gratton (U Laval) (NSERC)–Industrial Research Chair

CO-FUNDED BY: Fonds d’amorçage UQAR; Mérinov Inc.; Ressources Aquatiques Québec (RAQ)

PROJECT LEAD: Nathalie Le François (Montreal Biodome; U Laval)

PROJECT TEAM: Anne Tremblay-Gratton (U Laval); Grant Vandenberg (U Laval); Éric Tamigneaux (EPAQ)

CONTACT: [email protected]

Palmaria palmata. Biodome de Montréal. Palmaria palmata. Biodome de Montréal. Photo: Anne Tremblay-Gratton (U Laval) Photo: Anne Tremblay-Gratton (U Laval) 112 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

Biotic and Abiotic Determinants Lumpfish and Atlantic Halibut Aquaculture Operations Optimization Influencing Winter Flounder arming Atlantic Halibut (Hippoglossus optimize the various stages of production. The Feeding Behaviour and hippoglossus) and Lumpfish (Cyclopterus 4th generation should be produced in winter. Larval Growth Flumpus) represents an opportunity for Merinov trials have produced halibut eggs Quebec’s aquaculture industry to diversify its and larvae. To date, it has been impossible inter Flounder activities and markets with native species to maintain larvae beyond metamorphosis. (Pseudopleuronectes americanus) that tolerate captivity well. The project aims Further trials are scheduled for January 2017. W is a fish species that occurs off the to improve the survival rate of these two The project has contributed to the east coast of North America. This species is marine fish species. advancement of marine fish culture and of great interest for temperate aquaculture For Atlantic Halibut, the project focuses the training of highly qualified staff. and recreational fishing, which requires on the period between egg incubation and seed production in order sustain stocks in juvenile rearing because proficiency in larval DATE: JUN. 2014–JUN. 2017 coastal habitats. However, development of rearing of flatfish is a critical step influencing FUNDED BY: Fonds de Recherche du Québec en aquaculture production is limited by high performance in subsequent stages of the Nature et Technologies (FRQNT) mortalities in the initial benthic phase. Feed development cycle. quality plays an important role in limiting As lumpfish is a new farmed species, PROJECT LEAD: Marie-Hélène Fournier (Merinov; these mortalities. The purpose of this the project covers all stages of its life cycle. CÉGEP de la Gaspésie des et Îles) project is to verify the nutritional quality (in A method has been developed to breed PROJECT TEAM: Tony Grenier (Merinov) terms of fatty acids) of copepod nauplii as Lumpfish. From the first cohort of farmed CONTACT: [email protected] alternative live prey and compare it with Lumpfish, Merinov performed breeding trials traditional aquaculture feed (rotifers). In from the larval stage to sexual maturity. The WEBSITE: www.merinov.ca addition, flounder use shallow habitats organization is now producing 3rd generation where significant human activities occur. farmed larvae. Current trials are designed to Another objective of the project is to assess whether boat noise affects feeding behaviour in this species, particularly during the larval period, while individuals are still pelagic. Such information could assist in the selection of seeding areas. This study defines the impact of biotic parameters such as prey quality on Winter Flounder larval growth and the impact of anthropogenic noise on this species’ Lumpfish spawners. Photo: Marie-Hélène Fournier A Lumpfish larva. Photo: Marie-Hélène Fournier feeding behaviour. (Merinov; CÉGEP de la Gaspésie des et Îles) (Merinov; CÉGEP de la Gaspésie des et Îles)

DATE: APR. 2015–MAR. 2018 Physiology of Triploid Fish FUNDED BY: Fonds de Recherche du Québec en Nature et Technologies (FRQNT) team riploidy is the only management tool Understanding the physiological limitations research project currently available for ensuring of triploidy will allow for improvements in reproductive sterility of farmed fish. their culture protocols for commercial PROJECT LEAD: Réjean Tremblay (UQAR-ISMER) T Sterile populations can be of direct benefit to production. This will benefit the aquaculture PROJECT TEAM: Gilberte Gendron, industry since sexually mature fish often have industry in two ways: by eliminating early Maria Martínez-Silva, Céline Audet, reduced flesh quality and disease resistance. maturation of production fish and by ensuring Gesche Winkler (UQAR-ISMER) Sterility also addresses the risk of escaped that escaped fish cannot breed in the wild. COLLABORATORS: Aurélie Jolivet (CNRS fish breeding in the wild. However, triploids Research Unit 6539; TBM environnement); Fréderic are rarely used in aquaculture because of DATE: ONGOING Olivier (BOREA Research Unit 7208; CNRS; MNHN; performance limitations. We are investigating UPMC; IRD) FUNDED BY: NSERC–Discovery Grants Program the effects of triploidy on key physiological CONTACT: [email protected] processes to determine whether changes CO-FUNDED BY: New Brunswick Innovation in cell size and number, associated with Foundation (NBIF)–Research Assistantships Initiative triploidy, affect the ability of these animals PROJECT LEAD: Tillmann Benfey (UNB) to withstand chronic stress. Our research PROJECT TEAM: Chris Small, Nicole Nader, currently focuses on red blood cell structure Krista Latimer, Tillmann Benfey (UNB) and function, aerobic capacity, bioenergetics, [email protected] and environmental tolerances (high CONTACT: temperature and hypoxia). We have adopted WEBSITE: www2.unb.ca/biology/Faculty/Benfey.html zebrafish as a model species for some of this research because of the availability of stocks with fluorescent cells that are ideal biomarkers for cell location and function. Additional research is being done with Brook Charr, as a model salmonid that is easy to keep in our small-scale aquatic facility at the University of New Brunswick (UNB) campus. Adult male Brook Charr in a swim flume used for Research results will be translated to Atlantic measuring oxygen uptake at various temperatures. Salmon through industry partnerships. Photo: Krista Latimer (UNB) CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 113

Antifouling Control: Development of Non-Biocidal Techniques for Mariculture

ncreased proliferation of biofouling and natural competitors such as Periwinkle (amalgam of algae, bivalves, crustaceans, (Littorina littorea) and Hermit Crab (Pagurus Ior other invertebrates) on breeding spp.). Tests are performed in a natural and structures and organisms is a major a controlled environment to compare the challenge for sea farmers, particularly anti-fouling effectiveness of these treatments oyster and scallop farmers. In the Magdalen under different conditions. Islands, this problem is amplified by the This project provides an opportunity to proliferation of invasive aquatic species: test several innovative techniques to stop Golden Star Tunicate (Botryllus schlosseri) or reduce the development of biofouling and Violet Tunicate (Botrylloides violaceus). on stock structures. In the long term, these This colonization is having a significant advances will make companies more economic impact on the industry: cost-effective and competitive. They additional costs for maintaining and may also provide benefits for other Control structure, no treatment. Photo: Merinov cleaning structures, premature structural marine industries. degradation, deterioration in the quality of breeding stock organisms, etc. DATE: SEP. 2016–MAR. 2017 Current techniques used to attenuate FUNDED BY: DFO–Partnership Fund the impact of biofouling are often very inefficient. In response to a growing CO-FUNDED BY: Merinov phenomenon catalyzed by climate change, PROJECT LEAD: Madeleine Nadeau (Merinov) producers must identify new, more efficient PROJECT TEAM: Nicolas Toupoint (Merinov) processes, without risk to farmed organisms and consumers. This is why Merinov COLLABORATORS: Nathalie Simard (DFO); is working on this project to improve Biomer consortium management of mariculture structures CONTACT: [email protected] and survival of the breeding organisms, WEBSITE: www.merinov.ca Structure which received an antifouling coating oysters, and scallops. The techniques treatment. Photo: Merinov tested are non-biocidal antifouling paints

Engineering Project in Support of the Fishing and Aquaculture Industry

n order to be as efficient as possible and produce images of crab movement near a remain competitive, marine aquaculture cage for 20 to 24 hours. Icompanies need to meet significant Thanks to the new equipment and adaptation or technological development technologies installed in company facilities, needs. Merinov’s engineering team provides sea farmers will become more cost-effective. various services such as computer-assisted design, 3D modelling, and system and DATE: APR. 2015–MAR. 2017 process optimization. FUNDED BY: Ministère de l’Agriculture, des Among one if its many accomplishments, Pêcheries et de l’Alimentation du Québec (MAPAQ); Merinov modified an outdoor mussel spat Ministère du Développement Économique, de Mussel spat collector. Photo: Daniel Leblanc (Merinov) collector by adding a rotating drum with a l’Innovation et Exportation du Québec (MDEIE) hydraulic motor. This change significantly Lise Chevarie (Merinov) reduced labour costs. A job that once PROJECT LEAD: required three employees now requires two. PROJECT TEAM: Lise Chevarie, Daniel Leblanc, At a mussel farmer’s request, Merinov also Hubert Murray (Merinov) designed a mussel spat collection system COLLABORATORS: Private companies for conventional collectors. The collection CONTACT: [email protected] system was modelled. The mussel stripping system was modified to improve worker WEBSITE: www.merinov.ca ergonomics and reduce physical effort. This work greatly reduces travel time during operations. Mechanizing this work sped Design drawings of a rotating drum with a hydraulic up operations and provided a significant motor. Photo: Daniel Leblanc (Merinov) increase in performance. Many other initiatives by the Merinov engineering team have helped marine aquaculture companies in the Gaspé, Magdalen Islands, and North Shore areas optimize their farming methods. From time to time, Merinov engineering projects also cover some fishing industry needs. For example, a recently developed System for mussel sock dismantlement. Video: Merinov underwater camera housing is now used to 114 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

Service Viviers-Conseils: Innovation Service in Support of the Lobster Industry n recent years, lobster landings have Service Viviers-conseils promotes the increased. Since the fishing season is marketing of very high quality lobster, several Iopen for only about 10 weeks, lobster months after the fishing season. It makes marketing companies have to process and companies more productive and competitive market large volumes in a very short time. by increasing their containment capacity, During this time, various issues arise: labour providing superior product quality, and shortages, insufficient storage capacity, modernizing their equipment. reduced ability to obtain better prices from buyers, quality management issues, etc. DATE: APR. 2016–MAR. 2021 Service Viviers-conseils, created by FUNDED BY: Natural Sciences and Engineering Hemolymph sampling for blood protein analysis to verify lobster quality. Merinov–Centre collégial de transfert de Research Council of Canada (NSERC) technologie des pêches du CÉGEP de la Photo: Jean-François Laplante (Merinov) Gaspésie et des Îles, is addressing this CO-FUNDED BY: Emploi Québec; Private Sector industry problem by helping companies PROJECT LEAD: Jean-François Laplante (Merinov) innovate in order to optimize their systems PROJECT TEAM: Marie-Claude Côté-Laurin, and containment conditions. Francis Coulombe, Madeleine Nadeau It is necessary to innovate in this field since (Merinov);Marie-Hélène Bénard, 60% of Quebec lobster is marketed live. For Lisandre Solomon-Gilmore (Merinov; instance, producers can consult Merinov CÉGEP de la Gaspésie et des Îles); to diagnose mechanical and biological Marie-Hélène Fournier (EPAQ); Jacinthe Bourgeois parameters, set up new tanks, and monitor (Cégep de la Gaspésie et des Îles) lobster quality status prior to marketing. In, COLLABORATORS: Private Sector they also offer support for setting up an CONTACT: Jean-Franç[email protected] Extended lobster containment. automation system, implementing research and Photo: Jean-François Laplante (Merinov) development projects, and custom training. WEBSITE: www.merinov.ca

