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1. The emergence of Vibrio pathogens in Europe : ecology, evolution, and pathogenesis (Paris, 11-12th March 2015)

Author: Alexander K. T. Kirschner, Luigi Vezzulli, Stephan Huehn, Craig Baker-Austin, Eckhard Strauch, Tom Defoirdt, Felipe Cava, Carlos R. Osorio, Didier Mazel, Frédérique Le Roux, Delphine Destoumieux-Garzón, K. Mathias Wegner, Lone Gram, Jennifer M. Ritchie, Carmen Amaro, Melanie Blokesch, Carolin C. Wendling, Annick Jacq, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Université Pierre et Marie Curie - Paris 6 (UPMC) - Centre National de la Recherche Scientifique (CNRS), Unité Physiologie Fonctionnelle des Organismes marins, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Earth, Environmental and Life Sciences (DISTAV), Universita degli studi di Genova, Instituto de Acuicultura, Universidad de Santiago de Compostela, University of Valencia, University of Surrey (UNIS), UGent Aquaculture R&D Consortium, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD) - Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) - Université de Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS), Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Plasticité du Génome Bactérien, Institut Pasteur [Paris] - Centre National de la Recherche Scientifique (CNRS), Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11) - Centre National de la Recherche Scientifique (CNRS), Umea University (SWEDEN), Technical University of Denmark [Lyngby] (DTU), GEOMAR - Helmholtz Centre for Ocean Research Kiel (GEOMAR), Federal Institute for Risk Assessment, Medical University of Vienna, Universidade de Santiago de Compostela. Departamento de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela. Instituto de Acuicultura, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Coastal Ecology, Alfred Wegener Institute, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Università degli studi di Genova = University of Genoa (UniGe), Departamento de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela [Spain] (USC ), Faculty of Health and Medical Sciences, Universiteit Gent = Ghent University (UGENT), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Global Health Institute - Institut d'Infectiologie [Lausanne], Plasticité du Génome Bactérien - Bacterial Genome Plasticity (PGB), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Umeå University, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Bundesinstitut für Risikobewertung - Federal Institute for Risk Assessment (BfR), Institute for Hygiene and Applied Immunology, Medizinische Universität Wien = Medical University of Vienna, Free University of Berlin (FU), We warmly thank EUROMARINE, EMBRC-France, the Agence Nationale de la Recherche (ANR) for their financial support, Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Laboratoire de Biologie Intégrative des Modèles Marins ( LBI2M ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research ( AWI ), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] ( CEFAS ), Department of Earth, Environmental and Life Sciences ( DISTAV ), Instituto de Acuicultura, Universidade de Santiago de Compostela, University of Surrey ( UNIS ), Ghent University [Belgium] ( UGENT ), Interactions Hôtes-Pathogènes-Environnements ( IHPE ), Université de Perpignan Via Domitia ( UPVD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ), Ecole Polytechnique Fédérale de Lausanne ( EPFL ), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Technical University of Denmark [Lyngby] ( DTU ), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] ( GEOMAR ), Free University of Berlin ( FU ), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)
Subjects: Cell- och molekylärbiologi, lcsh:QR1-502, Network, PACIFIC OYSTERS, [ SDV.MP.BAC ] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, global warming, human health, genome plasticity, HORIZONTAL GENE-TRANSFER, lcsh:Microbiology, european network, OYSTERS CRASSOSTREA-GIGAS, Applied research, Food security, biology, Ecology, Genome plasticity, MARINE PHOTOBACTERIUM, Human health risks, aquaculture, SECRETION SYSTEM, Perspective, Vibrio-host interaction, VIRULENCE FACTORS, Microbiology (medical), Ecology (disciplines), Social issues, Microbiology, SDG 3 - Good Health and Well-being, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 14. Life underwater, SDG 14 - Life Below Water, SDG 2 - Zero Hunger, Bacterial disease, animal model, Global warming, Outbreak, Biology and Life Sciences, genome asticity, D-AMINO ACIDS, Animal model, Aquaculture, Biotic-abiotic interactions, Human health, interactions, biology.organism_classification, CLINICAL SOURCES, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, bacterial disease, Vibrio, DAMSELAE SUBSP DAMSELAE, 13. Climate action, networks, Cell and Molecular Biology, PHOTOBACTERIUM-DAMSELAE
Abstract: Global change has caused a worldwide increase in reports of Vibrio-associated diseases with ecosystem-wide impacts on humans and marine animals. In Europe, higher prevalence of human infections followed regional climatic trends with outbreaks occurring during episodes of unusually warm weather. Similar patterns were also observed in Vibrio-associated diseases affecting marine organisms such as fish, bivalves and corals. Basic knowledge is still lacking on the ecology and evolutionary biology of these bacteria as well as on their virulence mechanisms. Current limitations in experimental systems to study infection and the lack of diagnostic tools still prevent a better understanding of Vibrio emergence. A major challenge is to foster cooperation between fundamental and applied research in order to investigate the consequences of pathogen emergence in natural Vibrio populations and answer federative questions that meet societal needs. Here we report the proceedings of the first European workshop dedicated to these specific goals of the Vibrio research community by connecting current knowledge to societal issues related to ocean health and food security We warmly thank EUROMARINE, EMBRC-France, the Agence Nationale de la Recherche (ANR) for their financial support and EFOR organization to this first workshop SI
Published: 2015

2. The potential contribution of small coastal streams to the conservation of declining and threatened diadromous fishes, especially the European eel

Author: Tea Bašić, Françoise Daverat, Gordon H. Copp, Salmon & Freshwater Team (SFT), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre for Environment, Fisheries andAquaculture Science, Grant/Award Number:Science Excellence fund, and EuropeanCommission, Grant/Award Number: Interregproject DiadES - EAPA_18/2018
Subjects: flounder, 0106 biological sciences, Fish migration, juvenile fish nursery habitat, 010604 marine biology & hydrobiology, STREAMS, Biology, 010603 evolutionary biology, 01 natural sciences, Fishery, [SDE]Environmental Sciences, Threatened species, dune stream, Environmental Chemistry, 14. Life underwater, Pas-de-Calais, General Environmental Science, Water Science and Technology
Abstract: International audience; Human‐generated pressures are continuing to have a detrimental effect on diadromous fishes, resulting in legislative initiatives to conserve and manage these species. Field studies to inform these initiatives focus almost exclusively on larger marine, estuarine, and inland waters, neglecting the role of small coastal streams and tributaries in population recovery. As an example of the potential contribution of very small coastal streams to diadromous fish recruitment, we report here on the densities and distribution of European eel Anguilla anguilla L. and flounder Platichthys flesus (L.) in one such stream, “La Warenne,” in northeast France in October 1998 and 1999. Both species were found mainly in downstream sites in both years—flounder were captured in low numbers only, but mean CPUE values for eel were similar to the highest densities reported in the ICES WGEEL database for larger rivers of Great Britain, France and Spain in the Interreg Atlantic and North Sea areas. This small dataset illustrates that small coastal streams may represent an important, but overlooked, role in conservation strategies for European eel, and possibly flounder, indicating the need for further field studies and investigations of existing data sources to evaluate the contributions to diadromous fish recruitment of these poorly studied water courses.
Published: 2020

3. Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture

Author: Isabelle Arzul, Luigi Vezzulli, K. Mathias Wegner, Alberto Pallavicini, Christine Paillard, Yannick Gueguen, David Bass, Paillard, Christine, Gueguen, Yannick, Wegner, K Mathia, Bass, David, Pallavicini, Alberto, Vezzulli, Luigi, Arzul, Isabelle, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), Alfred Wegener Institute for Polar and Marine Research (AWI), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Life Sciences, Università degli studi di Trieste, National Institute of Oceanography and Applied Geophysics (OGS), Dipartimento di Scienze della Terra dell'Ambiente e della Vita (DISTAV), Universita degli studi di Genova, Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Università degli studi di Trieste = University of Trieste, Università degli studi di Genova = University of Genoa (UniGe), Laboratoire de Génétique et Pathologie des Mollusques Marins (LGPMM), Santé, Génétique et Microbiologie des Mollusques (SGMM), and ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017)
Subjects: Functional role, Biomedical Engineering, Bioengineering, Context (language use), [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Disease, Aquaculture, Biology, Animals, Host-Pathogen Interactions, Bivalvia, Microbiota, 03 medical and health sciences, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, 030306 microbiology, Ecology, Host (biology), business.industry, Animal, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Host-Pathogen Interaction, 13. Climate action, [SDE]Environmental Sciences, Disease prevention, business, Biotechnology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; In bivalves, no clear-cut functional role of microbiota has yet been identified, although many publications suggest that they could be involved in nutrition or immunity of their host. In the context of climate change, integrative approaches at the crossroads of disciplines have been developed to explore the environment-host-pathogen microbiota system. Here, we attempt to synthesize work on (1) the current methodologies to analyse bivalve microbiota, (2) the comparison of microbiota between species, between host compartments and their surrounding habitat, (3) how the bivalve microbiota are governed by environmental factors and host genetics and (4) how host-associated microorganisms act as a buffer against pathogens and/or promote recovery, and could thereby play a role in the prevention of disease or mortalities.
Published: 2022

4. Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

Author: Morga, Benjamin, Jacquot, Maude, Pelletier, Camille, Chevignon, Germain, Dégremont, Lionel, Biétry, Antoine, Pepin, Jean-François, Heurtebise, Serge, Escoubas, Jean-Michel, Bean, Tim, Rosani, Umberto, Bai, Chang-Ming, Renault, Tristan, Lamy, Jean-Baptiste, Santé, Génétique et Microbiologie des Mollusques (IFREMER SG2M), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie des Mollusques Marins, 17390 La Tremblade, France. (LGPMM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Génétique et Pathologie des Mollusques Marins - Ifremer (SG2M-LGPMM), Interactions Hôtes-Pathogènes-Environnements (IHPE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Perpignan Via Domitia (UPVD), The Roslin Institute and Royal (Dick), School of Veterinary Studies, University of Edinburgh, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (Cefas), University of Padua [Italy], Yellow Sea Fisheries Research Institute, and Chinese Academy of Fishery Sciences
Subjects: Microbiology (medical), shellfish farming, OsHV-1, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], measurably evolution, marine virus, Microbiology, ComputingMilieux_MISCELLANEOUS, Original Research, diversity
Abstract: The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.
Published: 2021
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5. pr2-primers: an 18S rRNA primer database for protists

Author: David Bass, Frédéric Mahé, Daniel Vaulot, Stefan Geisen, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Nanyang Technological University [Singapour], Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Wageningen University and Research [Wageningen] (WUR), Nanjing Agricultural University, Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Nanjing Agricultural University (NAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), and Terrestrial Ecology (TE)
Subjects: 0106 biological sciences, In silico, Biology, computer.software_genre, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, 18S ribosomal RNA, 03 medical and health sciences, metabrcoding, Genetics, RNA, Ribosomal, 18S, medicine, primers, Laboratorium voor Nematologie, Ecology, Evolution, Behavior and Systematics, database, 030304 developmental biology, protists, 0303 health sciences, Database, shiny, Eukaryota, Protist, Plan_S-Compliant_NO, PE&RC, Amplicon Size, 18S rRNA, PCR, international, metabarcoding, [SDE]Environmental Sciences, Primer (molecular biology), Laboratory of Nematology, computer, Biotechnology
Abstract: Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost uniquely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, a wise primer choice is needed as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few on-line resources available to list existing primers. We built a database listing 179 primers and 76 primer pairs that have been used for eukaryotic 18S rRNA metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR2 for eukaryotes and a subset of Silva for prokaryotes. This allowed to determine the taxonomic specificity of primer pairs, the location of mismatches as well as amplicon size. We developed a R-based web application that allows to browse the database, visualize the taxonomic distribution of the amplified sequences with the number of mismatches, and to test any user-defined primer set (https://app.pr2-primers.org). This tool will provide the basis for guided primer choices that will help a wide range of ecologists to implement protists as part of their investigations.
Published: 2021

6. Effects of Nutrient Management Scenarios on Marine Food Webs: A Pan-European Assessment in Support of the Marine Strategy Framework Directive

Author: Chiara Piroddi, Ekin Akoglu, Eider Andonegi, Jacob W. Bentley, Igor Celić, Marta Coll, Donna Dimarchopoulou, René Friedland, Kim de Mutsert, Raphael Girardin, Elisa Garcia-Gorriz, Bruna Grizzetti, P.-Y. Hernvann, Johanna J. Heymans, Bärbel Müller-Karulis, Simone Libralato, Christopher P. Lynam, Diego Macias, Svetla Miladinova, Fabien Moullec, Andreas Palialexis, Ove Parn, Natalia Serpetti, Cosimo Solidoro, Jeroen Steenbeek, Adolf Stips, Maciej T. Tomczak, Morgane Travers-Trolet, Athanassios C. Tsikliras, European Commission, Agencia Estatal de Investigación (España), Natural Environment Research Council (UK), BiodivERsA, Belmont Forum, National Academies of Sciences, Engineering and Medicine (US), European Commission - Joint Research Centre [Ispra] (JRC), Institute of Marine Sciences [Erdemli-Mersin] (IMS), Middle East Technical University [Ankara] (METU), United Nations Environment Programma World Conservation Monitoring Centre, School of Anthropology and Conservation [University of Kent], University of Kent [Canterbury], National Institute of Oceanography and Applied Geophysics (OGS), Marine Sciences Institute of Andalusia, Spanish Council for Scientific Research. ICMAN (CSIC), Laboratory of Ichthyology, School of Biology, Aristotle University of Thessalonik, Department of Fisheries, Animal and Veterinary Sciences, College of the Environment and Life Sciences, University of Rhode Island, Kingston, European Commission - Joint Research Centre [Geel] (JRC), Department of Environmental Science and Policy, University of California, USA, School of Marine Science and Ocean Engineering, University of New Hampshire (UNH), Laboratoire Ressources halieutiques Manche Mer du nord, IFREMER Centre Manche Mer du Nord, (HMMN), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité de recherche Sciences et Technologies Halieutiques (STH), University of California [Santa Cruz] (UCSC), University of California, European Marine Board, Baltic Sea Centre, Stockholm University, Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Center for Earth System Research and Sustainability (CEN), Universität Hamburg (UHH), Scottish Association for Marine Science (SAMS), Spain & Ecopath International Initiative Research Association, Institut de Ciències del Mar, Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), aboratory of Ichthyology, School of Biology, Aristotle University of Thessalonik, and OpenMETU
Subjects: 0106 biological sciences, lcsh:QH1-199.5, 010504 meteorology & atmospheric sciences, Ocean Engineering, lcsh:General. Including nature conservation, geographical distribution, Aquatic Science, Oceanography, Fish stock, Policy support, 01 natural sciences, hydrological modeling, Marine Strategy Framework Directive, ecological indicators, hydrodynamic and biogeochemical modeling, Ecosystem, Marine ecosystem, 14. Life underwater, lcsh:Science, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Water Science and Technology, Trophic level, higher trophic level modeling, Global and Planetary Change, Biomass (ecology), criteria, business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Pelagic zone, policy support, Ecological indicator, 13. Climate action, [SDE]Environmental Sciences, ecological modeling, Environmental science, lcsh:Q, business
Abstract: 18 pages, 7 figures, 2 tables, supplementary material https://www.frontiersin.org/articles/10.3389/fmars.2021.596797/full#supplementary-material.-- The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author/s, Eutrophication is one of the most important anthropogenic pressures impacting coastal seas. In Europe, several legislations and management measures have been implemented to halt nutrient overloading in marine ecosystems. This study evaluates the impact of freshwater nutrient control measures on higher trophic levels (HTL) in European marine ecosystems following descriptors and criteria as defined by the Marine Strategy Framework Directive (MSFD). We used a novel pan-European marine modeling ensemble of fourteen HTL models, covering almost all the EU seas, under two nutrient management scenarios. Results from our projections suggest that the proposed nutrient reduction measures may not have a significant impact on the structure and function of European marine ecosystems. Among the assessed criteria, the spawning stock biomass of commercially important fish stocks and the biomass of small pelagic fishes would be the most impacted, albeit with values lower than 2.5%. For the other criteria/indicators, such as species diversity and trophic level indicators, the impact was lower. The Black Sea and the North-East Atlantic were the most negatively impacted regions, while the Baltic Sea was the only region showing signs of improvement. Coastal and shelf areas were more sensitive to environmental changes than large regional and sub-regional ecosystems that also include open seas. This is the first pan-European multi-model comparison study used to assess the impacts of land-based measures on marine and coastal European ecosystems through a set of selected ecological indicators. Since anthropogenic pressures are expanding apace in the marine environment and policy makers need to use rapid and effective policy measures for fast-changing environments, this modeling framework is an essential asset in supporting and guiding EU policy needs and decisions, BM-K acknowledges funding from EU-H2020 project ClimeFish (grant agreement 677039), CL received support from the project CAMPUS funded by the Natural Environment Research Council and Defra (grant agreement NERC UK NE/RE007241/1). FM was funded by the SOMBEE project of the joint BiodivERsA and Belmont Forum call “BiodivScen 2018” (ANR-18-EBI4-0003-01). KD received support from the National Academies of Sciences Engineering and Medicine Gulf Research Program (Early Career Research Fellowship). MC acknowledges partial funding from the European Union’s Horizon 2020 Research and Innovation Programme under grant agreement no 869300 (FutureMARES project). This work acknowledges institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021

