The “Metacopepod” Project: Designing an Integrated DNA Metabarcoding and Image Analysis Approach to Study and Monitor Biodiversity of Zooplanktonic Copepods
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National Monitoring Program for Biodiversity and Non-Indigenous Species in Egypt
UNITED NATIONS ENVIRONMENT PROGRAM MEDITERRANEAN ACTION PLAN REGIONAL ACTIVITY CENTRE FOR SPECIALLY PROTECTED AREAS National monitoring program for biodiversity and non-indigenous species in Egypt PROF. MOUSTAFA M. FOUDA April 2017 1 Study required and financed by: Regional Activity Centre for Specially Protected Areas Boulevard du Leader Yasser Arafat BP 337 1080 Tunis Cedex – Tunisie Responsible of the study: Mehdi Aissi, EcApMEDII Programme officer In charge of the study: Prof. Moustafa M. Fouda Mr. Mohamed Said Abdelwarith Mr. Mahmoud Fawzy Kamel Ministry of Environment, Egyptian Environmental Affairs Agency (EEAA) With the participation of: Name, qualification and original institution of all the participants in the study (field mission or participation of national institutions) 2 TABLE OF CONTENTS page Acknowledgements 4 Preamble 5 Chapter 1: Introduction 9 Chapter 2: Institutional and regulatory aspects 40 Chapter 3: Scientific Aspects 49 Chapter 4: Development of monitoring program 59 Chapter 5: Existing Monitoring Program in Egypt 91 1. Monitoring program for habitat mapping 103 2. Marine MAMMALS monitoring program 109 3. Marine Turtles Monitoring Program 115 4. Monitoring Program for Seabirds 118 5. Non-Indigenous Species Monitoring Program 123 Chapter 6: Implementation / Operational Plan 131 Selected References 133 Annexes 143 3 AKNOWLEGEMENTS We would like to thank RAC/ SPA and EU for providing financial and technical assistances to prepare this monitoring programme. The preparation of this programme was the result of several contacts and interviews with many stakeholders from Government, research institutions, NGOs and fishermen. The author would like to express thanks to all for their support. In addition; we would like to acknowledge all participants who attended the workshop and represented the following institutions: 1. -
Bioluminescence of the Poecilostomatoid Copepod Oncaea Conifera
l MARINE ECOLOGY PROGRESS SERIES Published April 22 Mar. Ecol. Prog. Ser. Bioluminescence of the poecilostomatoid copepod Oncaea conifera Peter J. Herring1, M. I. ~atz~,N. J. ~annister~,E. A. widder4 ' Institute of Oceanographic Sciences, Deacon Laboratory, Brook Road Wormley, Surrey GU8 5UB, United Kingdom 'Marine Biology Research Division 0202, Scripps Institution of Oceanography, La Jolla, California 92093, USA School of Biological Sciences, University of Birmingham, Edgbaston. Birmingham B15 2TT, United Kingdom Harbor Branch Oceanographic Institution, 5600 Old Dixie Highway, Fort Pierce, Florida 34946, USA ABSTRACT: The small poecilostomatoid copepod Oncaea conifera Giesbrecht bears a large number of epidermal luminous glands, distributed primarily over the dorsal cephalosome and urosome. Bio- luminescence is produced in the form of short (80 to 200 ms duration) flashes from withrn each gland and there IS no visible secretory component. Nevertheless each gland opens to the exterior by a simple valved pore. Intact copepods can produce several hundred flashes before the luminescent system is exhausted. Individual flashes had a maximum measured flux of 7.5 X 10" quanta s ', and the flash rate follows the stimulus frequency up to 30 S" Video observations show that ind~vidualglands flash repeatedly and the flash propagates along their length. The gland gross morphology is highly variable although each gland appears to be unicellular. The cytoplasm contains an extensive endoplasmic reticulum. 0. conifera swims at Reynolds numbers of 10 to 50, and is normally associated with surfaces (e.g. marine snow). We suggest that the unique anatomical and physiological characteristics of the luminescent system arc related to the specialised ecological niche occupied by this species. -
Copepod Distribution and Production in a Mid-Atlantic Ridge Archipelago