Identification of Growth Stanzas and the Modification of the Body Weight Exponent in the Thermal-Unit Growth Coefficient (TGC) Model for Nile Tilapia (Oreochromis niloticus)

three growth stanzas (Model 3). Goodness- of-fit statistics (R2, CCC, RSS, etc.) and model selection criteria (AIC) determined Model 1 was superior to Model 3; Models 1 & 3 were superior to Model 2. The inclusion of growth stanzas improved the fit of the TGC model, with modification of the body weight exponent further improving the fit, resulted in a more realistic and biologically sound growth model. Growth functions are integral in farm production management, current growth functions used in aquaculture overlook the potential of difference in growth pattern (stanzas) during the production cycle. The proposed model incorporates growth Resulting growth trajectories from Model 1, 2, and 3 compared to observed sampled body weight values from stanzas, and differing body weight one production lot of Nile Tilapia. Photo: Christopher Powell (U Guelph) exponents in each growth stanza, in an effort to better represent growth at any given life stage of a fish. he ability to predict growth of aquaculture growth rates were calculated using the TGC species has improved with the model and regressed against body weights. DATE: SEP. 2015–ONGOING adoption of the thermal-unit growth Three growth stanzas, representing changes T FUNDED BY: MITACS Canada coefficient (TGC) model. However, the in growth patterns across life stages, were TGC model does not account for changes identified using spline and broken-line CO-FUNDED BY: Ontario Graduate Scholarship in growth patterns across life stages by analysis. A non-linear model was applied to (OGS) assuming a constant body weight exponent growth data and body weight exponents PROJECT LEADS: Christopher Powell, (b=1/3). The objective of this study is to iteratively solved for in each identified Dominique Bureau (U Guelph) improve the predicative ability of the TGC growth stanza. Analysis resulted in a growth model through the identification modified TGC model with body weight PROJECT TEAM: James France, Owen Skipper-Horton, Fiona Tansil (U Guelph) of growth stanzas and modification of the exponents (b) of 0.405, 0.798, and 0.956 body weight exponent in Nile Tilapia in each growth stanza. The modified TGC CONTACT: [email protected], (Oreochromis niloticus). model (Model 1) was compared to the [email protected] Growth data were collected from commercial traditional TGC growth model (Model 2), and tilapia culture operations (329 observations); the TGC model (b=1/3) modified to include CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 115

The Feasibility of Using Bacterial Community Profiling with Next-Generation DNA Sequencing to Assess Temporal and Spatial Environmental Disturbances

envision this as a broad-based tool that can be used across the country, in both marine and freshwater habitats, and on all bottom types. It is designed to mesh well with other techniques being developed in separate research initiatives, both nationally and internationally. We are entering a new era in biology where genetic technologies are allowing us insights, which were not available previously, into biological processes and characteristics of animals and the habitats they inhabit. If successful, this project will add another tool for scientists and managers to assess impacts of various practices and potentially Remotely operated vehicle (ROV) and bacterial syringe sampler taking a surface sediment sample on a rocky a mechanism to provide baseline information bottom in the Bay of Fundy. Photo: Shawn Robinson (DFO) for longer term climate change impacts to hanges to marine habitats, either from We feel that this new technique could be the ecosystem. natural or anthropogenic sources, will applicable to all bottom types, in all depths of Cbe reflected in the species diversity water, and may give an accurate overview of DATE: JUN. 2016–MAR. 2017 and the physiological traits of the organisms. the current benthic oxygen level that drives FUNDED BY: DFO–Program for Aquaculture This characteristic profile of species by much of the biodiversity of interest for the Regulatory Research (DFO–PARR) habitat is reflected at many different size management of industrial activities. Because scales ranging from bacteria to large mobile we will be sampling from the surface layers PROJECT LEAD: Shawn Robinson (DFO) marine animals. The goal of this study is to where the turnover of bacteria can be very PROJECT TEAM: Helen Gurney-Smith, test the concept that benthic conditions can rapid, the technique will allow us a view of Jonathan Day, Steve Neil, Craig Smith (DFO) be easily and cost-effectively monitored via the current environmental conditions of the COLLABORATORS: Ben Forward (RPC) bacterial populations using MiSeq, a rapid bottom. We propose to test this concept in DNA sequencing technology that is being the Bay of Fundy to develop an CONTACT: [email protected] adopted internationally and setting new understanding of the spatial and temporal WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ standards for environmental monitoring. limitations of this technique. Ultimately, we parr-prra/projects-projets/2016-M-10-eng.html

Metagenomic Approach to the Characterization of Microflora in Aquaculture Effluents that Induce Phytoprotection and Growth Promotion of Aquaponic and Hydroponic Plants nvironmental protection concerns microorganisms promoting plant growth are growing in the agri-food sector, and phytoprotection in hydroponics and Eparticularly in the aquaculture industry, aquaponics. This will allow the development where effluent capture and recovery have of a better understanding of their interactions become priorities. At the same time, the with plants and the impact they have on hydroponics sector is seeking more them. The characterization of a hydroponic sustainable nutrient sources and biological system’s unique microflora will allow for the methods for fighting specific pathogens. identification of beneficial species, and Aquaponics technology can be used in this foster their development and marketing context to produce vegetable plants from as phytopathogenic biocontrol agents or fish excrement, which microorganisms even organic fertilizers. convert into digestible nutrients. In return, the plants clean the water by catching DATE: APR. 2015–MAR. 2018 elements that are toxic to fish, so that 99% FUNDED BY: Ministère de l’Agriculture, des of the water can be recycled. Aquaculture Pêcheries et de l’Alimentation du Québec (MAPAQ) effluents promote the growth and performance of a wide range of hydroponic PROJECT LEAD: Grant Vandenberg (U Laval) plants. We recently demonstrated that the PROJECT TEAM: Benjamin Laramée, microflora present in aquaculture effluents Nicolas Derome, (U Laval); Martine Dorais (AAC) induces phytoprotection against Pythium COLLABORATORS: Youbin Zheng (U Guelph) ultimum and Fusarium oxysporum, two [email protected] significant pathogens in agriculture. CONTACT: However, there is little information providing WEBSITE: http://www.vrrc.ulaval.ca/fileadmin/ a taxonomic description of this specific ulaval_ca/Images/recherche/bd/chercheur/ fiche/424160.html Benjamin Laramée in front of his aquaponic system. microflora. This research project will Photo: Benjamin Laramée (U Laval) identify, through metagenomic methods, 116 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

NSERC-Cooke Industrial Research Chair in Sustainable Aquaculture arming of fish and shellfish in the ocean is equal in importance to harvest Ffisheries as a means of seafood production. Concerns about disease and waste management as well as interaction with commercial fisheries have led to controversy among the industry, government regulators, and coastal communities. There are, however, many avenues of environmental improvement feasible for ocean culture of salmon in net pens. Cooke Aquaculture, the largest locally owned aquaculture company in North America, has partnered with Dalhousie University, in a research program on aquaculture sustainability. Professor Jon Grant is the NSERC-Cooke Industrial Research Chair in Sustainable Aquaculture. An approach involving simulation modelling is being employed using computer models Simulation of benthic process allows estimation of assimilative Habitat map based on echosounder and mapping of aquaculture ecosystems to capacity (AC) of sediments near aquaculture sites. Sediment oxygen surveys of Shelburne Harbour. Colours is contoured as a function of waste deposition (fish feed and pellets) correspond to different bottom types as predict the transport of diseases and waste relative to hydrodynamic regime from highly depositional to highly separated statistically and groundtruthed particles by ocean currents. A field program dispersive. Red regions are low sediment oxygen due to high with bottom video. The most widespread of oceanographic instruments and sampling deposition and low dispersion. colour is sand. at coastal sites, including Cooke Aquaculture farm operations, is being used to check the reliability of the predictions. Various planning scenarios are explored with this method, which can be used to arrange farm sites to minimize the spread of disease or accumulation of waste. Dalhousie’s inclusion of training of highly qualified personnel in the research program furthers this cooperation with the aquaculture industry in a new chapter in the practice of environmentally conscious fish farming. This research into the sustainability of salmon farming includes an ecosystem approach to aquaculture and marine spatial planning.

DATE: JAN. 2014–DEC. 2018

FUNDED BY: Natural Sciences and Engineering Research Council (NSERC)–Industrial Research Drone used for mapping salmon habitat in Upper Salmon River, Fundy National Park. Chairs Grants Photo: Jon Grant (Dalhousie U) CO-FUNDED BY: Cooke Aquaculture Inc.

PROJECT LEAD: Jon Grant (Dalhousie U)

PROJECT TEAM: Ramon Filgueira (Dalhousie U)

COLLABORATORS: Tom Taylor (Cooke Aquaculture Inc.)

CONTACT: [email protected]

Sensor collaboration with Vemco Amirix (realtimeaquaculture.com) on cage-specific oxygen and temperature data, with wireless acoustic data logging and smartphone monitoring. CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 117

Evaluation of Different The Development of an FVCOM Fish Farm Site-to-Site Connectivity Biomasses for a Pilot Project to Hydrodynamic Model to Support Using GPS Tracked Surface Breed Fly Larvae, an Alternative Aquaculture on the West Coast Drifters and FVCOM-Based Source of Protein and Lipids in of Vancouver Island Particle Tracking Model Animal Feed revious hydrodynamic modelling in quaculture Bay Management Areas n Quebec, the management of organic the Broughton Archipelago and the (ABMAs) were implemented in waste recycling, aimed at reducing landfill PDiscovery Islands has demonstrated A southwest New Brunswick in 2006 use, is currently challenging. There is also the advantage of having a computer as part of a multi-faceted effort to manage I (numerical) model that provides accurate disease within fish farms and reduce the a critical need for alternative cost-effective and environmentally-friendly ingredients for three dimensional information on current potential for the spread of disease between livestock feed. Fish meal derived from the flow, temperature, and salinity. FVCOM (Finite farms and geographic areas. The boundaries overexploitation of marine ecosystems is Volume Coastal Ocean Model), when fully of the ABMAs were chosen so that the not sustainable, and the volumes produced developed for this area, promises to provide estimated exchange of water and associated cannot keep up with the growing demand accurate 3D information. Since FVCOM’s water borne pathogens between ABMAs on from the aquaculture industry. development process is complex, this a tidal time scale (~12.5 h) was minimized. Our approach combines the two issues, research project is using existing information Although the ABMA approach to disease using fly larvae to recycle organic waste into and new data collected specifically for this management seems to have been successful, quality feed that is high in protein and other project in order to further develop the model. the original ABMA structure imposed some nutrients. Fly larvae production is simple, The ultimate goal of the project is to be limitations that have operational and socio- low-cost, and environmentally friendly. able to apply the accurate FVCOM 3D economic consequences. Splitting some of The goal of this project in the first year is information to examine particle tracking, the ABMAs will increase the total number of to evaluate various ratios of feed substrates virus dispersion, and sea lice behaviour in the ABMAs in the southwest New Brunswick area produced from fruit and vegetable waste waters off the West Coast of Vancouver Island and may increase water exchange between and microbrewery grains on the growth and in and around aquaculture sites in the area. the new ABMAs but it could help provide nutritional composition of two species of fly The results of this project (the developed more operational flexibility to the industry. larvae (i.e., Black Soldier and Domestic Fly). model) will be important for the sustainable This approach could also offer more socio- The second year will focus on incorporating management of the aquaculture industry. economic stability to the residents of the area marine waste to assess its impacts on larval The data will inform mitigation actions that by providing more consistent and stable omega-3 content to enhance the nutritional can be recommended by management employment. This is particularly relevant quality of fish meal for carnivorous species. bodies in response to well characterized to the island of Grand Manan in the mouth Larval meal and oil production costs will risk. From an industry perspective, these of the Bay of Fundy where employees also be assessed to determine whether results can inform best management sometimes need to travel by ferry to and from they meet the constraints of aquaculture practices in order to offset possible impacts. work on the island because of the lack of a feed producers. third ABMA. Both industry and provincial This project will thereby validate the DATE: MAY 2015–JUN. 2017 government desire a better understanding of the potential for water exchange between success of establishing fly larva production FUNDED BY: DFO–Aquaculture Collaborative to recycle organic waste and make it fit for Research and Development Program (DFO–ACRDP) the farm sites within the existing ABMAs inclusion in fish feed for aquaculture species and the risk potential for disease-spread CO-FUNDED BY: Cermaq Canada Ltd.; between fish farms prior to decision making. A in Canada. Grieg Seafood BC Ltd. more advanced water circulation model, Finite PROJECT LEAD: Peter Chandler (DFO) DATE: MAY 2015–DEC. 2017 Volume Coastal Ocean Model (FVCOM), new PROJECT TEAM: Mike Foreman, Darren Tuele, particle tracking models, and new current FUNDED BY: Ministère de l’Agriculture, des John Morrison, Pramod Thupaki, Di Wan, Ming Guo, meter data from the offshore area of Eastern Pêcheries et de l’Alimentation du Québec (MAPAQ); Maxin Krassovski (DFO) Grand Manan will soon be available. When Mitacs COLLABORATORS: Kathleen Frisch (Cermaq these data are combined with the new drifter PROJECT LEAD: Grant Vandenberg (U Laval) Canada Ltd.); Barry Milligan (Grieg Seafood BC Ltd.) data collected under this project, a more PROJECT TEAM: Justine Richard-Giroux, substantial examination of the potential for CONTACT: [email protected] Marie-Hélène Deschamps (U Laval); water exchange between the fish farms in Marie-Pier Aubin, Charles Lavigne (CDBQ) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ the ABMAs will be possible. acrdp-pcrda/projects-projets/15-1-P-03-eng.html CONTACT: [email protected] DATE: APR. 2016–JUN. 2019 WEBSITE: http://www.vrrc.ulaval.ca/fileadmin/ ulaval_ca/Images/recherche/bd/chercheur/ FUNDED BY: DFO–Aquaculture Collaborative fiche/424160.html Research and Development Program (DFO–ACRDP) CO-FUNDED BY: Atlantic Canada Fish Farmers Association (ACFFA)