7. VHSV Single Amino Acid Polymorphisms (SAPs) Associated With Virulence in Rainbow Trout

Author: Francesco Pascoli, Michele Gastaldelli, Joëlle Cabon, Michel Brémont, Thierry Morin, Yannick Blanchard, David Ryder, Anna Toffan, Anna Luiza Farias Alencar, Valentina Panzarin, Niels Jørgen Olesen, Stéphane Biacchesi, Argelia Cuenca, Carlos P. Dopazo, Miriam Abbadi, Lénaïg Louboutin, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), DTU Aqua, National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Instituto de Acuicultura, Universidade de Santiago de Compostela, Virologie et Immunologie Moléculaires (VIM (UR 0892)), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Novimark Project (G88F13000660001) funded by the Animal Health and Welfare (Anihwa) ERA-Net Consortium., and UK’s Department for Environment, Food and Rural Affairs (Defra) under contract C7277
Subjects: Microbiology (medical), molecular markers, single amino acid polymorphism (SAP), animal diseases, lcsh:QR1-502, Host tropism, Virulence, Genome, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Genotype, SDG 14 - Life Below Water, 14. Life underwater, Pathogen, 030304 developmental biology, Original Research, Genetics, 0303 health sciences, biology, 030306 microbiology, VHSV, Molecular markers, biology.organism_classification, rainbow trout, virulence, Trout, Rainbow trout, Single amino polymorphism (SAP), [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Viral hemorrhagic septicemia
Abstract: International audience; The Viral Hemorrhagic Septicemia Virus (VHSV) is an OIE notifiable pathogen widespread in the Northern Hemisphere that encompasses four genotypes and nine subtypes. In Europe, subtype Ia impairs predominantly the rainbow trout industry causing severe rates of mortality, while other VHSV genotypes and subtypes affect a number of marine and freshwater species, both farmed and wild. VHSV has repeatedly proved to be able to jump to rainbow trout from the marine reservoir, causing mortality episodes. The molecular mechanisms regulating VHSV virulence and host tropism are not fully understood, mainly due to the scarce availability of complete genome sequences and information on the virulence phenotype. With the scope of identifying in silico molecular markers for VHSV virulence, we generated an extensive dataset of 55 viral genomes and related mortality data obtained from rainbow trout experimental challenges. Using statistical association analyses that combined genetic and mortality data, we found 38 single amino acid polymorphisms scattered throughout the complete coding regions of the viral genome that were putatively involved in virulence of VHSV in trout. Specific amino acid signatures were recognized as being associated with either low or high virulence phenotypes. The phylogenetic analysis of VHSV coding regions supported the evolution toward greater virulence in rainbow trout within subtype Ia, and identified several other subtypes which may be prone to be virulent for this species. This study sheds light on the molecular basis for VHSV virulence, and provides an extensive list of putative virulence markers for their subsequent validation.
Published: 2020

8. Neutron-induced damage simulations: Beyond defect production cross-section, displacement per atom and iron-based metrics

Author: D. Simeone, Petter Helgesson, Laurence Luneville, Y. Iwamoto, Stanislav Simakov, I. P. Bondarenko, R. Vila, Lawrence R. Greenwood, Patrick J. Griffin, C. J. Ortiz, A. Yu. Konobeyev, Henrik Sjöstrand, N. P. Lazarev, Dimitri Rochman, D. Terentyev, G. Bonny, Jeremy Lloyd Conlin, Fernando Mota, J.-Ch. Sublet, T. A. Khromyleva, V. A. Khryachkov, Mark R. Gilbert, Centre d'Etude de l'Energie Nucléaire (SCK-CEN), Université libre de Bruxelles (ULB), Fonds National de la Recherche Scientifique [Bruxelles] (FNRS), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Frontier Materials, Nagoya Institute of Technology, Nagoya Institute of Technology, CEA-Direction des Energies (ex-Direction de l'Energie Nucléaire) (CEA-DES (ex-DEN)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Centro de Investigaciones Energéticas Medioambientales y Tecnológicas [Madrid] (CIEMAT), Laboratoire de PHysique et Applications des SEmi-conducteurs (PHASE), Centre National de la Recherche Scientifique (CNRS), Paul Scherrer Institute (PSI), CEA- Saclay (CEA), and Université Paris-Saclay
Subjects: Fluid Flow and Transfer Processes, Physics, Nuclear reaction, [PHYS]Physics [physics], Complex system, General Physics and Astronomy, Nuclear data, Residual, 01 natural sciences, 010305 fluids & plasmas, Computational physics, Cascade, 0103 physical sciences, Neutron, 010306 general physics, Nucleon, Fermi Gamma-ray Space Telescope
Abstract: Nuclear interactions can be the source of atomic displacement and post-short-term cascade annealing defects in irradiated structural materials. Such quantities are derived from, or can be correlated to, nuclear kinematic simulations of primary atomic energy distributions spectra and the quantification of the numbers of secondary defects produced per primary as a function of the available recoils, residual and emitted, energies. Recoils kinematics of neutral, residual, charged and multi-particle emissions are now more rigorously treated based on modern, complete and enhanced nuclear data parsed in state of the art processing tools. Defect production metrics are the starting point in this complex problem of correlating and simulating the behaviour of materials under irradiation, as direct measurements are extremely improbable. The multi-scale dimensions (nuclear-atomic-molecular-material) of the simulation process is tackled from the Fermi gradation to provide the atomic- and meso-scale dimensions with better metrics relying upon a deeper understanding and modelling capabilities of the nuclear level. Detailed, segregated primary knock-on-atom metrics are now available as the starting point of further simulation processes of isolated and clustered defects in material lattices. This allows more materials, incident energy ranges and particles, and irradiations conditions to be explored, with sufficient data to adequately cover both standard applications and novel ones, such as advanced-fission, accelerators, nuclear medicine, space and fusion. This paper reviews the theory, describes the latest methodologies and metrics, and provides recommendations for standard and novel approaches.
Published: 2019