Anais da Academia Brasileira de Ciências (2014) 86(4): 1719-1733 (Annals of the Brazilian Academy of Sciences) Printed version ISSN 0001-3765 / Online version ISSN 1678-2690 http://dx.doi.org/10.1590/0001-3765201420130395 www.scielo.br/aabc Copepod distribution and production in a Mid-Atlantic Ridge archipelago PEDRO A.M.C. MELO1, MAURO DE MELO JÚNIOR2, SILVIO J. DE MACÊDO1, MOACYR ARAUJO1 and SIGRID NEUMANN-LEITÃO1 1Universidade Federal de Pernambuco, Departamento de Oceanografia, Av. Arquitetura, s/n, Cidade Universitária, 50670-901 Recife, PE, Brasil 2Universidade Federal Rural de Pernambuco, Unidade Acadêmica de Serra Talhada, Fazenda Saco, s/n, Zona Rural, 56903-970 Serra Talhada, PE, Brasil Manuscript received on October 3, 2013; accepted for publication on March 11, 2014 ABSTRACT The Saint Peter and Saint Paul Archipelago (SPSPA) are located close to the Equator in the Atlantic Ocean. The aim of this study was to assess the spatial variations in the copepod community abundance, and the biomass and production patterns of the three most abundant calanoid species in the SPSPA. Plankton samples were collected with a 300 µm mesh size net along four transects (north, east, south and west of the SPSPA), with four stations plotted in each transect. All transects exhibited a tendency toward a decrease in copepod density with increasing distance from the SPSPA, statistically proved in the North. Density varied from 3.33 to 182.18 ind.m-3, and differences were also found between the first perimeter (first circular distance band) and the others. The total biomass varied from 15.25 to 524.50 10-3 mg C m-3 and production from 1.19 to 22.04 10-3 mg C m-3d-1. -
Eggs of the Copepod Acartia Tonsa Dana Require Hypoxic Conditions to Tolerate Prolonged Embryonic Development Arrest Tue Sparholt Jørgensen1,2*, Per Meyer Jepsen1, H
Jørgensen et al. BMC Ecol (2019) 19:1 https://doi.org/10.1186/s12898-018-0217-5 BMC Ecology RESEARCH ARTICLE Open Access Eggs of the copepod Acartia tonsa Dana require hypoxic conditions to tolerate prolonged embryonic development arrest Tue Sparholt Jørgensen1,2*, Per Meyer Jepsen1, H. Cecilie B. Petersen1, Dennis Steven Friis1 and Benni Winding Hansen1* Abstract Background: Copepods make up the largest zooplankton biomass in coastal areas and estuaries and are pivotal for the normal development of fsh larva of countless species. During spring in neritic boreal waters, the copepod pelagic biomass increases rapidly from near absence during winter. In the calanoid species Acartia tonsa, a small fraction of eggs are dormant regardless of external conditions and this has been hypothesized to be crucial for sediment egg banks and for the rapid biomass increase during spring. Other eggs can enter a state of induced arrest called quies- cence when external conditions are unfavourable. While temperature is known to be a pivotal factor in the transition from developing to resting eggs and back, the role of pH and free Oxygen in embryo development has not been systematically investigated. Results: Here, we show in a laboratory setting that hypoxic conditions are necessary for resting eggs to maintain a near-intact rate of survival after several months of induced resting. We further investigate the infuence of pH that is realistic for natural sediments on the viability of resting eggs and document the efect that eggs have on the pH of the surrounding environment. We fnd that resting eggs acidify their immediate surroundings and are able to survive in a wide range of pH. -
Diversity and Life-Cycle Analysis of Pacific Ocean Zooplankton by Video Microscopy and DNA Barcoding: Crustacea
Journal of Aquaculture & Marine Biology Research Article Open Access Diversity and life-cycle analysis of Pacific Ocean zooplankton by video microscopy and DNA barcoding: Crustacea Abstract Volume 10 Issue 3 - 2021 Determining the DNA sequencing of a small element in the mitochondrial DNA (DNA Peter Bryant,1 Timothy Arehart2 barcoding) makes it possible to easily identify individuals of different larval stages of 1Department of Developmental and Cell Biology, University of marine crustaceans without the need for laboratory rearing. It can also be used to construct California, USA taxonomic trees, although it is not yet clear to what extent this barcode-based taxonomy 2Crystal Cove Conservancy, Newport Coast, CA, USA reflects more traditional morphological or molecular taxonomy. Collections of zooplankton were made using conventional plankton nets in Newport Bay and the Pacific Ocean near Correspondence: Peter Bryant, Department of Newport Beach, California (Lat. 33.628342, Long. -117.927933) between May 2013 and Developmental and Cell Biology, University of California, USA, January 2020, and individual crustacean specimens were documented by video microscopy. Email Adult crustaceans were collected from solid substrates in the same areas. Specimens were