PROJECT LEAD: Fred Page (DFO)

PROJECT TEAM: Susan Haigh, Sean Corrigan, Sarah Scouten, Frederick (Jack) Fife (DFO); Mike Beattie, Pat Mowatt (DAAF); Final checks prior to the deployment of a current Betty House (ACFFA) meter mooring from the CCGS John P. Tully off the west coast of Vancouver Island are made by Lucius COLLABORATORS: Sue Farquharson (ACFFA) Perreault and Roger Savoie. Data collected by a network of moorings are used to validate the currents CONTACT: [email protected] Adult Black Soldier Flies mating. simulated by the FVCOM hydrodynamic model. Photo: Justine Richard-Giroux (U Laval) Photo: David Spear (DFO) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ acrdp-pcrda/projects-projets/16-1-M-03-eng.html 118 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

Contribution to the Identification of a Locally Available Food Source for Sustainable Tilapia (Oreochromis niloticus) Production in the Democratic Republic of Congo performances compared to the Rcongo test feed, the cost-benefit analysis indicated that it was more economically advantageous because it reduced fish production costs by 36% compared to commercial feed. The project allowed the reduction of fish production costs through the informed use of vegetable protein sources and a food source that is easily accessible by farmers.

DATE: JUN. 2015–AUG. 2015 Final sampling of tilapia (O. niloticus) on day 28. Collection of feces by syphoning for tilapia Photo: Albert Tshinyama (U Laval) digestibility study. Photo: Albert Tshinyama (U Laval) FUNDED BY: Fonds Forestier pour le Bassin du Congo (FFBC); African Development Bank (AfDB)

CO-FUNDED BY: Programme Élargi de Formation ilapia farming is one alternative that protein sources would have on zootechnical en Gestion des Ressources Naturelles dans le Bassin can contribute to reducing food and nutritional performances (e.g., growth, du Congo (PEFOGRN-BC) insecurity in the Democratic Republic food use), as well as the cost of fish T PROJECT LEAD: Grant Vandenberg (U Laval) of Congo and in Africa as a whole, as this fish production. Tests were conducted on species is highly productive and adapts juvenile tilapia (Oreochromis niloticus) PROJECT TEAM: Albert Tshinyama, Emilie Proulx, better to low inputs in fish farming. However, (~ 15-20 g) at the aquatic sciences lab at Marie-Hélène Deschamps, Damase Khasa (U Laval); Freddy Okitayela (University of Kinshasa) the use of optimized feed with a high content Université Laval. Three diets were tested: of fish meal is not encouraged, given their 1) Rcongo: the main substitution test food COLLABORATORS: Mélodie Richard, high costs and their very limited availability made with African ingredients; 2) Rcanada: Corina Nagy (U Laval) to farmers. Identifying locally available the second test food made with the same CONTACT: [email protected] resources would make it possible to develop ingredients but acquired in Canada; and WEBSITE: http://www.vrrc.ulaval.ca/fileadmin/ fish farming and reduce production costs. 3) Rcommercial: a commercial control ulaval_ca/Images/recherche/bd/chercheur/ This study involved evaluating the effects feed made with fish meal. Although the fiche/424160.html that substituting fish meal with vegetable commercial feed had a higher zootechnical

Benthic Culture of Sea Cucumbers: Assessing Interactions Between Cultured and Wild Populations and the Mitigation of Environmental Impacts in Shellfish Co-Culture

associated environmental impacts of shellfish aquaculture. However, seasonal changes in sea cucumber density at our study site suggest that if preventing mixing of wild and cultured stocks is desired, some form of containment may be necessary. Expanding our knowledge of benthic ranching techniques for P. californicus and addressing issues such as containment of this species will be mutually beneficial to resource managers and industry partners.

DATE: APR. 2012–MAR. 2015

FUNDED BY: DFO–Aquaculture Collaborative Juvenile California Sea Cucumber, Parastichopus californicus, perched on an oyster clump amid a forest of Research and Development Program (DFO–ACRDP) oyster culture strings. Photo: Dan Curtis (DFO) CO-FUNDED BY: Fan Seafoods Ltd.; Klahoose First Nation; Pacific Sea Cucumbers Harvesters igh market demand has resulted between wild and benthic-ranched Association; Viking Bay Ventures in a great deal of interest in culturing individuals. The results of this project show Chris Pearce (DFO) the California Sea Cucumber promise for the development of sea cucumber PROJECT LEAD: H PROJECT TEAM: Dan Curtis, Nick Duprey, (Parastichopus californicus) in British Columbia aquaculture in BC. Juveniles have shown (BC). However, before these operations can good growth and survival when raised in Claudia Hand (DFO); Scott McKinley (UBC) proceed to full scale production, additional benthic cages both on and away from an COLLABORATORS: Fan Seafoods Ltd.; Klahoose base-line data are needed to determine the existing deep-water oyster farm. When First Nation; Pacific Sea Cucumbers Harvesters viability and potential impacts of culturing sea co-cultured with oysters, the nutrient rich Association; Viking Bay Ventures cucumbers. The primary aims of this project benthic habitat at these sites may allow for CONTACT: [email protected] are to determine: 1) the growth and survival higher growth rates and stocking densities. WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ of sea cucumbers in benthic culture; 2) the High densities of sea cucumbers often found acrdp-pcrda/projects-projets/P-14-02-003-eng.html environmental impact of sea cucumber at existing aquaculture sites may help to aquaculture; and 3) the potential interactions ameliorate some of the nutrient loading and CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 119

Optimization of Fly Co-Product Processing Methods for Repurposing Organic Waste in Quebec he production of insects from organic and Ultra-high temperature processing (UHT) of Canadian farmed fish as well as the waste is a sustainable approach or High pressure homogenization (HPH)) Canadian safety and hygiene criteria Tthat would allow the production of aimed at reducing/controlling the microbial of alternative feeds. alternative proteins and lipids meeting the load of the larvae. HPH optimization will needs of animal production. The goal of facilitate the extraction techniques of DATE: JUN. 2016–MAY 2019 this project is to improve the techniques for co-products such as protein, lipid, and chitin FUNDED BY: Ministère de l’Agriculture, des culling Black Soldier Fly larvae, as well as from fly larvae meal. Costs, performance, Pêcheries et de l’Alimentation du Québec (MAPAQ) fish meal processing processes, to optimize and product quality, such as lipid and amino the nutritional value, safety, and digestibility acid profiles, will be rigorously monitored at PROJECT LEAD: Grant Vandenberg (U Laval) of fish and chicken feed. each stage of processing to determine the PROJECT TEAM: Marie-Hélène Deschamps, Black Soldier Fly larvae will be produced at optimal processes to be retained. Finally, Jennifer Larouche, Justine Richard, Linda Saucier, the Centre de développement bioalimentaire two protein meals obtained through the Cristina Ratti, Alain Doyen, Lucie Beaulieu, du Québec (CDBQ), and various culling optimal techniques will be incorporated into Marie-Pierre Létourneau Montminy (U Laval); Marie-Pier Aubin, Charles Lavigne (CBDQ) techniques (i.e., CO2 anaesthesia, by oxygen experimental diets, and their digestibility and deprivation and/or freezing) will be tested. palatability compared to control diets during CONTACT: [email protected] The larvae will then be transferred to nutritional testing in fish and chickens. WEBSITE: http://www.vrrc.ulaval.ca/fileadmin/ Université Laval where various packaging This project will include the development ulaval_ca/Images/recherche/bd/chercheur/ techniques will be tested (i.e., pasteurization of insect products meeting nutritional needs fiche/424160.html

Operational diagram of Black Soldier Fly meal optimization. Photo: Marie-Hélène Deschamps (U Laval) 120 MISCELLANEOUS CANADIAN AQUACULTURE R&D REVIEW 2017

Comparative Genomics of the Salmonid Brook Charr for Establishing Zones for Managing Identifying Physiological/Expression QTL and Conserved Risks Related to Pathogens and/ Gene Regulatory Networks or Pollutants Originating on Finfish Aquaculture Facilities in n addition to their ecological, cultural and characterize gene expression networks and the Broughton Archipelago and commercial importance, salmonids are of central hub genes. Finally, we will anchor Discovery Islands Igreat interest for genetics research and assembled genomic scaffolds on the newly evolutionary biology due to their evolutionary developed genetic map and compare with ish farming in coastal waters characterized success and the occurrence of an ancestral other species. Collectively, this work will by strong and variable currents makes whole-genome duplication at the base of identify regions of the genome important for understanding the water circulation the lineage. Much research has been ecologically and evolutionary important traits, F important to sustain a healthy environment, conducted in salmonid genetics, and there and bring Brook Charr genetics into the both on and away from the farm. When many exist high-density genetic maps for at least genomic era. farms share a common environment, the eight species, chromosome-level genome This work will develop genomic tools for cumulative impacts may be surprisingly assemblies for two species, and many Brook Charr, including a high-density genetic complex, especially in an environment that transcriptome studies. However, most map, a draft genome assembly, and growth changes daily (tides and winds), seasonally of this work has been conducted on two and stress-resistance markers to be used for (snowmelt and river runoff), and yearly Salmo Oncorhynchus genera, and . The selective breeding. Additionally, this work will (climate change). A high precision model Salvelinus fontinalis Brook Charr ( ) is of put Brook Charr genomics into the context (FVCOM) that can represent temperature, great importance commercially (both from of the broader study of evolution post whole salinity, and water flow in three dimensions an aquaculture and an angling perspective) genome duplication, specifically in terms has been developed. The results of the but remains much less characterized. This of sex determination, important genomic model simulations (April to October 2010) are project aims to improve the genetic tools regions, and gene expression regulation. stored as 3D data fields at hourly intervals for and characterization of Brook Charr. 21 depth levels, at each of the 36,000 nodes First, we developed a high-density DATE: SEP. 2013–SEP. 2017 that comprise the model grid. Particle genetic map with 3826 single nucleotide FUNDED BY: Fonds de recherche du Québec– tracking models use the modelled currents polymorphism (SNP) markers and a new Nature et Technologies (FRQNT)–Projets de to determine the area of influence due to bioinformatics method to compare the recherché en équipe the release of virtual particles from fish farm map to all other published high-density Société de recherche et de locations. A field program using surface salmonid maps, as well as to a non- CO-FUNDED BY: développement en aquaculture continentale Inc. drifters designed at DFO has been used to duplicated outgroup, to identify chromosome (SORDAC) validate the model results with observed correspondence among the species. Second, surface currents. Tracked by a GPS we identified quantitative trait loci (QTL) PROJECT LEAD: Louis Bernatchez (U Laval); Céline Audet (UQAR) (global positioning system), the drifters associated with growth, reproductive and provided weeks of positional information PROJECT TEAM: Ben Sutherland (U Laval) stress-resistance traits. We also identified to compare with corresponding circulation the sex chromosome and confirmed striking CONTACT: [email protected]; and particle tracking model simulations. recombination rate differences between the [email protected] The hydrodynamic connectivity between sexes. Third, we will use RNA-sequencing to fish farms in regions such as the Broughton perform expression QTL (eQTL) analysis and Archipelago and Discovery Islands has been used to contribute to decisions involving pathogen transfer among fish farms, and from fish farms to wild fish. Management zones can then be established based on these criteria.