9. Consistency of impact assessment protocols for non-native species

Author: Johanna Witzell, João Canning-Clode, Alejandro Juárez-Escario, Wolf-Christian Saul, Franz Essl, Paulo A. V. Borges, Marius Skolka, Alberto Maceda-Veiga, Carmen Morales-Rodríguez, Elena Tricarico, Eleni Kytinou, Hélia Marchante, Triya Tessa Ramburn, Pablo González-Moreno, Stefanos Kalogirou, Angeliki F. Martinou, Rumen Tomov, Ciaran Laverty, C. Romeralo, Predrag Simonović, Konstantinos Tsiamis, Giuseppe Brundu, Claudia Giuliani, Ali Serhan Tarkan, Rory Sheehan, Vanessa Lozano, Naida Muhthassim, Jan Pergl, Hugo Verreycken, Carla Rego, António O. Soares, Ahmet Uludag, Greta Srėbalienė, Fabian Reichenbach, Niki Chartosia, Wolfgang Nentwig, Tim Adriaens, Mi-Jung Bae, Lucija Šerić Jelaska, Helen E. Roy, Ana Andjelković, Jonathan M. Jeschke, Gordon H. Copp, Lorenzo Lazzaro, Z. Á. Nagy, Miquel Jover, Marie-Anne Auger-Rozenberg, Stelios Katsanevakis, Montserrat Vilà, Emili García-Berthou, Leif Sundheim, Aleksandra Kočić, Swen Follak, Mário Boieiro, Toril Loennechen Moen, Øystein Wiig, Gritta Schrader, Johan van Valkenburg, Maria Cristina Morais, Elizabeth J. Cottier-Cook, Michel Bariche, Fried Guillaume, Øivind Gammelmo, Dan Minchin, Kęstutis Arbačiauskas, Wolfgang Rabitsch, Fabio Crocetta, Ana Montero-Castaño, Bram D'hondt, Sven Bacher, Nikica Ogris, Andrea Zanetta, Hüseyin Önen, Sylvaine Giakoumi, Sandro Meyer, Frances E. Lucy, Elizabete Marchante, Bruno Foggi, Anna Maria Vettraino, Riikka Puntila, Pieter Boets, Federico Cardigos, Sonia Vanderhoeven, Belinda Gallardo, Marc Kenis, Lluís Vilar, Venche Talgø, Cristina Preda, Centre for Agricultural and Biosciences International (CABI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Estación Biológica de Doñana (EBD), Department of Biology, Northern Arizona University [Flagstaff], Ovidius University of Constanta, Research Institute for Nature and Forest (INBO), Department of Agriculture, Università degli studi di Napoli Federico II, Salmon & Freshwater Team (SFT), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Bournemouth University [Poole] (BU), Division of Conservation, Vegetation and Landscape Ecology, University of Vienna [Vienna], Universitat de Girona (UdG), Department of Marine Sciences [Aegean], University of the Aegean, Norwegian Biodiversity Information Centre, Partenaires INRAE, Institute of Technology Sligo, Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Natural Environment Research Council (NERC), Klaipėda University [Lituanie] (KU), Norwegian Institute of Bioeconomy Research (NIBIO), Service Public de Wallonie, Institute for Plant Protection and Environment, University of Novi Sad, Nature Research Centre, Unité de recherche Zoologie Forestière (URZF), Institut National de la Recherche Agronomique (INRA), Nakdonggang National Institute of Biological Resources, American University of Beirut [Beyrouth] (AUB), Provincial Centre of Environmental Research, Centre for Ecology, Evolution and Environmental Changes (CE3C), Universidade dos Açores, Marine and Environmental Sciences Centre (MARE UC), Universidade de Coimbra [Coimbra], University of the Azores, Smithsonian Environmental Research Center, University of Cyprus, Scottish Marine Institute, Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn (SZN), Austrian Agency for Health and Food Safety, Applied and Restoration Ecology Group, Pyrenean Institute of Ecology, COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Università degli Studi di Milano [Milano] (UNIMI), Plant Health Laboratory, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Biology, Faculty of Science, University of Isfahan, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Freie Universität Berlin, Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Universitat de Lleida, Hellenic Centre for Marine Research (HCMR), J.J. Strossmayer University of Osijek, Queen's University [Belfast] (QUB), Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Instituto Politécnico de Coimbra, Royal Air Forces, Department of Environmental Sciences, University of California [Los Angeles] (UCLA), University of California-University of California, Marine Organism Investigations, Universidade de Trás-os-Montes e Alto Douro, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Slovenian Forestry Institute, Gaziosmanpaşa University, Department of Invasion Ecology, Institute of Botany, Czech Academy of Sciences [Prague] (CAS), Marine Research Centre (CIMA), Regional government of Galicia, Environment Agency Austria, Simon Fraser University (SFU.ca), Sustainable Forest Management Research Institute, Universitad de Valladolid, Swedish University of Agricultural Sciences (SLU), Julius Kühn-Institut (JKI), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Muğla Sıtkı Koçman University, University of Forestry (UF), European Commission's Joint Research Centre, and MÜ
Subjects: 0106 biological sciences, environmental impact, expert judgement, invasive alien species policy, management prioritization, risk assessment, socio-economic impact, Computer science, vaikutukset, PEST RISK ANALYSIS, protocols, Plant Science, Medi ambient -- Anàlisi d'impacte, 01 natural sciences, Environmental impact, udc:630*44:630*44, Socio economic impact, SUPPORT, Statistics, Milieux et Changements globaux, lcsh:QH301-705.5, asiantuntijuus, Risk assessment, CALIBRATION, Introduced organisms, evaluation, Ecology, VDP::Landbruks- og Fiskerifag: 900, Ecological Modeling, tulokaslajit, riskinarviointi, Pest Risk Analysis, humanities, družbeno ekonomski vpliv, yhtenäisyys, ympäristövaikutukset, expertise, invazivne tujerodne vrste, Expert judgement, Espècies introduïdes, politika, tarpeet, [SDE.MCG]Environmental Sciences/Global Changes, education, INVASIVENESS SCREENING TOOL, ukrepanje, Aquatic Science, 010603 evolutionary biology, vpliv na okolje, CLASSIFICATION, Ecology and Environment, ENVIRONMENTAL-IMPACT, ocena tveganja, Invertebrate Zoology, Environmental Impact, lajit, Biological invasions, Invasions biològiques, Ecology, Evolution, Behavior and Systematics, sosioekonomiset tekijät, strokovna ocena, needs, ALIEN PLANTS, Environmental impact, expert judgement, invasive alien species policy, management prioritization, risk assessment, socio-economic impact, consistency, Impact assessment, 010604 marine biology & hydrobiology, Biology and Life Sciences, 500 Naturwissenschaften und Mathematik::590 Tiere (Zoologie)::590 Tiere (Zoologie), types and species, ECOLOGICAL IMPACTS, FRAMEWORK, Zoologie des invertébrés, protokollat, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, Environmental impact analysis, lcsh:Biology (General), Insect Science, Animal Science and Zoology, arviointi, SYSTEM
Abstract: Standardized tools are needed to identify and prioritize the most harmful non-native species (NNS). A plethora of assessment protocols have been developed to evaluate the current and potential impacts of non-native species, but consistency among them has received limited attention. To estimate the consistency across impact assessment protocols, 89 specialists in biological invasions used 11 protocols to screen 57 NNS (2614 assessments). We tested if the consistency in the impact scoring across assessors, quantified as the coefficient of variation (CV), was dependent on the characteristics of the protocol, the taxonomic group and the expertise of the assessor. Mean CV across assessors was 40%, with a maximum of 223%. CV was lower for protocols with a low number of score levels, which demanded high levels of expertise, and when the assessors had greater expertise on the assessed species. The similarity among protocols with respect to the final scores was higher when the protocols considered the same impact types. We conclude that all protocols led to considerable inconsistency among assessors. In order to improve consistency, we highlight the importance of selecting assessors with high expertise, providing clear guidelines and adequate training but also deriving final decisions collaboratively by consensus
Published: 2019
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10. Validation of EN ISO method 15216 - Part 1 – Quantification of hepatitis A virus and norovirus in food matrices

Author: Joanna Ollivier, Gwenola Hardouin, P.H. in’t Veld, Sophie Butot, Alexandre Leclercq, Bertrand Lombard, S.A. Rutjes, James A. Lowther, Albert Bosch, D. Mäde, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Universitat de Barcelona (UB), Nestlé Institute of Health Sciences SA [Lausanne, Switzerland], Laboratoire de Microbiologie, Environnement, Microbiologie et Phycotoxines (EMP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Lower Saxony State Office for Consumer Protection and Food Safety, National Institute for Public Health and the Environment [Bilthoven] (RIVM), Association Française de Normalisation (AFNOR), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Netherlands Food and Consumer Product Safety Authority (NVWA), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Biologie des Infections - Biology of Infection, Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), The validation of International Standard EN ISO 15216-1 was carried out under the framework of European Mandate No. M381 of DG SANTE and DG GROW (European Commission)., DIAKITE, andrée, Laboratoire de Microbiologie, IFREMER, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: 0301 basic medicine, Bivalve molluscan shellfish, Standardization, [SDV]Life Sciences [q-bio], MESH: Bivalvia, medicine.disease_cause, Limit of Detection, MESH: Reverse Transcriptase Polymerase Chain Reaction, Validation, Vegetables, MESH: Animals, Risk management, MESH: Shellfish, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.MHEP] Life Sciences [q-bio]/Human health and pathology, Reverse Transcriptase Polymerase Chain Reaction, General Medicine, Bottled water, Hepatitis a virus, 3. Good health, Surfaces, MESH: Reproducibility of Results, [SDV] Life Sciences [q-bio], [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, MESH: Fruit, MESH: Norovirus, 030106 microbiology, MESH: Limit of Detection, Biology, Microbiology, 03 medical and health sciences, Environmental health, MESH: Hepatitis A virus, Soft fruit, medicine, MESH: European Union, Food microbiology, Animals, Humans, European Union, MESH: Food Microbiology, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Shellfish, MESH: Humans, business.industry, International standard, Norovirus, Reproducibility of Results, Virology, MESH: Vegetables, Bivalvia, Real-time RT-PCR, [SDV.AEN] Life Sciences [q-bio]/Food and Nutrition, Fruit, Food Microbiology, Hepatitis A virus, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, [SDV.MHEP]Life Sciences [q-bio]/Human health and pathology, Food Science
Abstract: International audience; Hepatitis A virus (HAV) and norovirus are important agents of food-borne human viral illness, with common vehicles including bivalve molluscan shellfish, soft fruit and various vegetables. Outbreaks of viral illness due to contamination of the surfaces of foods, or food preparation surfaces by for example infected food handlers are also common. Virus analysis of food matrices can contribute towards risk management for these hazards and a two-part technical specification for determination of Hepatitis A virus and norovirus in food matrices (ISO/TS 15216:2013) was published jointly by the European Committee for Standardisation and the International Organization for Standardization in 2013.As part of the European Mandate No. M381 to validate 15 standards in the field of food microbiology, an international validation study involving 18 laboratories from 11 countries in Europe was conducted between 2012 and 2014. This study aimed to generate method characteristics including limit of detection, limit of quantification, repeatability and reproducibility for ISO 15216 – Part 1, the method for quantification, in seven food matrices.The organization and results of this study, including observations that led to improvements in the standard method are presented here. After its conclusion, the method characteristics generated were added to the revised international standard, ISO 15216-1:2017, published in March 2017.
Published: 2019

11. A new phylogeny and environmental DNA insight into paramyxids: an increasingly important but enigmatic clade of protistan parasites of marine invertebrates