preserved in ethanol and sent to the Canadian Centre for DNA Barcoding at the Received: June 03, 2021 | Published: July 26, 2021 University of Guelph, Ontario, Canada for sequencing of the COI DNA barcode. From 1042 specimens, 544 COI sequences were obtained falling into 199 Barcode Identification Numbers (BINs), of which 76 correspond to recognized species. For 15 species of decapods (Loxorhynchus grandis, Pelia tumida, Pugettia dalli, Metacarcinus anthonyi, Metacarcinus gracilis, Pachygrapsus crassipes, Pleuroncodes planipes, Lophopanopeus sp., Pinnixa franciscana, Pinnixa tubicola, Pagurus longicarpus, Petrolisthes cabrilloi, Portunus xantusii, Hemigrapsus oregonensis, Heptacarpus brevirostris), DNA barcoding allowed the matching of different life-cycle stages (zoea, megalops, adult). -
Marine Biological Association Occasional Publications No. 21
Identification of the copepodite developmental stages of twenty-six North Atlantic copepods David V.P. Conway Marine Biological Association Occasional Publications No. 21 (revised edition) 1 Identification of the copepodite developmental stages of twenty-six North Atlantic copepods David V.P. Conway Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, PL1 2PB Marine Biological Association of the United Kingdom Occasional Publications No. 21 (revised edition) Cover picture: Nauplii and copepodite developmental stages of Centropages hamatus (from Oberg, 1906). 2 Citation Conway, D.V.P. (2012). Identification of the copepodite developmental stages of twenty-six North Atlantic copepods. Occasional Publications. Marine Biological Association of the United Kingdom, No. 21 (revised edition), Plymouth, United Kingdom, 35 pp. Electronic copies This guide is available for free download, from the National Marine Biological Library website - http://www.mba.ac.uk/nmbl/ from the “Download Occasional Publications of the MBA” section. © 2012 Marine Biological Association of the United Kingdom, Plymouth, UK. ISSN 02602784 This publication has been compiled as accurately as possible, but corrections that could be included in any revisions would be gratefully received. email: [email protected] 3 Contents Preface Page 4 Introduction 5 Copepod classification 5 Copepod body divisions 5 Copepod appendages 6 Copepod moulting and development 8 Sex determination in late gymnoplean copepodite stages 9 Superorder Gymnoplea: Order Calanoida -
Taxonomy, Biology and Phylogeny of Miraciidae (Copepoda: Harpacticoida)
TAXONOMY, BIOLOGY AND PHYLOGENY OF MIRACIIDAE (COPEPODA: HARPACTICOIDA) Rony Huys & Ruth Böttger-Schnack SARSIA Huys, Rony & Ruth Böttger-Schnack 1994 12 30. Taxonomy, biology and phytogeny of Miraciidae (Copepoda: Harpacticoida). - Sarsia 79:207-283. Bergen. ISSN 0036-4827. The holoplanktonic family Miraciidae (Copepoda, Harpacticoida) is revised and a key to the four monotypic genera presented. Amended diagnoses are given for Miracia Dana, Oculosetella Dahl and Macrosetella A. Scott, based on complete redescriptions of their respective type species M. efferata Dana, 1849, O. gracilis (Dana, 1849) and M. gracilis (Dana, 1847). A fourth genus Distioculus gen. nov. is proposed to accommodate Miracia minor T. Scott, 1894. The occurrence of two size-morphs of M. gracilis in the Red Sea is discussed, and reliable distribution records of the problematic O. gracilis are compiled. The first nauplius of M. gracilis is described in detail and changes in the structure of the antennule, P2 endopod and caudal ramus during copepodid development are illustrated. Phylogenetic analysis revealed that Miracia is closest to the miraciid ancestor and placed Oculosetella-Macrosetella at the terminal branch of the cladogram. Various aspects of miraciid biology are reviewed, including reproduction, postembryonic development, verti cal and geographical distribution, bioluminescence, photoreception and their association with filamentous Cyanobacteria {Trichodesmium). Rony Huys, Department of Zoology, The Natural History Museum, Cromwell Road, Lon don SW7 5BD, England. - Ruth Böttger-Schnack, Institut für Meereskunde, Düsternbroo- ker Weg 20, D-24105 Kiel, Germany. CONTENTS Introduction.............. .. 207 Genus Distioculus pacticoids can be carried into the open ocean by Material and methods ... .. 208 gen. nov.................. 243 algal rafting. Truly planktonic species which perma Systematics and Distioculus minor nently reside in the water column, however, form morphology .......... -