DATE: APR. 2011–APR. 2016

FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR)

PROJECT LEAD: Peter Chandler (DFO)

PROJECT TEAM: Mike Foreman, Diane Masson, Kyle Garver, Dario Stucchi, Darren Tuele, Michael Ikonomou, Stewart Johnson, Marc Trudel (DFO)

CONTACT: [email protected] Brook Charr alevins. Photo: Céline Audet (UQAR) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2011-P-08-eng.html CANADIAN AQUACULTURE R&D REVIEW 2017 MISCELLANEOUS 121

Development of Environmental Assimilation Capacity of Organic Evaluation of Genetic DNA (eDNA)-Based Matter from Salmon Aquaculture Structuring of California Sea Biosurveillance for Aquatic (ACOM): Improving Model Cucumber (Parastichopus Invasive Species (AIS) to Inform Predictions of Benthic Impacts californicus) Across Transfer Management and Policy Decision- Zones in British Columbia he spatial scale, magnitude and Making Associated with Shellfish persistence of benthic, or seabed, Aquaculture Movements isheries and Oceans Canada (DFO) Teffects from the release of organic regulates the introduction and transfer wastes are influenced by a range of factors hellfish movements associated with of fish and shellfish into and between that control waste deposition, recycling, and F aquaculture activities are a known facilities in British Columbia so as not to transport. Previous research has shown that vector for aquatic invasive species (AIS) adversely affect local aquatic species and S a relationship exists between the deposition habitats. Requests for introductions and introduction and spread. For example, the rate of organic matter from salmon net-pens transfer of harvested shellfish has been transfers to and from aquaculture facilities are and benthic community effects. However, established as a vector for the spread of risk-assessed for possible disease, ecological this simple cause-effect relationship neglects invasive tunicates, bryozoans, and European and and genetic effects on native species to consider many important physical, Green Crab. Even with mitigation measures and ecosystems, and to ensure the regulations chemical, and biological processes that are like rinsing in place, which is currently used are met. There may be a requirement for responsible for the manifestation of benthic for Green Crab areas, some degree of risk mitigation measures to minimize any risks effects. An important, but poorly understood of translocating invasive species is intrinsic associated with transfer activities (e.g., egg factor is the inherent capacity of different to all shellfish movements. As such, informed disinfection, quarantine of stock). benthic habitats to mineralize (recycle) this decision-making around shellfish movements In British Columbia, five distinct shellfish material without significantly altering the is an important management activity to transfer zones (STZs) span the Pacific Region. natural state of the seabed. This organic mitigate risk of new invasions in geographic STZs are used to manage the movement enrichment threshold is commonly referred areas in BC that currently lack AIS that are of cultured shellfish to prevent gene flow to as the “assimilative capacity”. Ongoing present at other locations. Along the coast of between farmed and wild populations, and multidisciplinary research in Canada and British Columbia, collecting spatial data on AIS to manage the transfer of potential parasites/ Norway aims to increase scientific expertise distributions is challenged by high variability pathogens. Introducing or translocating and knowledge on the major processes in the geographic distribution of AIS at cultured individuals can lead to gene flow with that determine benthic assimilative capacity relatively small spatial scales. These patchy wild populations, and can result in a loss of under a range of environmental settings AIS distributions also create a challenge for genetic variation or adaptive genes found in and seabed types (mud, sand, and mixed management because it is not feasible to the wild populations. Therefore, understanding substrate). This work includes studies on manage shellfish movements in BC at the the spatial scales at which shellfish populations waste deposition and dispersion dynamics, level of individual AIS or individual bays. are genetically distinct can help to optimize the the decay rates of organic matter, and DNA metabarcoding of complex (i.e., boundaries of STZs to meet both ecological oxygen exchanges with the seabed. A mixed-species or environmental DNA) and socio-economic objectives. separate objective of this research is the samples generates millions of sequence Currently, an Introductions and Transfers development of a model that will provide reads from the majority of species present Licence is required for both between and increased accuracy in predicting the within the sample simultaneously and with within zone transfer activities of sea cucumbers spatial scale and the magnitude of benthic high sensitivity. Using reference DNA sequence in British Columbia. This study will assess community effects from ocean-based libraries, metabarcoding reads can be the genetic structure of the California Sea finfish farms. Parastichopus californicus translated into biodiversity data with a relatively Cucumber ( ) and high level of taxonomic resolution and can be compare the location of genetic discontinuities used for detection of cryptic, rare, and small DATE: APR. 2014–MAR. 2017 with current STZ boundaries. Information on their genetic structure will also contribute taxa, including AIS. The main objective of FUNDED BY: DFO–Program for Aquaculture this project is to transfer into DFO an eDNA- Regulatory Research (DFO–PARR) important spatial information for informing fisheries management and the design of Marine based metabarcoding tool developed by the PROJECT LEAD: Peter Cranford (DFO) Canadian Aquatic Invasive Species Network Protected Area (MPA) networks. The results of PROJECT TEAM: Brent Law, Fred Page, (CAISN) and perform optimization and this project will contribute to science advice that Terri Sutherland, Shawn Robinson, can be used to enhance the scientific basic for field-validation for its use as an AIS Herb Vandermeulen, Susan Haigh (DFO) biosurveillance tool to aid decision-making, STZs and the sustainable management of the COLLABORATORS: Raymond Bannister shellfish aquaculture industry. including around shellfish aquaculture (Institute of Marine Research, Norway) movements in BC. CONTACT: [email protected] DATE: APR. 2015–MAR. 2017

DATE: APR. 2016–MAR. 2019 WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ FUNDED BY: DFO–Program for Aquaculture parr-prra/projects-projets/2014-M-06-eng.html Regulatory Research (DFO–PARR) FUNDED BY: DFO–Program for Aquaculture Regulatory Research (DFO–PARR) PROJECT LEAD: Janelle Curtis (DFO)

PROJECT LEAD: Cathryn Abbott (DFO) PROJECT TEAM: Nicholas Duprey, Chris Pearce, Dan Curtis (DFO) PROJECT TEAM: Kristen Marie Westfall, Tom Therriault, Kristi Miller-Saunders, COLLABORATORS: Marie-Josée Fortin, Kara Aschenbrenner, Geoff Lowe, Amanda Xuereb (U of T); Louis Bernatchez (U Laval) Scott Gilmore (DFO); Melania Cristescu (McGill U); CONTACT: [email protected] Guang Zhang (McGill U; DFO) WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ CONTACT: [email protected] parr-prra/projects-projets/2015-P-03-eng.html WEBSITE: www.dfo-mpo.gc.ca/aquaculture/rp-pr/ parr-prra/projects-projets/2016-P-03-eng.html 122 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

ORGANIZATIONS

Atlantic Canada Opportunities Agency (ACOA) Fonds de recherche du Québec – Nature et National Sciences and Engineering Research Technologies (FRQNT) Council (NSERC) »» Atlantic Innovation Fund (AIF) Genome Canada (GC) »» Discovery Grants Program British Columbia Salmon Farmers Association (BCSFA) – Marine Environmental Research »» Genome Atlantic »» Industrial Research Chairs (IRC) Grants Program (MERP) »» Genome British Columbia »» Industrial Research Chairs for Colleges Fisheries and Oceans Canada (DFO) (IRCC) Grants »» Genome Québec »» Aquaculture Collaborative Research and »» Postdoctoral Fellowship (PDF) Program »» Ontario Genomics Development Program (ACRDP) »» Strategic Partnership Grants for Networks Hakai Institute »» Centre for Aquatic Animal Health Research (SPG-N) and Diagnostics (CAAHRD) Ministere de l’Agriculture, des Pecheries Pacific Salmon Commission (PSC) et de l’Alimentation du Québec (MAPAQ) »» Genomics Research and Development Pacific Salmon Foundation (PSF) Initiative (GRDI) National Research Council (NRC) Canada Ressources Aquatiques Québec (RAQ) »» National Contaminants Advisory »» Industrial Research Assistance Program (IRAP) Group (NCAG) Sea Pact »» Algal Carbon Conversion (ACC) Program »» Partnership Fund Social Sciences and Humanities Research Council of Canada (SSHRC) »» Program for Aquaculture Regulatory Research (PARR) CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 123

Atlantic Canada Opportunities Agency (ACOA) Atlantic Innovation Fund (AIF) part of the Government of Canada’s he Atlantic Canada Opportunities • Policy, advocacy and co-ordination – commitment to increasing business Agency works to create opportunities being a champion for Atlantic Canada A productivity, growth and competitiveness, for economic growth in Atlantic by representing the region’s interests T the AIF is helping Atlantic Canada compete Canada by helping businesses become at the national level in areas like policy at home and abroad by supporting the more competitive, innovative and productive, development, research and analysis and development of innovative products and by working with diverse communities to in work with other departments to ensure services that lead to commercial success. develop and diversify local economies, and coordination of policies and programs. The AIF helps Atlantic Canadians develop by championing the strengths of Atlantic We will also continue to play an essential and bring to market new products and services Canada. Together, with Atlantic Canadians, role in the co-ordination and development that lead to market success, help grow we are building a stronger economy. of the Atlantic Gateway and lead trade strategic sectors, or lead to the creation of With our many partners in economic development initiatives that increase the research and commercialization partnerships. development, ACOA works to strengthen exposure of Atlantic Canadian firms in (2017, www.acoa-apeca.gc.ca) the Atlantic economy through: foreign markets, thereby generating • Enterprise development – helping new economic opportunities. improve the business climate and lending a hand for individual business start-ups, modernizations and expansions; • Community development – working with communities to nurture economic growth, improve local infrastructure and develop opportunities in the local economy; and

Aerial view of salmon net-pens in Doctor’s Cove, New Brunswick. (Photo: Kobb Media) 124 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

British Columbia Salmon Farmers Association (BCSFA) – Marine Environmental Research Program (MERP)

he BC Salmon Farmers Association to the program between 2015 and 2020 to (BCSFA) is a forum for communication be utilized in partnership with government, Tand cooperation within the salmon academic and independent research farming sector, and the focal point for liaison institutions. The program was created with between the industry and government. the aim to gain a better understanding of the BCSFA also provides information to the marine environment and BC’s wild marine public and stakeholders about salmon species, particularly wild salmon stocks. The farming, and coordinates industry-wide BCSFA has developed a formalized Call for activities, research, and community events. Proposals process, overseen by an external Our members include both farmed salmon body – producers and many of the companies the BCSFA Science Advisory Council. who provide services and supplies to them. Annually, the BCSFA hosts the The BCSFA was established in 1984 and is Collaborations on the Coast workshop based in Campbell River, British Columbia. in Nanaimo, BC which brings together The BCSFA holds research and representatives from the industry, and farm-raised fish health, as well as development as one of the top priorities scientific community, government and the changing coastal environment. in maintaining a sustainable industry. In conservation groups to discuss and For further information, please visit December 2014, the BCSFA developed review current research (including MERP www.bcsalmonfarmers.ca/ the Marine Environmental Research Program funded research) to further improve the research-innovation (MERP) and committed $1.5 million in funding industry’s understanding of both wild

Fisheries and Oceans Canada (DFO)

isheries and Oceans Canada (DFO) aquaculture also provides a solid scientific ecosystems. We also invest in aquatic delivers programs and services foundation for the conservation and animal health research to understand how Fthat support the sustainable use protection of fish and fish habitat in marine or best to prevent, mitigate, and treat disease. and development of Canada’s waterways freshwater ecosystems. On-going research As species diversification is often seen and aquatic resources. On behalf of the contributes to scientific certainty with respect as a means of increasing Canada’s global Government of Canada, DFO is responsible to aquaculture operations and how they market share, DFO scientists also play a for developing and implementing policies interact with the aquatic environment. key role in innovative research. and programs in support of Canada’s In recent years, DFO’s research effort (2017, www.dfo-mpo.gc.ca) scientific, ecological, social, and economic has been directed at understanding The following DFO programs are currently interests in oceans and fresh waters. It is environmental effects of aquaculture supporting Canadian aquaculture research: DFO’s mission to deliver to Canadians the on freshwater and marine habitat and following outcomes: • Economically Prosperous Maritime Sectors and Fisheries; • Sustainable Aquatic Ecosystems; and • Safe and Secure Waters. In working toward these outcomes, the Department is guided by the principles of sound scientific knowledge and effective management. DFO is the lead federal department for the sustainable management of fisheries and aquaculture. Responsibility for aquaculture management and development (governance) is shared between the federal, provincial, and territorial governments. We work together, with many other partners, to ensure that the legislative and regulatory framework for aquaculture is responsive to the public’s and industry’s needs. DFO’s aquaculture research aims to address regulatory knowledge gaps, and collaborative research and development with the aquaculture industry. Collaborative research facilitates the transfer of the latest technologies to the aquaculture industry. Research on the environmental effects of A CTD (conductivity, temperature, and depth) rosette taking water samples in Baynes Sound, British Columbia. Photo: Dan McPhee (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 125