Author: Georgia M. Ward, David Bass, Stephen W. Feist, Grant D. Stentiford, Rose Kerr, Suzanne T. Williams, Martyn Bennett, Cédric Berney, Kelly S. Bateman, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), The Natural History Museum [London] (NHM), University of Exeter, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), and Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Paramyxa, 0106 biological sciences, 0301 basic medicine, Paraphyly, Annelida, Zoology, Biology, DNA, Ribosomal, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Microscopy, Electron, Transmission, Marteilioides, Phylogenetics, Crustacea, Marteilia, RNA, Ribosomal, 18S, Animals, Cercozoa, Clade, Phylogeny, 18S rDNA phylogeny, Paramyxida, Phylogenetic tree, DNA, Protozoan, biology.organism_classification, Type species, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Infectious Diseases, Taxon, Mollusca, Eomarteilia, Parasitology, Paramarteilia, eDNA
Abstract: International audience; Paramyxida is an order of rhizarian protists that parasitise marine molluscs, annelids and crustaceans. They include notifiable pathogens (Marteilia spp.) of bivalves and other taxa of economic significance for shellfish production. The diversity of paramyxids is poorly known, particularly outside of commercially important hosts, and their phylogenetic position is unclear due to their extremely divergent 18S rDNA sequences. However, novel paramyxean lineages are increasingly being detected in a wide range of invertebrate hosts, and interest in the group is growing, marked by the first ‘Paramyxean Working Group’ Meeting held in Spain in February 2015. We review the diversity, host affiliations, and geographical ranges of all known paramyxids, present a comprehensive phylogeny of the order and clarify its taxonomy. Our phylogenetic analyses confirm the separate status of four genera: Paramarteilia, Marteilioides, Paramyxa and Marteilia. Further, as including M. granula in Marteilia would make the genus paraphyletic we suggest transferring this species to a new genus, Eomarteilia. We present sequence data for Paramyxa nephtys comb. n., a parasite of polychaete worms, providing morphological data for a clade of otherwise environmental sequences, sister to Marteilioides. Light and electron microscopy analyses show strong similarities with both Paramyxa and Paramyxoides, and we further discuss the validity of those two genera. We provide histological and electron microscopic data for Paramarteilia orchestiae, the type species of that genus originally described from the amphipod Orchestia; in situ hybridisation shows that Paramarteilia also infects crab species. We present, to our knowledge, the first known results of a paramyxid-specific environmental DNA survey of environmental (filtered water, sediment, etc.) and organismally-derived samples, revealing new lineages and showing that paramyxids are associated with a wider range of hosts and habitat types than previously known. On the basis of our new phylogeny we propose phylogenetic hypotheses for evolution of lifecycle and infectivity traits observed in different paramyxid genera.
Published: 2016

12. Radiation dose estimation for marine mussels following exposure to tritium: Best practice for use of the ERICA tool in ecotoxicological studies

Author: Bruno Fiévet, Alexandre Devos, Lorna J. Dallas, Brett P. Lyons, Awadhesh N. Jha, Andrew Turner, Plymouth University, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and Interreg 4059European Regional Development Fund, FEDER
Subjects: Water Pollutants, Radioactive, Tritiated water, [SDV]Life Sciences [q-bio], Health, Toxicology and Mutagenesis, 010501 environmental sciences, Ecotoxicology, Radiation Dosage, Tritium, 01 natural sciences, 030218 nuclear medicine & medical imaging, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Animals, Environmental Chemistry, Seawater, Waste Management and Disposal, 0105 earth and related environmental sciences, Mytilus, Radionuclide, biology, Radiation dose, General Medicine, biology.organism_classification, Pollution, chemistry, 13. Climate action, Environmental chemistry, Whole Organism
Abstract: International audience; Accurate dosimetry is critically important for ecotoxicological and radioecological studies on the potential effects of environmentally relevant radionuclides, such as tritium (3H). Previous studies have used basic dosimetric equations to estimate dose from 3H exposure in ecologically important organisms, such as marine mussels. This study compares four different methods of estimating dose to adult mussels exposed to 1 or 15 MBq L-1 tritiated water (HTO) under laboratory conditions. These methods were (1) an equation converting seawater activity concentrations to dose rate with fixed parameters; (2) input into the ERICA tool of seawater activity concentrations only; (3) input into the ERICA tool of estimated whole organism concentrations (woTACs), comprising dry activity plus estimated tissue free water tritium (TFWT) activity (TFWT volume × seawater activity concentration); and (4) input into the ERICA tool of measured whole organism activity concentrations, comprising dry activity plus measured TFWT activity (TFWT volume × TFWT activity concentration). Methods 3 and 4 are recommended for future ecotoxicological experiments as they produce values for individual animals and are not reliant on transfer predictions (estimation of concentration ratio). Method 1 may be suitable if measured whole organism concentrations are not available, as it produced results between 3 and 4. As there are technical complications to accurately measuring TFWT, we recommend that future radiotoxicological studies on mussels or other aquatic invertebrates measure whole organism activity in non-dried tissues (i.e. incorporating TFWT and dry activity as one, rather than as separate fractions) and input this data into the ERICA tool. © 2016 Elsevier Ltd.
Published: 2016

13. Taxonomy of the order Mononegavirales: update 2018

Author: Kang Seuk Choi, Nikos Vasilakis, Claudio Verdugo, Janusz T. Paweska, Thomas Briese, Víctor Manuel Neira Ramírez, Andrew J. Bennett, Masayuki Horie, Charles H. Calisher, Robert Kityo, Anthony R. Fooks, Martin Schwemmle, Sunil K. Mor, Nidia G. Aréchiga Ceballos, Timothy H. Hyndman, Ayato Takada, Yíngyún Caì, Robert A. Lamb, Alexander Bukreyev, Paul A. Rota, Tony L. Goldberg, Lin-Fa Wang, Benhur Lee, Kartik Chandran, Hideki Ebihara, Michael R. Wiley, Ralf G. Dietzgen, Anna E. Whitfield, Mark D. Stenglein, Piet Maes, Andrew J. Easton, Jean L. Patterson, Valerian V. Dolja, Olga Dolnik, Eugene V. Koonin, James F. X. Wellehan, Ralf Dürrwald, Peter L. Collins, Qisheng Song, Susan Payne, Jonathan S. Towner, Sina Bavari, Sonia Vázquez-Morón, Pierre Formenty, Sophie J. Smither, Keizō Tomonaga, Leslie L. Domier, Dàohóng Jiāng, Gael Kurath, Robert B. Tesh, Sergey V. Netesov, Elodie Ghedin, Andrea Maisner, Denise A. Marston, Cristine Campos Lawson, Elke Mühlberger, Christopher F. Basler, Conrad M. Freuling, Yǒng Zhèn Zhāng, Dennis Rubbenstroth, Peter J. Walker, Gōngyín Yè, David Wang, Ron A. M. Fouchier, Gustavo Palacios, Gary P. Kobinger, Yuri I. Wolf, Timothy Song, Hideki Kondō, Mart Krupovic, Karla Prieto, David M. Stone, Luciano M. Thomazelli, Colin A. Chapman, Ashley C. Banyard, Jens H. Kuhn, Stuart G. Siddell, Noël Tordo, John M. Dye, Terry Fei Fan Ng, Charles Y. Chiu, Kim R. Blasdell, Bertus K. Rima, Victoria Wahl, Eric M. Leroy, Gaya K. Amarasinghe, Juan Emilio Echevarría, Norbert Nowotny, Roger Hewson, Thomas Müller, Viktor E. Volchkov, Washington University School of Medicine (WUSM), University of Washington [Seattle], Laboratorio de Rabia, Instituto de Diagnóstico y Referencias Epidemiológicos, Animal and Plant Health Agency [Weybridge] (APHA), Georgia State University, University System of Georgia (USG), U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), School of Veterinary Medicine, Department of Pathobiological Sciences, University of Wisconsin-Madison-Influenza Research Institute, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, Columbia University [New York], The University of Texas Medical Branch (UTMB), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Department of Anthropology [Montréal], McGill University = Université McGill [Montréal, Canada], Wildlife Conservation Society (WCS), Primate Research Institute, Kyoto University, University of California [San Francisco] (UC San Francisco), University of California (UC), Avian Disease Research Division, Animal and Plant Quarantine Agency, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Department of Botany and Plant Pathology, Oregon State University (OSU), Center for Genome Research and Biocomputing, Philipps Universität Marburg = Philipps University of Marburg, University of Chicago, IDT Biologika, School of Life Sciences, University of Warwick [Coventry], Department of Biochemistry and Molecular Biology, University of Rochester [USA], Institute of Health Carlos III, Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Institute of Molecular Virology and Cell Biology, Federal Research Institute for Animal Health - Friedrich-Loeffler-Institut, Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Public Health England [Salisbury] (PHE), Kagoshima University, Murdoch University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University [Wuhan] (HZAU), Makerere University [Kampala, Ouganda] (MAK), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, National Center for Biotechnology Information (NCBI), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Neuromuscular Diagnostic Laboratory, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Universidad de Chile = University of Chile [Santiago] (UCHILE), Novosibirsk State University (NSU), Department of Medicine [San Francisco], University of California (UC)-University of California (UC), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], University of Bristol [Bristol], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri [Columbia] (Mizzou), University of Missouri System, Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Universidade de São Paulo - USP (BRAZIL), Institute for Virus Research, Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Facultad de Ciencias Veterinarias [Buenos Aires], Universidad de Buenos Aires [Buenos Aires] (UBA), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], University of Florida [Gainesville] (UF), University of Nebraska Medical Center, University of Nebraska System, Kansas State University, State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Albert Einstein College of Medicine, McGill University, Kyoto University [Kyoto], University of California [San Francisco] (UCSF), University of California, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Philipps University of Marburg, Warwick University, Public Health England [Porton Down, Salisbury], Huazhong Agricultural University, Makerere University (MAK), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Institut Pasteur [Paris], Centre International de Recherches Médicales de Franceville, University of Minnesota [Twin Cities], Universidad de Chile, University of California-University of California, Texas Biomedical Research Institute [San Antonio, Texas], National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], University of Bristol (School of Cellular and Molecular Medicine), University of Missouri [Columbia], Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, University of Florida [Gainesville], and Virology
Subjects: 0301 basic medicine, Order Mononegavirales, 040301 veterinary sciences, Mononegavirales Infections, 04 agricultural and veterinary sciences, General Medicine, Biology, Data science, Virology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Article, 0403 veterinary science, 03 medical and health sciences, 030104 developmental biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Humans, Animals, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), Mononegavirales, Phylogeny
Abstract: International audience; In 2018, the order Mononegavirales was expanded by inclusion of 1 new genus and 12 novel species. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV) and summarizes additional taxonomic proposals that may affect the order in the near future.
Published: 2018