Fatty Acid and Alcohol Composition of the Small Polar Copepods, Oithona and Oncaea : Indication on Feeding Modes
Polar Biol (2003) 26: 666–671 DOI 10.1007/s00300-003-0540-x ORIGINAL PAPER G. Kattner Æ C. Albers Æ M. Graeve S. B. Schnack-Schiel Fatty acid and alcohol composition of the small polar copepods, Oithona and Oncaea : indication on feeding modes Received: 2 April 2003 / Accepted: 28 July 2003 / Published online: 27 August 2003 Ó Springer-Verlag 2003 Abstract The fatty acid and alcohol compositions of the (Paffenho¨ fer 1993). They occur from the polar seas to Antarctic copepods Oithona similis, Oncaea curvata, tropical regions at both hemispheres. Species of both Oncaea antarctica and the Arctic Oncaea borealis were genera can reach high concentrations, exceeding 5,000 determined to provide the first data on their lipid bio- individuals m)3 (Dagg et al. 1980; Koga 1986; chemistry and to expand the present knowledge on their Paffenho¨ fer 1993; Metz 1996). The high abundance of feeding modes and life-cycle strategies. All these tiny these tiny species compensates for the low biomass and, species contained high amounts of wax esters (on average thus, the populations can reach biomass levels of the 51.4–86.3% of total lipid), except females of Oithona same order as dominant calanoid species (Metz 1996). In similis (15.2%). The fatty-acid composition was clearly the Southern Ocean, Oithonidae and Oncaeidae can dominated by 18:1(n-9), especially in the wax-ester-rich account for between 20 and 24% of the total copepod Oncaea curvata (79.7% of total fatty acids). In all species, biomass (Schnack-Schiel et al. 1998). 16:0 and the polyunsaturated fatty acids 20:5(n-3) and The epipelagic species, Oithona similis, has been de- 22:6(n-3), which are structural components of all mem- scribed as the most numerous and widely distributed branes, occurred in significant proportions. -
Comparison of Seasonal Trends Between Reef and Offshore Zooplankton Communities in the Northern Gulf of Aqaba (Red Sea)
Comparison of seasonal trends between reef and offshore zooplankton communities in the northern Gulf of Aqaba (Red Sea) Manuel Olivares Requena Master thesis Supervision by: Dr. Astrid Cornils (AWI, Germany) Prof. Dr. Stefanie M. H. Ismar (GEOMAR, Germany) Kiel, January 2016 Index Summary ……………….…………………………………………………………………………………………………3 Introduction…………….…………………………………………….…………………………………………………4 1. Introduction…………………………………………………………………………………………………….…………..4 2. Objectives…………………………………………………………………………………………………………….……..5 Material and Methods…………………………………………………………………………………… .….……6 1. Study area: The Gulf of Aqaba ……………………………………………………………………………………..6 2. Sample collection……………………………………………………………………………………………………..….8 3. Sample analysis………………………………………………………………………………………………..……….. 10 4. Data analysis………………………………………………………………………………………………………………12 Results…………………………………………………………………………………………………………………...14 A. Environmental parameters ………………………………………………………………………………………..14 B. Community patterns…………………………………………………………………………………………….…… 15 B1. Mesozooplankton ………………………………………………………………...………………………15 B2. Copepods……………………………………………………………………………………………………..20 C. Patterns of dominant taxa…………………………………………………………………………………. .……. 25 D. Carbon and nitrogen analysis……………………………………………………………………………………. 26 Discussion…………………………………………………………………………………………………….………..27 1. Mesozooplankton composition……………………………………………………………………….……..…. 27 2. Mesozooplankton abundance and biomass... ……………………………………………………….……29 3. Seasonal patterns ………………………………………………………………………………….…………..……..30 4. Spatial patterns: reef vs. -
Species of the Genera Temora and Tortanus from Indonesian Coastal Waters
Berk. Penel. Hayati: 14 (125–135), 2009 SPECIES OF THE GENERA TEMORA AND TORTANUS FROM INDONESIAN COASTAL WATERS Mulyadi Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences Jl. Raya Bogor Km. 46 Cibinong 16911, Indonesia E-mail: [email protected] ABSTRACT During taxonomic studies on the pelagic copepods of Indonesian waters, three species of Temora, T. discaudata Giesbrecht, 1882, T. discaudata n. var. and T. turbinata (Dana, 1849), and three species of Tortanus, T. (Tortanus) barbatus, T. (Tortanus) forcipatus and T. (Tortanus) gracilis were described and figured on specimens collected from 8 sites along Indonesian coastal waters. Descriptions, measurements and figures are given for those species, along with a review of their distribution over the world oceans, and with taxonomic remarks, ecological notes, and restricted synonymies. Key words: taxonomy, Temora, Tortanus, Indonesian waters INTRODUCTION MATERIALS AND METHODS Family Temoridae Giesbrecht, 1893 comprises of The present plankton samples were obtained from 8 35 species from four genera, Epischura Forbes, 1882; sites during 1994–2007 (Figure 1). Sampling was done Eurytemora Giesbrecht, 1881; Heterocope Sars, 1863; and by surface and vertical hauls (10 m and 20 m depth to the Temora Baird, 1850. The genus Temora presently comprises surface) with plankton net (0.33 mm mesh size, 0.45 m of five species (Boxshall & Halsey, 2004). Among them two mouth diameter). The samples were fixed and preserved species, T. discaudata Giesbrecht, 1882 and T. turbinata in 5% buffered formaldehyde/sea water solution. As far (Dana, 1849) have been reported from Indonesian waters as possible, the specimens were identified to species level. -
Fecundity and Survival of the Calanoid Copepod <I>Acartia Tonsa
The University of Southern Mississippi The Aquila Digital Community Master's Theses Spring 5-2007 Fecundity and Survival of the Calanoid Copepod Acartia tonsa Fed Isochrysis galeana (Tahitian Strain) and Chaetoceros mulleri Angelos Apeitos University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/masters_theses Part of the Aquaculture and Fisheries Commons, and the Marine Biology Commons Recommended Citation Apeitos, Angelos, "Fecundity and Survival of the Calanoid Copepod Acartia tonsa Fed Isochrysis galeana (Tahitian Strain) and Chaetoceros mulleri" (2007). Master's Theses. 276. https://aquila.usm.edu/masters_theses/276 This Masters Thesis is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Master's Theses by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi FECUNDITY AND SURVIVAL OF THE CALANOID COPEPOD ACARTIA TONSA FED ISOCHRYSIS GALEANA (TAHITIAN STRAIN) AND CHAETOCEROS MULLER! by Angelos Apeitos A Thesis Submitted to the Graduate Studies Office of the University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Master of Science May2007 ABS1RACT FECUNDITY AND SURVIVAL OF THE CALANOID COPEPOD ACARTIA TONSA FED ISOCHRYSIS GALEANA (TAHITIAN STRAIN) AND CHAETOCEROS MULLER! Historically, red snapper (Lutjanus campechanus) larviculture at the Gulf Coast Research Lab (GCRL) used 25 ppt artificial salt water and mixed, wild zooplankton composed primarily of Acartia tonsa, a calanoid copepod. Acartia tonsa was collected from the estuarine waters of Davis Bayou and bloomed in outdoor tanks from which it was harvested and fed to red sapper larvae. -
A Comparison of Copepoda (Order: Calanoida, Cyclopoida, Poecilostomatoida) Density in the Florida Current Off Fort Lauderdale, Florida
Nova Southeastern University NSUWorks HCNSO Student Theses and Dissertations HCNSO Student Work 6-1-2010 A Comparison of Copepoda (Order: Calanoida, Cyclopoida, Poecilostomatoida) Density in the Florida Current Off orF t Lauderdale, Florida Jessica L. Bostock Nova Southeastern University, [email protected] Follow this and additional works at: https://nsuworks.nova.edu/occ_stuetd Part of the Marine Biology Commons, and the Oceanography and Atmospheric Sciences and Meteorology Commons Share Feedback About This Item NSUWorks Citation Jessica L. Bostock. 2010. A Comparison of Copepoda (Order: Calanoida, Cyclopoida, Poecilostomatoida) Density in the Florida Current Off Fort Lauderdale, Florida. Master's thesis. Nova Southeastern University. Retrieved from NSUWorks, Oceanographic Center. (92) https://nsuworks.nova.edu/occ_stuetd/92. This Thesis is brought to you by the HCNSO Student Work at NSUWorks. It has been accepted for inclusion in HCNSO Student Theses and Dissertations by an authorized administrator of NSUWorks. For more information, please contact [email protected]. Nova Southeastern University Oceanographic Center A Comparison of Copepoda (Order: Calanoida, Cyclopoida, Poecilostomatoida) Density in the Florida Current off Fort Lauderdale, Florida By Jessica L. Bostock Submitted to the Faculty of Nova Southeastern University Oceanographic Center in partial fulfillment of the requirements for the degree of Master of Science with a specialty in: Marine Biology Nova Southeastern University June 2010 1 Thesis of Jessica L. Bostock Submitted in Partial Fulfillment of the Requirements for the Degree of Masters of Science: Marine Biology Nova Southeastern University Oceanographic Center June 2010 Approved: Thesis Committee Major Professor :______________________________ Amy C. Hirons, Ph.D. Committee Member :___________________________ Alexander Soloviev, Ph.D.