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The Infection Dynamics of Sea Lice on Atlantic Salmon (Salmo Salar) in Cobscook Bay

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The Infection Dynamics of Sea Lice on Atlantic Salmon (Salmo Salar) in Cobscook Bay The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library Winter 12-27-2018 The nfecI tion Dynamics of Sea Lice on Atlantic Salmon (Salmo Salar) in Cobscook Bay, Maine, USA Catherine Anne Frederick University of Maine, [email protected] Follow this and additional works at: https://digitalcommons.library.umaine.edu/etd Part of the Aquaculture and Fisheries Commons, and the Parasitology Commons Recommended Citation Frederick, Catherine Anne, "The nfeI ction Dynamics of Sea Lice on Atlantic Salmon (Salmo Salar) in Cobscook Bay, Maine, USA" (2018). Electronic Theses and Dissertations. 3018. https://digitalcommons.library.umaine.edu/etd/3018 This Open-Access Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. THE INFECTION DYNAMICS OF SEA LICE ON ATLANTIC SALMON (SALMO SALAR) IN COBSCOOK BAY, MAINE, USA. By Catherine Ann Frederick B.S. Coastal Carolina University, 2010 M.S. Kentucky State University, 2013 A DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy In Marine-Bio Resources The Graduate School The University of Maine December 2018 Advisory Committee: Ian Bricknell, Professor of Aquaculture Biology, Advisor Gayle Zydlewski, Associate Professor of Marine Biology Heather Hamlin, Associate Professor Aquaculture Damian Brady, Assistant Professor Aquaculture Mark Fast, Associate Professor Pathobiology © 2018 Catherine Frederick THE INFECTION DYNAMICS OF SEA LICE ON ATLANTIC SALMON (SALMO SALAR) IN COBSCOOK BAY, MAINE, USA. By Catherine Frederick Dissertation Advisor: Dr. Ian Bricknell An Abstract of the Dissertation Presented in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (In Marine-Bio Resources) December 2018 Sea lice (Lepeophtheirus and Caligus spp) are parasitic copepods that infect the external surfaces of fish hosts. Salmon lice (L. salmonis) outbreaks are commonly reported by operations in Canada, Norway, Scotland, Ireland, and the United States and are a primary concern in aquaculture because of their fish health and economic impacts. When farmed fish mortalities and treatments are accounted for, annual losses from sea louse infestations exceed $300,000,000 (Costello 2009). Farms experiencing sea lice infections risk on-site re-infection and transmission to wild populations and other farms that are hydrographically connected. In Maine, Atlantic salmon farms are located in the northeast, with major operations in Machiasport and Cobscook Bay. The primary aim of this study was to establish the infection dynamics of sea lice in Cobscook because it is positioned at the mouth of the Bay of Fundy, where outbreaks are increasingly common but are not well described in the available literature. Sentinel cages housed Atlantic salmon juveniles for a total of 7 days every month to monitor sea lice settlement at 4 sites within Cobscook Bay: Broad Cove, Comstock Cove, Prince Cove, and Pembroke Landing. The survey revealed a pre-season (early summer) and season (autumn) peak for sea lice prevalence (percent infected fish) and abundance (lice/fish). Spatial differences in prevalence and abundance were also detected for most months of the study and Pembroke Landing became a site of interest because the observed infection trends were unique relative to the remaining coves. Copepodid and chalimus stages were not detected in the late winter or early spring in 2014 because temperatures were not supportive of egg hatching, naupliar survival, or copepodid attachment. The source of the infections observed over the course of 18 months was unclear and farm counts from the time of the study were not made available for farm to sentinel comparisons. The relationship between environmental factors and total sea lice counts were investigated using generalized linear mixed effect models (GLMMs) with a negative binomial distribution and a log link function. A mathematical model estimating body surface area of Atlantic salmon juveniles was designed and then used to generate fish morphometric data for GLMM development. Data from individual sites were initially pooled to generate a general model for the entire bay, but the significance of Pembroke Landing as an individual site prompted a need to generate site-specific GLMMs. Temperature had a positive relationship on total sea lice count at all sites, which was expected because of its biological relevance in expediting sea louse development and growth. Current velocity had a negative relationship with sea lice at Prince Cove and Pembroke Landing, likely because average velocities were within a