14. Understanding and managing fish populations: keeping the toolbox fit for purpose

Author: J R, Paris, K D, Sherman, E, Bell, C, Boulenger, C, Delord, M B M, El-Mahdi, E A, Fairfield, A M, Griffiths, C, Gutmann Roberts, R D, Hedger, L E, Holman, L H, Hooper, N E, Humphries, I, Katsiadaki, R A, King, A, Lemopoulos, C J, Payne, G, Peirson, K K, Richter, M I, Taylor, C N, Trueman, B, Hayden, J R, Stevens, Biosciences, Swansea University, School of Life Sciences, University of Sussex, University of East Anglia, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), South Valley University, Partenaires INRAE, Bournemouth University [Poole] (BU), Norwegian Institute for Nature Research (NINA), University of Southampton, Marine Biological Association of the United Kingdom (MBA), Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Environmental and Biological Sciences, University of Eastern Finland, Department of Biology, Northern Arizona University [Flagstaff], University of Stirling, Environment Agency, BioArch-Department of Archaeology, and University of New Brunswick (UNB)
Subjects: Conservation of Natural Resources, [SDV]Life Sciences [q-bio], Population Dynamics, telemetry, Fisheries, Fishes, stable isotopes, archaeology, Congresses as Topic, Models, Biological, modelling, Policy, surveys, Animals, Interdisciplinary Communication, genetics
Abstract: 50th Anniversary Annual Symposium of the Fisheries-Society-of-the-British-Isles (FSBI) - Understanding Fish Populations Jul 03-07, 2017 Symposium paper SAMARCH project; International audience; Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of The Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50years of fisheries research.
Published: 2018

15. 1D morphodynamic modelling using a simplified grain size description

Author: André Paquier, C. Beraud, Jérôme Le Coz, Benoît Camenen, RiverLy (UR Riverly), Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Lowestoft Laboratory, and Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS)
Subjects: Field (physics), 0208 environmental biotechnology, hydraulics, Sorting, Sediment, 02 engineering and technology, Numerical models, Mechanics, Grain size, one-dimensional model, MODELE UNIDIMENSIONNEL, Physics::Geophysics, 020801 environmental engineering, sediment, Aggradation, Particle-size distribution, [SDE]Environmental Sciences, Geotechnical engineering, HYDRAULIQUE, Sediment transport, Geology, Water Science and Technology, Civil and Structural Engineering
Abstract: International audience; This paper introduces an 1D numerical code RubarBE for hydraulic and mobile-bed simulations. The code's ability to reproduce the downstream fining of a gravel-sand mixture in response to bed aggradation is tested against laboratory experiments. Unlike in most numerical models, grain size distribution in each sediment layer is not represented using a multi-class model, but using the median diameter d50 and a sorting coefficient σ. The comparison of numerical results with experimental data shows that the adaptation length La, classically used for non-equilibrium sediment transport, is an essential parameter of the model to accurately reproduce the evolution of the deposit front. Empirical laws for adjustments of d50 and σ are proposed to reproduce sediment sorting through two grain-size related adaptation lengths (Ld, Lσ ). They are scaled by the length of the reach in morphological equilibrium, which is a useful result for field applications.
Published: 2018

16. A pan-European ring trial to validate an International Standard for detection of Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus in seafoods

Author: Craig Baker-Austin, B. Serbruyns, E. Strauch, William Keay, Donatella Ottaviani, Gwenola Hardouin, Stéphanie Copin, J.-P. Rosec, E. Gyurova, Rachel Hartnell, C. Blanco, Bertrand Lombard, S. Denayer, L. Stockley, Francesca Leoni, Kinga Wieczorek, M. Lopatek, Gergana Krumova-Valcheva, Dominique Hervio-Heath, A. Britova, F. Georgsson, Alexandre Leclercq, U. Henigman, P.H. in’t Veld, H. van den Berg, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Laboratoires Ministère de l'Economie et des Finances [Montpellier], Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche (IZSUM), Institute for food hygiene and bromatology [Ljubljana, Slovenia], Institut Scientifique de Santé Publique [Belgique] - Scientific Institute of Public Health [Belgium] (WIV-ISP), Réseau International des Instituts Pasteur (RIIP), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Association Française de Normalisation (AFNOR), Netherlands Food and Consumer Product Safety Authority (NVWA), Centre National de Référence Listeria - National Reference Center Listeria (CNRL), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre collaborateur de l'OMS Listeria / WHO Collaborating Centre Listeria (CC-OMS / WHO-CC), Institut Pasteur [Paris]-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), DIAKITE, andrée, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), and Institut Pasteur [Paris] (IP)-Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], 030106 microbiology, Conventional PCR, Vibrio vulnificus, Computational biology, medicine.disease_cause, Real-Time Polymerase Chain Reaction, Microbiology, Vibrios, Oysters, 03 medical and health sciences, Hemolysin Proteins, Pan european, Species level, Isolation techniques, medicine, Animals, Biochemical methods, European Union, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Vibrio cholerae, Vibrio, biology, Vibrio parahaemolyticus, International standard, Prawns, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV] Life Sciences [q-bio], Europe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Seafood, Food Microbiology, [SDV.MP.BAC] Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Real-time PCR, Food Science
Abstract: Globally, vibrios represent an important and well-established group of bacterial foodborne pathogens. The European Commission (EC) mandated the Comite de European Normalisation (CEN) to undertake work to provide validation data for 15 methods in microbiology to support EC legislation. As part of this mandated work programme, merging of ISO/TS 21872–1:2007, which specifies a horizontal method for the detection of V. parahaemolyticus and V. cholerae, and ISO/TS 21872–2:2007, a similar horizontal method for the detection of potentially pathogenic vibrios other than V. cholerae and V. parahaemolyticus) was proposed. Both parts of ISO/TS 21872 utilized classical culture-based isolation techniques coupled with biochemical confirmation steps. The work also considered simplification of the biochemical confirmation steps. In addition, because of advances in molecular based methods for identification of human pathogenic Vibrio spp. classical and real time PCR options were also included within the scope of the validation. These considerations formed the basis of a multi-laboratory validation study with the aim of improving the precision of this ISO technical specification and providing a single ISO standard method to enable detection of these important foodborne Vibrio spp.. To achieve this aim, an international validation study involving 13 laboratories from 9 countries in Europe was conducted in 2013. The results of this validation have enabled integration of the two existing technical specifications targeting the detection of the major foodborne Vibrio spp., simplification of the suite of recommended biochemical identification tests and the introduction of molecular procedures that provide both species level identification and discrimination of putatively pathogenic strains of V. parahaemolyticus by the determination of the presence of theromostable direct and direct related haemolysins. The method performance characteristics generated in this have been included in revised international standard, ISO 21872:2017, published in July 2017.
Published: 2017

17. Validation of the OECD reproduction test guideline with the New Zealand mudsnail Potamopyrgus antipodarum using trenbolone and prochloraz