Aquaculture Collaborative Research Centre for Aquatic Animal Genomics Research and and Development Program (ACRDP) Health Research and Diagnostics Development Initiative (GRDI) he Aquaculture Collaborative Research (CAAHRD) FO uses genomics for the aquaculture Tand Development Program (ACRDP) is he Centre for Aquatic Animal Health Dindustry and in the management of the a DFO initiative that promotes collaborative TResearch and Diagnostics (CAAHRD) wild fishery. These tools lead to better disease research and development activities oversees DFO’s research in support of the identification and control, development of between the aquaculture industry and the National Aquatic Animal Health Program techniques to accurately determine the department. The Program teams industry (NAAHP). The centre directs and coordinates population structure of wild marine fish, and representatives with DFO researchers. The targeted research, the development of to identify invasive or endangered species projects are primarily conducted within DFO quality diagnostics and the provision of as well as minimize illegal or unregulated research facilities but field work may also sound scientific advice in support of the harvesting. As an enabling technology, take place at industry or other partner Government of Canada’s efforts to protect genomics provides powerful tools and precise facilities. Potential projects are proposed our aquatic resources from the introduction information to support operational mandates by aquaculture producers and funded or spread of serious infectious diseases. and upon which policy and regulatory jointly through the ACRDP as well as the The Canadian Food Inspection Agency decisions can be based. participating aquaculture producer partners. (CFIA) has listed 42 aquatic animal diseases The GRDI was established for the purpose The key goals of the program are to: of concern — for which Canada has potential of building and maintaining capacity inside Improve the competitiveness and sustainability host species — that could severely impact government departments to do genomics of the Canadian aquaculture industry; wild and cultured finfish, shellfish, and research. Through targeted investments the Increase collaborative research between crustaceans. Some of these aquatic diseases Initiative has enabled the establishment of the department and industry; Facilitate occur throughout Canada, others are critical mass in genomics research that the process of technology transfer and endemic to specific regions and watersheds, supports innovation in key Canadian sectors, knowledge mobilization; and Increase while others are exotic (foreign) to Canada. and ensures that federal departments can scientific capacity of the Canadian CAAHRD’s three main areas of research mobilize their support for the overall, national aquaculture industry for essential are: 1) development and validation of genomics effort (e.g., projects funded by aquaculture research and development. diagnostic tests (e.g., validation as per Genome Canada, Canadian Institutes of The program has two broad Research and OIE guidelines, prioritization of regulated Health Research, etc.). Programs funded under Development Objectives. The first is Optimal diseases, development of molecular tests, the GRDI are also used to augment human Fish Health. The sustainability of the marine and others); 2) improvement of laboratory resources and help create partnerships with and freshwater aquaculture industry in processes (e.g., mitigation measures for false other government departments, universities, Canada is dependent on the health and positives, comparability studies, optimisation, and industry (where applicable) through the proper health management of the farmed etc.); and 3) knowledge generation (e.g., host sharing of technology platforms and by aquatic animals (fish, shellfish, and seaweed). susceptibility, host-pathogen interactions, collaborating in research areas that cut Funded research is intended to assist etc.). This research enables DFO’s National across traditional departmental sectors. the aquaculture sector in improving Aquatic Animal Health Laboratory System For information visit www.dfo-mpo.gc.ca/ fish health management practices and (NAAHLS) to meet the Department’s science/biotech-genom/index-eng.htm better understand pathogen and disease obligations as a partner in the NAAHP. interactions. The second objective is CAAHRD research is conducted by Environmental Performance. This objective scientists at the four NAAHLS facilities: is aimed at supporting research that the Gulf Biosecurity Unit – Aquatic Animal will enhance the overall environmental Health Lab (AAHL) in Charlottetown PEI, sustainability of aquaculture operations the Gulf Fisheries Centre – AAHL (Moncton, in Canada with the goal of enhancing New Brunswick), the Freshwater Institute – environmental responsibility while AAHL (Winnipeg, Manitoba), and the Pacific ensuring economic viability and optimal Biological Station – AAHL (Nanaimo, product quality. British Columbia). Since the program’s inception in 2001, For more information please visit approximately 460 projects have been www.dfo-mpo.gc.ca/science/coe-cde/ approved and funded. Over the last five caahrd-cesaard/index-eng.html years, DFO and collaborators have invested approximately $10 M into research collaborations for the ACRDP. For more information, please go to: www.dfo-mpo.gc.ca/aquaculture/acrdp- pcrda/index-eng.htm

A Fisheries and Oceans Canada (DFO) diver entering the water to collect samples in the Magdalen Islands. Photo: Dan McPhee (DFO) 126 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

National Contaminants Advisory Program for Aquaculture Regulatory Research (PARR) Group (NCAG) he Program for Aquaculture Regulatory between farmed and wild fish s a science-based federal government T Research (PARR) funds research projects populations in order to better Adepartment, DFO requires scientific within the Department to advance our understand the risks and inform evidence to inform the management understanding of environmental and policies and regulatory decisions, of Canada’s fisheries, and to advance biological interactions between aquaculture improving the overall sustainability sustainable aquatic ecosystems while and the aquatic environment. The Program of the industry. is designed to increase our scientific fostering economic prosperity across –– Release of Organic Matter knowledge in order to inform regulatory maritime sectors and fisheries. The National Research aimed at characterizing the decision-making and policy development. Contaminants Advisory Group (NCAG) impact of released organic matter from First established in 2008, this program facilitates the provision of scientific aquaculture (e.g., unconsumed feed, forms one of three pillars under the information and advice to DFO on priority fecal matter), developing and validating Sustainable Aquaculture Program at issues specific to the biological effects of methods and performance indicators DFO. The PARR’ s research priorities are contaminants on aquatic ecosystems. The to predict and measure these impacts driven by knowledge gaps and research main functions of the group are to fund in different marine and freshwater recommendations identified in DFO’ s external research projects that are aligned environments. with NCAG’s priorities, to synthesize results, Aquaculture Pathways of Effects, which and to develop science advice in support describes the linkages between aquaculture –– Other Habitat Impacts of DFO decision-making. Current priority related activities and their impacts in the Research examining the relationships research themes are: 1) oil and gas; 2) aquatic environment, and by specific between aquaculture and marine pesticides; 3) aquaculture therapeutants; regulatory and policy questions from habitats to better inform both and 4) contaminants and issues of emerging federal and provincial aquaculture management and regulatory concern. The NCAG has funded a variety regulators and policy makers. decisions, particularly related to of multiyear research projects at Canadian There are five broad themes or topics siting of aquaculture facilities. universities and not-for-profit research that the scientific research projects that are –– Cumulative Effects and institutions. funded through PARR address: Ecosystem Management –– Fish Pest and Pathogen Treatment Research to characterize and and Management predict the cumulative impacts from Partnership Fund Research that furthers our aquaculture activities, including understanding of diseases and s part of the Government of Canada’s developing models to evaluate and infestations, the mechanism of new investments in science, DFO predict the amount of aquaculture A on-farm infection and spread, has established a Partnership Fund that activities that the aquatic ecosystem and the effect on the environment provides $5 million per year in support of can sustainably accommodate, and and other fish species from collaborative research and increasing identify indicators that can be used to different treatment options. collective understanding of our oceans monitor whether an ecosystem is at and freshwater. –– Interactions with Wild Populations or near this carrying capacity. This is managed by the Department’s Research related to characterizing the www.dfo-mpo.gc.ca/aquaculture/parr-prra/ Office of Partnership and Collaboration. ecological and genetic interactions index-eng.html It will support new partnerships and collaborations within the ocean and freshwater sciences community (including Fonds de recherche du Québec – Nature et Technologies (FRQNT) universities, aquatic research networks, environmental organizations, Indigenous he Fonds de recherche du Québec groups and other stakeholders, both in – Nature et technologies (FRQNT) is Canada and abroad). These partnerships a non-profit agency, administered by will contribute to the best available science T a board of directors whose members are that will support decision-making about appointed by the Cabinet. Canada’s oceans, lakes, and rivers. Since July 1, 2011, the FRQNT has worked Fisheries and Oceans Canada is committed with the Fonds de recherche du Québec to fostering and leveraging these important – Santé (FRQS) and the Fonds de recherche postgraduate students and to persons who partnerships and the fund will support a du Québec – Société et culture (FRQSC) engage in postdoctoral research, through number of scientific research projects and under the banner Fonds de recherche du professional development scholarships to activities across the country, including those Québec. Their mandates are as follows: persons who wish to re-enter the research related to: science data collection and • To promote and provide financial support community, and through grants that allow integration; ocean and freshwater monitoring; for research in the fields of natural the teaching duties of college level and science in support of ocean literacy, sciences, mathematical sciences and professors engaging in research activities and the management, conservation, engineering. to be reduced. protection, and promotion of ocean • To create any necessary partnerships, in and freshwater resources. • To promote and provide financial support particular with universities, colleges, and http://www.dfo-mpo.gc.ca/science/ for the dissemination of scientific industry, and the government departments collaboration/partnership-fund-eng.html knowledge in fields of research relating to natural sciences, mathematical sciences and public and private bodies concerned. and engineering. (2017, adapted from www.frqnt.gouv.qc.ca/en/ • To promote and provide financial support accueil) for the training of researchers through achievement scholarships for graduate and CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 127

Genome Canada (GC)

enome Canada is a not-for-profit the benefit of all Canadians. We make organization, funded by the strategic investments in large-scale science, GGovernment of Canada. We act leading-edge technology and translation as a catalyst for developing and applying programs and initiatives to ensure genomics genomics and genomic-based technologies knowledge is applied to maximum benefit to create economic and social benefits for for Canada. Canadians. We: connect ideas and people Our programs are designed based across public and private sectors to find on engagement with a broad range of new uses for genomics; invest in large-scale stakeholders, including sector-specific users science and technology to fuel innovation; of genomics, especially in the private sector. and translate discoveries into solutions They are implemented through a rigorous on partnership both at the program and across key sectors of national importance, international peer-review system, which research project levels. In this way, Genome including health, agriculture and agri-food, ensures only the highest-quality research Canada catalyzes a collaborative, thriving forestry, fisheries and aquaculture, the proposals with the greatest potential for genomics enterprise across the country and environment, energy, and mining. impact are funded. internationally. Genome Canada aims to harness the Partnerships are an integral component of (2017, adapted from www.genomecanada.ca) transformative power of genomics for our model. We do nothing alone. We insist

Genome Atlantic enome Atlantic is a not-for-profit identify, develop or manage results-focused Gcorporation with a mission to help genomics R&D projects. Atlantic Canada reap the economic and We have extensive connections to social benefits of genomics and associated Genome Canada, the Genome Centres technologies. Since our inception in 2000, (Genome BC, Genome Alberta, Genome we have worked with a range of partners to Prairie, Ontario Genomics, and Genome enable over $90 million in new genomics Québec ) and the network of universities, R&D in the region. research institutions, companies, We aim to develop genomics R&D projects government departments, and other in seven key sectors – agriculture, fisheries agencies that are involved in genomics and aquaculture, energy, the environment, and related research. forestry, mining, and human health. We We receive financial support from the strategic partners to increase the impact work with a range of public Government of Canada through Genome of genomics innovation. and private partners to help companies Canada, the National Research Council We help companies, government and organisations use genomics to solve – Industrial Research Assistance Program, departments and researchers pursue problems in these sectors. Our services and the Atlantic Canada Opportunities genomics-based solutions to real-world are diverse and highly flexible, but are Agency – Business Development Program. problems. generally focused on helping teams We are always interested in working with (2017, www.genomeatlantic.ca)