range that limits sea lice attachment. Results from the survey and the mathematical model were linked with previous work on sea lice infection dynamics to develop scenarios that describe potential sources of infection for Cobscook Bay. These data and scenarios will be used to inform future bio-physical models and assist in developing hypotheses that can be tested once models are validated and confirmed. ACKNOWLEDGEMENTS I would first like to thank my advisor, Ian and colleagues Mike and Sarah B. for their supervision and mentorship. Ian for having nothing but the upmost faith in my academic pursuits and for actively encouraging my endeavors. Mike for continually pushing my personal expectations on how I should think of science, for your liaison ship with involved stakeholders, and for your driving to and from work sites when my sleepy eyes could not. Sarah for navigating and helping with the organization of 2.5 years of field and lab in addition to your own research and growing family. To Mike, Sarah B, and Sarah Turner for spending countless hours examining fish for sea lice and for enduring my random music playlists even when not up to taste; I still feel confident on my choice of playing heavy metal in the early morning. Thanks to my committee: Gayle and Heather for your insight as fellow women in S.T.E.M., for your assistance and guidance in experimental design, and for your enthusiasm as mentors, researchers, and teachers. Damian for your continued effort towards my self-preservation in statistical analyses and for attempting to pull me out the rabbit holes. Mark for your insight as a sea louse biologist and for the input you have provided over the last half decade. To my army of assistants for the countless hours you spent under my direction in the field and lab. This project required so many hands to complete and I had the assistance of so many wonderful undergraduate and high school students, many of whom have moved onto their own research and projects. I would like to acknowledge financial support from NOAA Maine Sea Grant for covering research expenses, APHIS for partial coverage of my research assistantship, and the School of Biology and Ecology for my teaching assistantship. Thanks to Farahad and Julia for addressing the needs of their TAs and for providing the opportunity to share my knowledge and skills in a formal instructional setting. To my wonderful tribe of strong, intelligent, fierce, weirdos that have made this journey exceptionally easier. I am forever grateful to the Ladybugs, Tough Enders, Successful Queens, Red Haus-ers, iii Polevaulters, and IMRC folk for the positivity and support in my academic life and for hosting dinners, dances, spaces of expression to explore non-scientific interests so that I may maintain my sanity. To the wonderful humans at Mabel Wadsworth Center for giving me a voice and the ability to give back to the greater Bangor Area. To the skaters, NSOs, SOs, and volunteers of Central Maine Derby and my trainer Vanessa Sanders for encouraging me to be the best Glam I can be. To my family for the longevity of their support and their unwavering confidence that I can and am able to do whatever I set my mind to. To my past mentors: I did this crazy thing and you all led me here in some way. Jean, to this day you remain number one as my most favorite teacher. I remember the dynamics of your classroom to this day and so glad to have kept in touch after all these years. I’m proud to say that my 3rd (and 4th) grade teacher is a friend of mine. Preston, I never said much to this effect, but the foundation of your lectures and the message you send every day has had such a tremendous effect on me and the way in which I approach my life and work. Erin, I would not be here today if you had not taken a chance on an undergrad that probably had no business doing half the work you allowed me to do. Thank you for your faith and confidence, I hope I did you proud! iv TABLE OF CONTENTS ACKNOWLEDGEMENTS ................................................................................................................................ iii LIST OF TABLES ........................................................................................................................................... viii LIST OF FIGURES ........................................................................................................................................... ix 1. A GENERAL INTRODUCTION TO SEA LICE BIOLOGY AND ECOLOGY ......................................................... 1 1.1. Biology of sea lice, a group of parasitic copepods ...................................................................... 7 1.1.1. Life history and reproductive biology
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