Author: Lennart Weltje, Paula Kajankari, Thomas H. Hutchinson, Laurent Lagadic, Clare Askem, Paula Sánchez-Marín, Karin Lund Kinnberg, Katharina Ruppert, Virginie Ducrot, Jörg Oehlmann, Maurine Neiman, Cornelia Geiß, Carlos M. Barroso, Daniel Faber, Peter Matthiessen, Henrik Holbech, Steve Morris, Matthias Teigeler, Olli-Pekka Penttinen, Publica, Department Aquatic Ecotoxicology, Goethe-Universität Frankfurt am Main, Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Department of Biology and CESAM, Universidade de Aveiro, Bayer Pharma AG [Berlin], Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Biology, University of Southern Denmark (SDU), University of Plymouth, Department of Environmental Sciences, Old School House, University of Iowa [Iowa City], Universidade de Vigo, Fraunhofer Institute for Molecular Biology and Applied Ecology (Fraunhofer IME), Fraunhofer (Fraunhofer-Gesellschaft), Crop Protection – Ecotoxicology, and BASF SE
Subjects: 0301 basic medicine, Health, Toxicology and Mutagenesis, [SDV]Life Sciences [q-bio], Snails, fathead minnow, standardisation, Test validity, 010501 environmental sciences, Endocrine Disruptors, Toxicology, 01 natural sciences, Anabolic Agents, Trenbolone, snail, Organisation for Economic Co-Operation and Development, media_common, biology, zebrafish danio-rerio, Reproduction, Imidazoles, General Medicine, endocrine disruption, Test (assessment), Fecundity, Female, Mollusc, Trenbolone Acetate, Potamopyrgus antipodarum, medicine.drug, Environmental Monitoring, media_common.quotation_subject, Guidelines as Topic, Management, Monitoring, Policy and Law, Risk Assessment, 03 medical and health sciences, Toxicity Tests, medicine, Animals, Gastropod, 0105 earth and related environmental sciences, fish, Test design, sexual development test, marisa-cornuarietis, mollusca hydrobiidae, toxicity, Reproducibility of Results, Guideline, biology.organism_classification, Prochloraz, Fungicides, Industrial, 030104 developmental biology, 17-beta-trenbolone, exposure, Water Pollutants, Chemical, New Zealand
Abstract: International audience; The Organisation for Economic Cooperation and Development (OECD) provides several standard test methods for the environmental hazard assessment of chemicals, mainly based on primary producers, arthropods, and fish. In April 2016, two new test guidelines with two mollusc species representing different reproductive strategies were approved by OECD member countries. One test guideline describes a 28-day reproduction test with the parthenogenetic New Zealand mudsnail Potamopyrgus antipodarum. The main endpoint of the test is reproduction, reflected by the embryo number in the brood pouch per female. The development of a new OECD test guideline involves several phases including inter-laboratory validation studies to demonstrate the robustness of the proposed test design and the reproducibility of the test results. Therefore, a ring test of the reproduction test with P. antipodarum was conducted including eight laboratories with the test substances trenbolone and prochloraz and results are presented here. Most laboratories could meet test validity criteria, thus demonstrating the robustness of the proposed test protocol. Trenbolone did not have an effect on the reproduction of the snails at the tested concentration range (nominal: 10-1000 ng/L). For prochloraz, laboratories produced similar EC10 and NOEC values, showing the inter-laboratory reproducibility of results. The average EC10 and NOEC values for reproduction (with coefficient of variation) were 26.2 A mu g/L (61.7%) and 29.7 A mu g/L (32.9%), respectively. This ring test shows that the mudsnail reproduction test is a well-suited tool for use in the chronic aquatic hazard and risk assessment of chemicals.
Published: 2017

18. Taxonomy of the order Mononegavirales : update 2017

Author: Andrew J. Easton, Gael Kurath, Jonathan S. Towner, Qi Fang, Calogero Terregino, Noël Tordo, Jean L. Patterson, John H. Werren, John M. Dye, Andrea Maisner, Qisheng Song, Peter J. Walker, Benhur Lee, Pierre Formenty, Richard E. Randall, Ralf Dürrwald, Kim R. Blasdell, Alisa Bochnowski, Bertus K. Rima, Robert A. Lamb, Paul A. Rota, Kartik Chandran, Ralf G. Dietzgen, David M. Stone, Norbert Nowotny, Hideki Kondo, Roger Hewson, Anna E. Whitfield, Janusz T. Paweska, Masayuki Horie, Peter L. Collins, Keizo Tomonaga, Martin Schwemmle, Anthony P. James, Olga Dolnik, Gary P. Kobinger, Beibei Wang, Michael N. Pearson, Nicolás Bejerman, Susan Payne, Ming Li, Jian Hong, Fei Wang, Christopher F. Basler, Robert M. Harding, Jens H. Kuhn, Ron A. M. Fouchier, Charles H. Calisher, Eric M. Leroy, Viktor E. Volchkov, Hideki Ebihara, Lin-Fa Wang, Dàohóng Jiāng, Sina Bavari, Gaya K. Amarasinghe, Ayato Takada, Sergey V. Netesov, Elke Mühlberger, Sophie J. Smither, David Wang, Gongyin Ye, Peter Revill, Martin Beer, Colleen M. Higgins, Yīmíng Bào, Robert B. Tesh, Victoria Wahl-Jensen, Thomas Briese, Zhichao Yan, Dennis Rubbenstroth, Elodie Ghedin, Alexander Bukreyev, Nikos Vasilakis, Virology, Washington University School of Medicine (WUSM), University of Washington [Seattle], National Center for Biotechnology Information (NCBI), Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute of Diagnostic Virology (IVD), Friedrich-Loeffler-Institut (FLI), Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de la Patagonia Austral (UNPA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Columbia Mailman School of Public Health, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Department of Biochemistry and Molecular Biology, University of Rochester [USA], State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Public Health England [Salisbury] (PHE), Auckland University of Technology (AUT), Infections Virales et Pathologie Comparée - UMR 754 (IVPC), Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Icahn School of Medicine at Mount Sinai [New York] (MSSM), Centre International de Recherches Médicales de Franceville (CIRMF), Institute for Applied Ecology New Zealand (AENZ), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), University of Auckland [Auckland], Biomedical Sciences Research Complex [St Andrews, Scotland] (BSRC), University of St Andrews [Scotland], Victorian Infectious Diseases Reference Laboratory, Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), University of Missouri School of Medicine, University of Missouri System, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur [Paris], Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Washington University School of Medicine, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Department of Biology, Kansas State University, Albert Einstein College of Medicine, Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Institut National de la Recherche Agronomique (INRA)-École pratique des hautes études (EPHE)-Université Claude Bernard Lyon 1 (UCBL), Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Institute for Applied Ecology New Zealand, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), The University of Auckland, Centre for Experimental Medicine [Queen’s University of Belfast], Hokkaido University, Istituto Zooprofilattico Sperimentale delle Venezie, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Queensland University of Technology [Brisbane] (QUT), Institut National de la Recherche Agronomique (INRA)-École Pratique des Hautes Études (EPHE), Huazhong Agricultural University [Wuhan] (HZAU), Victorian Infectious Diseases Reference Laboratory [Melbourne, Australia] (VIDRL), Kyoto University, Institut Pasteur [Paris] (IP), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Biomedical Sciences Research Complex
Subjects: 0301 basic medicine, 030106 microbiology, Genome, Viral, Article, 03 medical and health sciences, Species Specificity, Genus, Phylogenetics, Virology, Gene Order, Viral, Mononegavirales, Phylogeny, Order Mononegavirales, Genome, biology, General Medicine, Pneumovirus, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Evolutionary biology, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology)
Abstract: International audience; In 2017, the order Mononegavirales was expanded by the inclusion of a total of 69 novel species. Five new rhabdovirus genera and one new nyamivirus genus were established to harbor 41 of these species, whereas the remaining new species were assigned to already established genera. Furthermore, non-Latinized binomial species names replaced all paramyxovirus and pneumovirus species names, thereby accomplishing application of binomial species names throughout the entire order. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Published: 2017

19. Hepatocellular adenoma in a European flatfish (Limanda limanda): genetic alterations in laser-capture micro-dissected tissue and global transcriptomic approach †a Adélaïde Lerebours, †

Author: Lerebours, Adélaïde, Chapman, Emma, Lyons, Brett, Bignell, John, Stentiford, Grant, Rotchell, Jeanette, University of Hull [United Kingdom], Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and School of Biological, Biomedical and Environmental Sciences
Subjects: fish, liver cancer, genetic changes, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, retinoblastoma gene, contaminants, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Liver tumours in flatfish have been diagnosed using histopathology for decades to monitor the impacts of marine pollution. Here we describe the application of specific gene (retinoblastoma, Rb) profiling in laser capture micro-dissected samples, and a suppression subtractive hybridization (SSH) approach to isolate differentially expressed genes in hepatocellular adenoma (HCA) samples from dab, Limanda limanda.The Rb profiles from apparently normal and HCA micro-dissected samples of fish from the North Sea showed no significant difference, and genotypic heterogeneity within defined histological phenotypes was observed. In the SSH, sequences associated with cell signalling, cell cycle, gene expression regulation, protein transport and protein degradation were isolated. These included up-regulation of arrestin domain containing 3 (arrdc3), Rac-1 and tribbles, and down-regulation of ankyrin repeat/sterile alpha-motif domain-containing protein 1B-like (ANKS1B-like), c-fos, CDKN1B and RhoA-like sequences, previously implicated in mammalian HCA. This study offers new candidates involved in fish liver tumour development.
Published: 2017