Genome British Columbia enome British Columbia is a non-profit high quality personnel; and deliver Gresearch organization that invests socio-economic benefits to BC, Canada, in and manages large-scale genomics and other parts of the world. and proteomics research projects and Our major investors are the Province of enabling technologies focused on British Columbia and the Government of areas of strategic importance such as human Canada through Genome Canada and health, forestry, fisheries and aquaculture, Western Economic Diversification Canada. energy and mining, and agri-food. This funding is complemented by other cluster; strategic international collaborations; Our research projects have attracted private and public investments. and proactive leadership in exploring over 300 major international co-funders societal impacts of genome sciences. Our Mission: and partner organizations, including many (2017, www.genomebc.ca) Genome BC leads academia, government, multinational corporations, pharmaceutical and industry to develop a world-class and biotechnology companies, worldwide genome sciences region that will deliver charitable foundations, and top-tier research social and economic benefits to British institutions. Such investments have helped Columbia, Canada, and beyond, through: us build internationally recognized enabling excellent projects and technology platforms; technologies; recruit, train, and retain innovative applications for the life sciences 128 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Genome Québec Ontario Genomics Hakai Institute enome Québec is an economic ntario Genomics (formerly the Ontario he Hakai Institute is a scientific development organization that Genomics Institute) is a not-for-profit G O research institution that conducts contributes to strengthening the intermediary organization funded by the long-term research at remote competitiveness of the genomics Ontario government and the federal T locations on the coastal margin of innovation system in order to maximize research funding agency Genome Canada. British Columbia, Canada. its socioeconomic impact in Québec. Established in 2000, Ontario Genomics is The name Hakai is inspired by the Hakai It does so by funding major genomic the only entity focused solely on stimulating, Lúxvbálís Conservancy, the largest marine research initiatives and putting in place enabling, and nurturing genomics innovation protected area on the BC coast, located the tools necessary for scientific and in the province of Ontario. We act as a about 400 kilometers north of Vancouver. strategic development in the field. catalyst for developing and applying The Hakai Institute includes the following Genome Québec is helping to accelerate genomic technologies across seven key elements: the original field station on Calvert the discovery of new applications for sectors – agriculture, bioproducts, energy, Island on the BC Central Coast; a second genomics in strategic areas such as health, forestry, health, mining, and water – to grow field station on Quadra Island at the north forestry, the environment, and agrifood. the province’s knowledge-based economy end of the Strait of Georgia; the Institute’s The funds invested by Genome Québec and create jobs and social benefits for own scientific research staff and equipment; are provided by the ministère de l'Économie, all Ontarians. and a large network of affiliated faculty and de la Science et de l'Innovation du Québec Our Vision other collaborators at universities, (MESI), the Government of Canada through • More funds for genomics research government agencies, and First Nations. Genome Canada, and private partners. in Ontario; Our research is inspired by Long Term (2017, www.genomequebec.com) • Genomics contributing to the Ecological Research (LTER) network, establishment of effective and cost- originally launched by the US National conscious public services, such as Science Foundation in 1980. We pool our healthcare; information with other coastal research sites—most notably in BC, Alaska, • Established genomics companies Washington, and Oregon—to gain an investing and operating in Ontario; and understanding of the dynamics of the • An innovative milieu in which genomics broader landscape. start-ups develop, mature, and accelerate Given the unique nature of our study area along the business growth pipeline, on the coastal margins of British Columbia, creating jobs and wealth in Ontario our scope includes the history of ecological change since the region became ice-free (2017, www.ontariogenomics.ca) roughly 15,000 years ago and the influence of humans on the landscape. The coastal margins of British Columbia, Canada are among the most productive areas in the world. Water flowing from the glaciers, snow packs, forests, and bogs of the temperate rainforest pours massive quantities of inorganic and organic nutrients into the surrounding estuaries and inlets. This nutrient-rich cocktail drives primary production, which in turn fuels complex marine food webs. Coastal productivity and biodiversity have also served as a magnet for settlement since humans first came to the coast. For millennia, humans have depended on the coast for travel, work, and sustenance – all the elements of life – which remains true today. (2017, www.hakai.org)

Dan McPhee setting the firing mechanism on a CTD rosette to collect samples in Baynes Sound, British Columbia. Photo: Terri Sutherland (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 129

Ministere de l’Agriculture, des National Research Council (NRC) Canada Pecheries et de l’Alimentation he National Research Council (NRC) is du Québec (MAPAQ) the Government of Canada's premier organization for research and Innovamer Program T development. y supporting research and innovation NRC partners with Canadian industry to in the commercial fisheries and take research impacts from the lab to the Baquaculture sector, the program marketplace, where people can experience aims to: the benefits. This market-driven focus delivers • Increase the industry's ability to use the innovation faster, enhances people's lives, and knowledge at its disposal to design or addresses some of the world's most pressing links to our corporate publications and significantly improve technologies, problems. We are responsive, creative, and financial statements. products, processes or services; uniquely placed to partner with Canadian Our vision industry, to invest in strategic R&D • Improve business competitiveness, meet To be the most effective research and programming that will address critical issues requirements, take advantage of business technology organization in the world, for our future. opportunities or solve a business-specific stimulating sustainable domestic prosperity. problem; Each year our scientists, engineers, and business experts work closely with thousands Our mission • Promote the acquisition of new scientific of Canadian firms, helping them bring new Working with clients and partners, we and technological knowledge and design technologies to market. We have the people, provide innovation support, strategic research, generic products and processes to make expertise, services, licensing opportunities, and scientific and technical services to them accessible to all companies and national facilities, and global networks to develop and deploy solutions to meet partners in the sector; support Canadian businesses. Canada's current and future industrial and • Stimulate networking between innovation In this section, you will find more information societal needs. agents and private sector actors to foster about how NRC is organized and governed, (2017, www.nrc-cnrc.gc.ca) knowledge acquisition and dissemination; where we are located across Canada, and The following NRC programs are currently and supporting Canadian aquaculture research: • Improve the innovation capacity of the sector and support the reinforcement Algal Carbon Conversion (ACC) Program of the complementary actions of the he Government of Canada is committed to identifying the most appropriate algae strains Ministry and its partners in this field. Taddressing the issue of CO2 emissions for industrial deployment, increasing the The Innovamer program has four while simultaneously generating economically productivity and reducing energy costs of components: and environmentally-sustainable opportunities photobioreactors, identifying ways to reduce Strand 1 – Business innovation projects – for Canadian companies. The Algal Carbon energy costs for processing algal biomass, Eligible customers: business. Conversion (ACC) flagship program positions and assisting in the development of high- Strand 2 – Targeted calls for sectoral Canada as a world leader in converting carbon value, sustainable products from algal innovation projects – Eligible customers: dioxide emissions into algal biomass, biomass. The full impacts of this initiative are research organizations; and business renewable biofuels, and other value-added projected to lead the deployment of enough associations using the necessary scientific products through integrated algal algal biorefinery facilities to divert up to 20% of experts; and biorefineries. Canadian carbon dioxide emissions from large Strand 3 – Networking, Dissemination The ACC program addresses a number final emitters by 2060. and Monitoring – Eligible clients: research of factors which influence the commercial (2017, www.nrc-cnrc.gc.ca/eng/solutions/ Institutes; business associations; and potential of ACC technology, including collaborative/algal_index.html) networking organizations Strand 4 – Partnership Initiatives – Eligible customers: research institutes; and Industrial Research Assistance Program (IRAP) networking organizations he National Research Council-Industrial and understand technology issues and (2017, adapted from www.mapaq.gouv.qc.ca/fr/ TResearch Assistance Program (NRC-IRAP) opportunities and provides linkages to Peche/md/Programmes/Pages/innovamer. is Canada's premier innovation assistance the best business and aspx) program for small and medium-sized R&D expertise in Canada. enterprises (SMEs). It is a vital component of Our strategic objectives the NRC, a cornerstone in Canada's innovation • Provide support to small and medium-sized system, regarded world-wide as one of the enterprises in Canada in the development best programs of its kind. and commercialization of technologies. For nearly 70 years, the NRC-IRAP has been stimulating wealth creation for Canada • Collaborate in initiatives within regional through technological innovation. This is and national organizations that support the largely accomplished by providing technology development and commercialization of assistance to small and medium-sized technologies by small and medium-sized enterprises (SMEs), at all stages of the enterprises. innovation process, to build their innovation (2017, www.nrc-cnrc.gc.ca/eng/irap/index.html) capacity and successfully take their ideas to market. NRC-IRAP helps SMEs identify 130 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

National Sciences and Engineering Research Council (NSERC)

SERC aims to make Canada a country to increase Canada’s scientific and of discoverers and innovators for technological capabilities for the benefit Nthe benefit of all Canadians. The of all Canadians. NSERC invests in people agency supports university students in their by supporting postsecondary students and advanced studies, promotes and supports postdoctoral fellows in their advanced discovery research, and fosters innovation studies. We promote discovery by funding by encouraging Canadian companies to research conducted by postsecondary participate and invest in postsecondary professors and foster innovation by between postsecondary institutions and research projects. NSERC researchers encouraging Canadian companies to industry, and the training of Canada’s next are on the vanguard of science, building participate and invest in postsecondary generation of scientists and engineers. on Canada’s long tradition of scientific research and training. (2017, www.nserc-crsng.gc.ca) excellence. Over the last 10 years, NSERC has The following NSERC programs are NSERC’s role is to make investments invested more than $7 billion in basic currently supporting Canadian aquaculture in people, discovery, and innovation research, projects involving partnerships research:

Discovery Grants Program he Discovery Grants Program assists in: are considered ‘grants in aid’ of research as in their applications, but may pursue new Tpromoting and maintaining a diversified they provide long term operating funds to research interests, provided they are within base of high-quality research capability in support the costs of a research program. As NSERC’s mandate. This provides researchers the natural sciences and engineering in a grant in aid of research, Discovery Grants with the flexibility to pursue promising Canadian universities; fostering research are not meant to support the full costs of research avenues as they emerge and the excellence; and providing a stimulating a research program and they can facilitate opportunity to address higher-risk (higher environment for research training. access to funding from other programs. reward) topics. Researchers can use their The Discovery Grants Program supports NSERC recognizes that, while being of a grants to participate in collaborative efforts. ongoing programs of research (with grant in aid nature, Discovery Grants must (2017, www.nserc-crsng.gc.ca/ long-term goals) rather than a single be sufficient to support a program of quality Professors-Professeurs/Grants-Subs/ short-term project or collection of projects. research that can have a meaningful impact DGIGP-PSIGP_eng.asp) These grants recognize the creativity on the field of study. and innovation that are at the heart of Recipients of Discovery Grants are not all research advances. Discovery Grants restricted to the specific activities described

Industrial Research Chairs (IRC) Grants ndustrial Research Chairs (IRC) are NSERC offers three types of IRCs: their activities on conducting research I intended to: assist universities in • Senior Industrial Research Chairs for and training highly qualified personnel, building on existing strengths to achieve distinguished senior researchers (five-year while carrying a reduced administrative the critical mass required for a major appointment, renewable); and teaching load. research endeavour in natural sciences and IRCs are funded jointly by NSERC and • Associate Industrial Research Chairs engineering of interest to industry; and/or industry. Provincial or federal government for early-stage researchers demonstrating assist in the development of research efforts departments and agencies may also exceptional promise (five-year in fields that have not yet been developed in co-sponsor/support an IRC, but only the appointment, renewable once); and Canadian universities but for which there is industrial contributions are taken into an important industrial need; and provide • Executive Industrial Research Chairs for account when NSERC determines its an enhanced training environment for outstanding R&D professionals (five-year funding level. graduate students and, where appropriate, appointment, non-renewable). (2017, adapted from www.nserc-crsng.gc.ca/ postdoctoral fellows by exposing them to An IRC grant provides funding for the professors-professeurs/cfs-pcp/irc-pci_eng. research challenges unique to industry and salary of the Chairholder, infrastructure, asp) the opportunity for significant ongoing research tools, instruments, and general interactions with the industrial partner(s). expenses related to the Chair’s program of research. Chairholders are expected to focus CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 131

Industrial Research Chairs for Postdoctoral Fellowship (PDF) Program Colleges (IRCC) Grants he Postdoctoral Fellowships (PDF) qualified Canadians with leading edge ndustrial Research Chairs for Colleges TProgram provides support to a core of scientific and research skills for Canadian I(IRCC) Grants support Chair programs the most promising researchers at a pivotal industry, government and universities. across the spectrum of natural and social time in their careers. The fellowships are (2017, www.nserc-crsng.gc.ca/Students- sciences, engineering, humanities, and/or also intended to secure a supply of highly Etudiants/PD-NP/PDF-BP_eng.asp) health sciences fields. Grants are given by NSERC, with the exception of funded proposals exclusively in the social sciences, Strategic Partnership Grants for Networks (SPG-N) humanities, and/or health sciences, which trategic Partnership Grants for Canada’s industrial base, generate will be given by SSHRC or CIHR, as SNetworks (SPG-N) fund large-scale, wealth, create employment, and/or appropriate. multidisciplinary research projects in influence Canadian public policy; IRCC Grants support applied research targeted research areas that require • Increase the number of highly leaders and their development of business- a network approach and that involve qualified personnel in the specified focused applied research programs at collaboration between academic target areas; and colleges. It is expected that the establishment researchers and Canadian-based of applied research leaders will enable the organizations. The applicant should • Enable the transfer of knowledge/ realization of the following objectives: be an established researcher with a solid technology and expertise to Canadian- • Increased delivery of innovative applied track record in collaborative research, based companies that are well-positioned research solutions to local companies at student training, and grant management, and to apply the results for economic gain or the community and/or regional level; who demonstrates the leadership and other to government organizations to strengthen public policy. • Enhanced teaching and curricula; skills necessary for managing a complex, interdisciplinary, multi-institutional project. (2017, adapted from www.nserc-crsng.gc.ca/ • Increased participation of faculty and other It is expected that these grants will: Professors-Professeurs/RPP-PP/SPG-SPS_ college staff in applied research activities; • Generate new knowledge/technology with eng.asp) • Increased opportunities for students to the strong potential to strengthen gain industrial problem-solving experience; and Pacific Salmon Commission (PSC) • Increased knowledge and technology transfer between colleges and companies, he Pacific Salmon Commission (PSC) It has responsibility for all salmon with the objective of increasing the is an international decision-making originating in the waters of one country productivity and competitiveness of organization, composed of four which are subject to interception by the local companies, particularly small and T Commissioners (and four alternates) from other, affect management of the other medium-sized enterprises (SMEs). the United States and Canada. This body country’s salmon, or affect biologically IRCC Grants assist colleges to develop handles ongoing administration of the the stocks of the other country. In addition, new or significantly enhance existing applied Pacific Salmon Treaty through advice from the Pacific Salmon Commission is charged research efforts and capacity in areas that four regional Panels of fisheries experts. with taking into account the conservation meet local or regional socio-economic Scientific advice on salmon populations of steelhead trout while fulfilling its needs. Chairholders are expected to and appropriate fishery controls comes other functions. conduct a program of applied research from several joint technical committees (2017, www.psc.org) with partner companies. Candidates should of salmon scientists from each country. therefore have a strong track record in As a treaty organization, the PSC conducting and managing industry-focused facilitates implementation of the Treaty applied research projects. The applied through research and regular meetings research projects will provide an enhanced between national, provincial/state, First training environment for students and Nation, and U.S. tribal delegates to manage college personnel by giving them the commercial, sport, and subsistence fisheries opportunity to address applied research in both countries. challenges with the private sector and to participate in significant ongoing interactions with business partners. (2017, adapted from www.nserc-crsng.gc.ca/ Professors-Professeurs/RPP-PP/IRCC- CRIC_eng.asp) 132 ORGANIZATIONS CANADIAN AQUACULTURE R&D REVIEW 2017

Pacific Salmon Foundation (PSF) Ressources Aquatiques Sea Pact Québec (RAQ) he Pacific Salmon Foundation, founded in 1987, is a federally essources Aquatiques Québec is Tincorporated non-profit charitable an interinstitutional grouping for the organization dedicated to the conservation sustainable development of the and restoration of wild Pacific Salmon and R aquaculture and fisheries industry in their natural habitats in British Columbia and Québec. It brings together about forty the Yukon. Operating independently from Québec researchers with a large network government, The Foundation facilitates of collaborators at the provincial, national dialogue and undertakes positive initiatives and international levels. in support of Pacific salmon amongst all The regular members of RAQ are from levels of government including First Nations; nine universities (Université du Québec à as well as industry, communities, individual Rimouski, Université Laval, Université de volunteers, and all fishing interests. Montréal, Université de Sherbrooke, Institut ea Pact will improve the sustainability The Pacific Salmon Foundation exists National de la Recherche Scientifique The of global seafood by using the to support ‘salmon communities’ in their École Polytechnique de Montréal, the Scollective power of like-minded North efforts, promote awareness of this keystone Université du Québec à Chicoutimi and American seafood companies to improve species, and guide the sustainable future the Université du Québec à Montréal), the fishing and fish farming systems we of wild Pacific Salmon and their habitat. a college-level institution (Cégep de la procure from. Sea Pact was created by the The Foundation partnered with British Gaspésie et des Îles), the Ministère des six founding members: Albion Fisheries, Columbia MP’s to secure $1 million more in Forêts, Faune et Parks, Fisheries and Fortune Fish & Gourmet, Ipswich Shellfish funds for community projects by increasing Oceans Canada, Agriculture and Agri-Food Group, Santa Monica Seafood, Seacore its share of Salmon Stamp user fees and Canada and the Canadian Museum of Seafood and Seattle Fish Co. Sea Pact worked with Fisheries and Oceans Canada Nature, Merinov, the Montreal Biodome now consists of nine members. on creation of the federal Recreational and the MBRC. Sea Pact is a group of leading North Fisheries Conservation Partnerships RAQ has been financially supported American Seafood Companies dedicated Program. since 2006 by the Québec Research to driving stewardship and continuous We steward the investment of our Fund – Nature and Technologies (Strategic improvement of social, economic, and available resources – both human and Grouping Program). RAQ is the only environmental responsibility throughout financial – to optimize our collective return. inter-institutional organization in Québec the global seafood supply chain. We are a vocal advocate, speaking as the whose objective is to participate actively Sea Pact strives to advance voice of the salmon community to articulate in the sustainable development of the environmentally sustainable fisheries the issues affecting our mandate. aquaculture industry and the fishing industry and aquaculture practices and provide With ongoing education, partnership and in Québec. It brings together Québec's the building blocks for a long term and collaboration, we will positively transform freshwater and coastal expertise, as sustainable seafood industry. To accomplish people’s outlook to realize the connection well as the skills on shellfish and fish, this, Sea Pact has pledged to financially wild Pacific Salmon have with everything in a single forum involving industry contribute to selected projects that are that is British Columbia. and decision-makers, biotechnology, aligned with Sea Pact’s mission. Sea Pact (2017, www.psf.ca) economic, legal, and ethical issues. wishes to place an emphasis on projects (2017, raq.uqar.ca) that are engaging in efforts relating to bycatch reduction, innovations in aquaculture, or social responsibility within the seafood supply chain. Projects impacting the top seafood species consumed on a global level are preferred. (2017, www.seapact.org) CANADIAN AQUACULTURE R&D REVIEW 2017 ORGANIZATIONS 133

Social Sciences and Humanities Research Council of Canada (SSHRC)

he Social Sciences and Humanities Research Council of Canada T(SSHRC) is the federal research funding agency that promotes and supports postsecondary-based research and research training in the humanities and social sciences. By focusing on developing Talent, generating Insights, and forging Connections across campuses and communities, SSHRC strategically supports world-leading initiatives that reflect a commitment to ensuring a better future for Canada and the world. SSHRC-supported research in the social sciences and humanities enhances our understanding of modern social, cultural, technological, environmental, economic, and wellness issues. It raises profound questions about who we are as human beings, what we need in order to thrive in complex and challenging times, and where we are headed in the new millennium. The work SSHRC supports encourages the deepest levels of inquiry. It spurs innovative researchers to learn from one another’s disciplines, delve into multiparty collaborations, and achieve common goals for the betterment of Canadian society. Research outcomes are shared with communities, businesses, and governments, who use this new knowledge to innovate and improve people’s lives. SSHRC also invests directly in Canada’s future. Through the social sciences and humanities, students receive the best possible training in critical thinking, complex decision-making, and creative exploration. By investing in scholarships, fellowships, and research training, SSHRC helps develop Canada’s best and brightest scholars and researchers into Canada’s future leaders. SSHRC-funded research builds understanding that can help change the world. As such, it has taken its place as a central component of Canadian innovation. (2017, www.sshrc-crsh.gc.ca/)

A seaside boardwalk in the Madgalen Islands, Quebec. Photo: Ingrid Burgetz (DFO) 134 GLOSSARY CANADIAN AQUACULTURE R&D REVIEW 2017 GLOSSARY AAFC Agriculture and Agri-Food Canada CIHR Canadian Institutes of GRDI Genomics Research and AAR Aquaculture Activity Regulations Health Research Development Initiative (DFO) AARS Alma Aquaculture Research Station (U CIMTAN Canadian Integrated Multi-Trophic GWAS Genome-Wide Association Studies Guelph) Aquaculture Network HC Health Canada AC Assimilative Capacity COSEWIC Committee on the Status of HMSC Huntsman Marine Science Centre Endangered Wildlife in Canada ACC Algal Carbon Conversion HPLC High Performance Liquid CRCP Canada Research Chairs Program ACFFA Atlantic Canada Fish Farmers Chromatography Association CTD Conductivity, Temperature, and Depth HQP Highly Qualified Personnel ACOA Atlantic Canada Opportunities Agency Cu Copper HSMI Heart and Skeletal Muscle Inflamation ACOA-AIF Atlantic Canada Opportunities CyHV-3 Cyprinid Herpesvirus 3 iBoF Inner Bay of Fundy Agency – Atlantic Innovation Fund CZRI Coastal Zones Research Institute ICAM Integrated Coastal Area Management ACRDP Aquaculture Collaborative Research DAAF Department of Agriculture, IFREMER French Research Institute for and Development Program (DFO) Aquaculture, and Fisheries Exploration of the Sea (New Brunswick) ADCP Acoustic Doppler Current Profiler IHN Infectious Haematopoietic Necrosis Dalhousie U Dalhousie University AGD Amoebic Gill Disease IHNV Infectious Haematopoietic AIF Atlantic Innovation Fund DEB Dynamic Energy Budget Necrosis Virus AIS Aquatic Invasive Species DELG Department of the Environment and IMTA Integrated Multi-Trophic Aquaculture Local Government (New Brunswick) Al Aluminum IPC Internal positive control DFA Department of Fisheries and APC Artificial Positive Control Aquaculture of Newfoundland IPMP Integrated Pest Management ARM Artificial Reference Material and Labrador Practices As Arsenic DFARD Department of Fisheries, Aquaculture, IRAP Industrial Research Assistance Program (NRC) AVC Atlantic Veterinary College (UPEI) and Rural Development (PEI) IRC Industrial Research Chairs (NSERC) BC British Columbia DFO Fisheries and Oceans Canada DIDSON Dual frequency IDentification SONar IRCC Industrial Research Chairs for BCSFA British Columbia Salmon Colleges (NSERC) Farmers Association DNA Deoxyribonucleic Acid ISA Infectious Salmon Anemia BCSGA British Columbia Shellfish Duke U Duke University ISAV Infectious Salmon Anemia Virus Grower’s Association EB Emamectin Benzoate BDP Business Development Program ISMER Institut des Sciences de la ECC Ecological Carrying Capacity Mer de Rimouski (UQAR) BHA Bassin du Havre Aubert ECCC Environment and Climate ISO International Organization for BKD Bacterial Kidney Disease Change Canada Standards BOD Biochemical Oxygen Demand / eDNA Environmental DNA ITC Introductions and Transfers Biochemical Oxygen Demanding Eh Redox Potential Committee Ca Calcium ELISA Enzyme-Linked Immunosorbent Assay K Potassium CAAHRD Centre for Aquatic Animal Health ENGO Environmental Non-Governmental KCS Kelly Cove Salmon Ltd. Research and Diagnostics (DFO) Organization KHVD Koi Herpes Virus Disease CAISN Canadian Aquatic Invasive EPAQ École des Pêches de l'Aquaculture LED Light Emitting Diode Species Network et du Québec LTER Long Term Ecological Research CARTI Centre for Applied Research, FAP Fonds d'Amorçage de Partenariat Technology, and Innovation (NIC) MAPAQ Quebec Department of Agriculture, Fe Iron CAT Center for Aquaculture Technologies Fisheries, and Food FFAW Fish, Food, and Allied Workers Union CATC Center for Aquaculture MAS Marker Assisted Selection Technologies Canada FIMTA Freshwater Integrated Multi-Trophic McGill U McGill University Aquaculture CCA Closed Containment Aquaculture MDEIE Ministère du Développement FL Fork Length CCGS Canadian Coast Guard Ship économique, de l'Innovation FRQNT Fonds de recherche du et de l'Exportation, Québec CCH Centre for Coastal Health Québec – Nature et technologies MÉES Ministère de l’éducation et de CCI College and Community Innovation FRQS Fonds de recherche du l’enseignement supérieur du Québec Program (NSERC) Québec – Santé [Québec Ministry of Higher Education Cd Cadmium FRQSC Fonds de recherche du and Training] CDBQ Centre de développement Québec – Société et culture MERP Marine Environmental Research Bioalimentaire du Québec FSWEP Federal Student Work Program (BCSFA) CÉGEP General and Vocational Experience Program Mg Magnesium College (Québec) FVCOM Finite Volume Coastal Ocean Model MIMTA Marine Integrated Multi-Trophic CERC Canada Excellence Research Chair Glasgow U Glasgow University Aquaculture CFIA Canadian Food Inspection Agency GPS Global Positioning System CANADIAN AQUACULTURE R&D REVIEW 2017 GLOSSARY 135

MITACS Mathematics of Information PEI Prince Edward Island U of M University of Manitoba Technology and Complex Systems PEIAA Prince Edward Island U of T University of Toronto Mn Manganese Aquaculture Alliance U Turku University of Turku MNRF Ontario Ministry of Natural Resources PEI-DFARD Prince Edward Island Department of U Washington University of Washington and Forestry Fisheries, Aquaculture, and Rural U Waterloo University of Waterloo Mount Allison U Mount Allison University Development U Windsor University of Windsor MPA Marine Protected Area PGD Proliferative Gill Disease/Disorder UBC Univeristy of British Columbia MSX Multinucleate Sphere X PGI Proliferative Gill Inflammation UBO University of Western Brittany Brest MUN Memorial University of Newfoundland ppm Parts per million UdeM University of Montréal Na Sodium ppt Parts per thousand UNB University of New Brunswick NAAHLS National Aquatic Animal Health PRV Piscine Reovirus Laboratory System (DFO) PSC Pacific Salmon Commission UNBF University of New Brunswick – Fredericton NAAHP National Aquatic Animal Health PSF Pacific Salmon Foundation Program (DFO) UNBSJ University of New Brunswick – qPCR Quantitative (Real-Time) Saint John NaPi Sodium phosphate Polymerase Chain Reaction UPEI Univeristy of Prince Edward Island NB New Brunswick QTL Quantitative Trait Loci UPEI – AVC University of Prince Edward Island – NBDAAF New Brunswick Department RAQ Ressources Aquatiques Québec Atlantic Veterinary College of Agriculture, Aquaculture, RAS Recirculating Aquaculture System and Fisheries UQAC University of Quebec – Chicoutimi RNA Ribonucleic Acid NBIF New Brunswick Innovation Foundation UQAR University of Quebec – Rimouski ROV Remotely Operated Vehicle NBRPC New Brunswick Research US-EPA United States Environmental Productivity Council RPC Research and Productivity Protection Agency Council (NB) NCAG National Contaminants Advisory USFWS United States Fish and Group (DFO) RT-qPCR Reverse Transcriptase Quantitative Wildlife Services Polymerase Chain Reaction NCLDV Nucleo-Cytoplasmic Large DNA Virus USGS United States Geological Survey SABM Société des Amis du Biodôme UV Ultraviolet NCP National Conservation Plan de Montréal UVic University of Victoria NIC North Island College SAV Salmon Alphavirus NL Newfoundland and Labrador UW University Centre of the SFU Simon Fraser University Westfjords (Iceland) NOAA US National Oceanographic and SGPV Salmon Gill Poxvirus Atmospheric Administration VHS Viral Hemorrhagic Septicemia SIMCorp Sweeney International Marine Corp. Nord U Nord University VHSV Viral Hemorrhagic Septicemia Virus SME Small and Medium-Sized Enterprises NRC National Research Council VIU Vancouver Island University sNCLDV Sturgeon Nucleo-Cytoplasmic WLU Wilfrid Laurier University NSCC Nova Scotia Community College Large DNA Virus WSIV White Sturgeon iridovirus NSDFA Nova Scotia Department of Fisheries SNP Single Nucleotide Polymorphism and Aquaculture WSSV White Spot Syndrome Virus SODIM Société de Développement de NSERC Natural Sciences and Engineering l’Industrie Maricole Inc. Zn Zinc Research Council SORDAC Société de Recherche et de NV Namao Virus Développement en Aquaculture OA Ocean Acidification Continentale Inc. OGS Ontario Graduate Scholarship SPDV Salmon Pancreas Disease Virus OIE World Organization for Animal Health SSHRC Social Sciences and Humanities OMAFRA Ontario Ministry of Agriculture, Food Research Council of Canada and Rural Affairs (now Ontario Ministry StFX St. Francis Xavier University of Agriculture and Food) STZ Shellfish Transfer Zone OPC Opportunistic Polychaete Complex SVCV Spring Veremia of Carp Virus OTN Ocean Tracking Network TFM 3-trifluoromethyl-4-nitrophenol P Phosphorus Trent U Trent University PARR Program for Aquaculture U Geneva University of Geneva Regulatory Research U Guelph University of Guelph Pb Lead U Laval University of Laval PCR Polymerase Chain Reaction U Maine University of Maine PDF Postdoctoral Fellowship U Moncton University of Moncton 136 INDEX OF PROJECT LEADS CANADIAN AQUACULTURE R&D REVIEW 2017 INDEX OF PROJECT LEADS

Abbott, Cathryn 47, 48, 54, 121 Ferguson, Moira 8 Miller-Saunders, Kristi 38, 50 Audet, Céline 120 Filgueira, Ramón 109 Moccia, Richard 6, 9, 10(2), 11 Balfry, Shannon 27 Flaherty, Mark 89 Murray, Harry 32, 92, 94 Barker, Duane 5, 21, 24, 30 Fontaine, Pierre-Olivier 68 Nadeau, Madeleine 113 Benfey, Tillmann 59, 112 Forster, Ian 22, 35 Niles, Monique 106 Bernatchez, Louis 14, 120 Fournier, Marie-Hélène 112 Ouellette, Marc 96, 107 Bliar, Pierre 12 Fréchette, Marcel 94 Page, Fred 44, 55(2), 77, 117 Bocking, Stephen 20 Gagné, Nellie 39, 41, 42, 44(2), 48(2), 51 Patterson, Michele 15 Boudreau, Monica 59 Garber, Amber 14, 21, 22, 24 Pearce, Chris 83, 107, 118 Boulding, Elizabeth 18, 52 Garver, Kyle 37, 45, 46(2), 50, 52 Pee Ang, Keng 18 Bourque, Daniel 101, 103, 105 Gauthier, Stéphane 19 Pelletier, Claude 9 Bradbury, Ian 16(2), 19, 23(3) Gilmore-Solomon, Lisandre 60, 110 Podemski, Cheryl 6, 70, 71, 77 Brager, Lindsay 73 Goulet, Pierre 22 Pohle, Gerhard 71 Bureau, Dominique 114 Grant, Jonathan 85, 116 Polinski, Mark 48 Byrne, Philip 49 Greenwood, Spencer 49 Powell, Christopher 114 Chandler, Peter 117, 120 Gurney-Smith, Helen 69, 107 Ratsimandresy, Andry 42, 57, 72 Charette, Steve 35 Guyondet, Thomas 91, 101, 105 Reid, Gregor 84, 85 Chevarie, Lise 93, 113 Hamoutene, Dounia 21(2), 22, 28, 55, Revie, Crawford 28 57, 73, 77 Chopin, Thierry 80,81,86 Ribble, Carl 37 Hewison, Tim 40 Clarke, Corey 17 Robinson, Shawn 29, 31, 33, 70, 75, Hicks, Carla 91 82, 88, 115 Clouthier, Sharon 43, 45, 46, 47 Johnson, Stewart 20, 32, 46 Ronquillo, Jesse 7, 41 Comeau, Luc 62, 78, 93, 102 Jones, Simon 29, 36(2), 39, 43, 45 Runighan, Dawn 16 Cooper, Andrew 71, 82 Jørgenson, Sven Martin 15 Schmutz, Anthony 97 Costa, Maycira 87 Kennedy, Chris 65(2), 66(2) Sephton, Dawn 96 Cournoyer, Marie-Line 48 Kidd, Karen 84 Sonier, Rémi 58, 78 Courtenay, Simon 76 Knowler, Duncan 89 Speare, Dave 83 Cranford, Peter 57, 121 LaFlamme, Mark 51, 102 Stannard, Jason 18 Crawford, Curran 88 Landry, Thomas 67, 91, 106 Stephenson, mary 48, 101 Cross, Stephen 64, 67 LaPlante, Jean-François 114 St-Hilaire, Sophie 50 Curtis, Janelle 121 Leadbeater, Steven 30, 36, 38, 42 Sutherland, Terri 54, 105 Daoud, Dounia 61(2), 62, 63 LeBlanc, Angeline 105, 106 Tibbetts, Sean 110 Davidson, William 14 Le François, Nathalie 12, 111 Toupoint, Nicolas 92 Donnet, Sebastien 72 Loftus, Kevin 4(2) Tremblay, Réjean 35, 112 Dudas, Sarah 107 Lowe, Geoff 47 Trudel, Marc 32 Duston, Jim 5 Lyons, Monica 74 Vandenberg, Grant 8, 115, 117, 118, 119 Enders, Eva 56 MacDonald, Bruce 81 Evans, Wiley 69, 109 McKindsey, Chris 74, 76, 95, 98, 99 Farrell, Anthony 15 Méthé, Denise 96, 103 Fast, Mark 26 CANADIAN AQUACULTURE R&D REVIEW 2017 137

Section Title Pages–Photos (Page 3 Finfish: Freshwater) Rainbow Trout in a stream. Photo: Shutterstock (Page 13 Finfish: Salmon) Salmon net-pen on the Pacific Coast. Photo: Bill Pennell (Page 25 Sea Lice) Lepeophtheirus salmonis, Nauplii II Stage, produced in the sea lice hatchery at SABS. Photo: Emily Nelson (DFO) (Page 34 Fish Health) Immunostained ISAV infected cells. Photo: Mélanie Roy (DFO) (Page 53 Environmental Interactions) Juvenile crab obtained during benthic sampling in Desolation Sound, BC. Photo: Dan McPhee (DFO) (Page 79 CIMTAN) California Sea Cucumber, Parastichopus californicus. Photo: Dominique Bureau (DFO) (Page 90 Shellfish: Mussels) Cultured Blue Mussels. Photo: Shawn Robinson (DFO) (Page 100 Shellfish: Oysters) Eastern Oyster, Crassostrea virginica, cultivated in Cocogne Bay, NB. Photo: Tara Donaghy (DFO) (Page 104 Shellfish: Other) Close-up of a Sea Scallop, Placopecten magellanicus. Photo: Shawn Robinson (DFO) (Page 108 Miscellaneous) Researchers working from the CCGS Octopus in the Magdalen Islands, QC. Photo: Dan McPhee (DFO) (Page 122 Organizations) Aquaculture site in the Bay of Fundy, New Bruswick. Photo: Johannie Duhaime (DFO) CANADIAN AQUACULTURE R&D REVIEW 2017 SPECIAL PUBLICATION 25 AQUACULTURE ASSOCIATION OF CANADA