20. Epidemiological characteristics of infectious hematopoietic necrosis virus (IHNV): a review

Author: Birgit Oidtmann, Richard Paley, P. F. Dixon, Raúl Alegría-Morán, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and Universidad de Chile = University of Chile [Santiago] (UCHILE)
Subjects: Infectious hematopoietic necrosis virus, 0301 basic medicine, [SDV]Life Sciences [q-bio], Salmo salar, Context (language use), Review, Fish Diseases, 03 medical and health sciences, Rhabdoviridae Infections, Animals, media_common.cataloged_instance, 14. Life underwater, European union, Salmo, Pathogen, media_common, Subclinical infection, General Veterinary, biology, Transmission (medicine), Infectious dose, biology.organism_classification, veterinary(all), Virology, 3. Good health, 030104 developmental biology, Oncorhynchus mykiss, Immunology
Abstract: Infectious hematopoietic necrosis virus (IHNV, Rhabdoviridae), is the causative agent of infectious hematopoietic necrosis (IHN), a disease notifiable to the World Organisation for Animal Health, and various countries and trading areas (including the European Union). IHNV is an economically important pathogen causing clinical disease and mortalities in a wide variety of salmonid species, including the main salmonid species produced in aquaculture, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss). We reviewed the scientific literature on IHNV on a range of topics, including geographic distribution; host range; conditions required for infection and clinical disease; minimum infectious dose; subclinical infection; shedding of virus by infected fish; transmission via eggs; diagnostic tests; pathogen load and survival of IHNV in host tissues. This information is required for a range of purposes including import risk assessments; parameterisation of disease models; for surveillance planning; and evaluation of the chances of eradication of the pathogen to name just a few. The review focuses on issues that are of relevance for the European context, but many of the data summarised have relevance to IHN globally. Examples for application of the information is presented and data gaps highlighted. Electronic supplementary material The online version of this article (doi:10.1186/s13567-016-0341-1) contains supplementary material, which is available to authorized users.
Published: 2016

21. Empirical observations of the spawning migration of European eels: The long and dangerous road to the Sargasso Sea

Author: Kim Aarestrup, Finn Økland, Anthony Acou, Janek Simon, Håkan Westerberg, David Righton, Thomas Trancart, Eric Feunteun, Niklas Sjöberg, Patrick G. Gargan, Uwe Brämick, Marisa Vedor, Elsa Amilhat, Alan Walker, Javier Lobón-Cerviá, Julian D. Metcalfe, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Institute of Freshwater Research, Department of Aquatic Resources, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), Muséum national d'Histoire naturelle (MNHN), Norwegian Institute for Nature Research (NINA), Inland Fisheries Ireland, Centre de Formation et de Recherche sur les Environnements Méditérranéens (CEFREM), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Inland Fisheries, Universidade do Porto, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Technical University of Denmark [Lyngby] (DTU), Université de Perpignan Via Domitia (UPVD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), European Commission, Department for Environment, Food & Rural Affairs (UK), Ministère de l'Écologie, du Développement durable et de l'Énergie (France), Federal Ministry of Food and Agriculture (Germany), Norwegian Institute for Nature Research, Institute of Marine Research (Sweden), Fundação para a Ciência e a Tecnologia (Portugal), Ministério da Educação e Ciência (Portugal), Generalitat Valenciana, and CSIC - Unidad de Recursos de Información Científica para la Investigación (URICI)
Subjects: 0106 biological sciences, Male, electronic tags, oceanic migration, Oceans and Seas, eel, spawning, ComputingMilieux_LEGALASPECTSOFCOMPUTING, tagging, escapement, 010603 evolutionary biology, 01 natural sciences, Predation, Behavioral Ecology, European eels, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Sargasso sea, Animals, 14. Life underwater, education, vertical migration, Diel vertical migration, Escapement, Research Articles, Electronic tags, animal migration, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, Multidisciplinary, Eels, Ecology, 010604 marine biology & hydrobiology, Reproduction, SciAdv r-articles, Spawn (biology), Fishery, Geography, Oceanography, Electronic tagging, Fish and Aquacultural Science, electronic tagging, Female, predation, Zoology, Sargasso Sea, Research Article
Abstract: This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license.-- et al., The spawning migration of the European eel (Anguilla anguilla L.) to the Sargasso Sea is one of the greatest animal migrations. However, the duration and route of the migration remain uncertain. Using fishery data from 20 rivers across Europe, we show that most eels begin their oceanic migration between August and December. We used electronic tagging techniques to map the oceanic migration from eels released from four regions in Europe. Of 707 eels tagged, we received 206 data sets. Many migrations ended soon after release because of predation events, but we were able to reconstruct in detail the migration routes of >80 eels. The route extended from western mainland Europe to the Azores region, more than 5000 km toward the Sargasso Sea. All eels exhibited diel vertical migrations, moving from deeper water during the day into shallower water at night. The range of migration speeds was 3 to 47 km day−1. Using data from larval surveys in the Sargasso Sea, we show that spawning likely begins in December and peaks in February. Synthesizing these results, we show that the timing of autumn escapement and the rate of migration are inconsistent with the century-long held assumption that eels spawn as a single reproductive cohort in the springtime following their escapement. Instead, we suggest that European eels adopt a mixed migratory strategy, with some individuals able to achieve a rapid migration, whereas others arrive only in time for the following spawning season. Our results have consequences for eel management., Most of the work described in this paper was funded under Grant Agreement GOCE-2008212133 (EELIAD) of the European Union FP7 research program on the environment (including climate change) and prepared under project no. 212133 (eeliad). National and regional governments also provided in-kind funding to support the work including the U.K. Department for Environment, Food, and Rural Affairs (to D.R., J.D.M., and A.W.); the French Ministry of Ecology, Sustainable Development, and Energy (to E.A.); the German Ministry of Agriculture and Environment of the federal state Saxony-Anhalt; the German Ministry of Agriculture, Environment, and Consumer Protection Mecklenburg-Vorpommern (to J.S. and U.B.); the Inland Fisheries Ireland (to P.G.); the Norwegian Institute for Nature Research (to F.Ø.); the Swedish Board of Fisheries (latterly Swedish University of Agricultural Sciences to H.W. and N.S.); the Villum Kann Rasmussen/Elisabeth and Knud Petersen’s Foundations (to K.A.); the Fundo Social Europeu/Ministério da Educação e Ciência; and the Portuguese Science and Technology Foundation (FCT) through PhD grant PD/BD/52603/2014 (to M.V.). In-kind support was provided by the Consejeria de Medio Ambiente de la Generalitat de Valencia, Spain., We acknowledge support of the publication fee by the CSIC Open Access Publication Support Initiative through its Unit of Information Resources for Research (URICI).
Published: 2016

22. Taxonomy of the order Mononegavirales: update 2016

Author: Ralf Dürrwald, Krisztián Bányai, Robert A. Lamb, Hideki Kondo, Alexander Bukreyev, Anna N. Clawson, Calogero Terregino, Robert B. Tesh, Andrew J. Easton, Andrea Maisner, Paul A. Rota, Gael Kurath, Kartik Chandran, Charles H. Calisher, Ralf G. Dietzgen, Janusz T. Paweska, Szilvia Marton, Dennis Rubbenstroth, Masayuki Horie, Juliana Freitas-Astúa, Bertus K. Rima, Jonathan S. Towner, Viktor E. Volchkov, Eric M. Leroy, David M. Stone, Susan Payne, Kwok-Yung Yuen, Hideki Ebihara, Lin-Fa Wang, Lìjiāng Liú, C. Li, Nikos Vasilakis, Olga Dolnik, Gaya K. Amarasinghe, Gary P. Kobinger, Jean L. Patterson, Sergio Lenardon, Xian Dan Lin, Leslie L. Domier, Mang Shi, Pierre Formenty, Ben Longdon, Anna E. Whitfield, Sina Bavari, Timothy H. Hyndman, Martin Verbeek, E. W. Kitajima, Elke Mühlberger, Peter J. Walker, Ayato Takada, Mark D. Stenglein, François Xavier Briand, David Wang, Elodie Ghedin, Jiāsēn Chéng, Keizo Tomonaga, Norbert Nowotny, Roger Hewson, Noël Tordo, Jun Hua Tian, Nicolás Bejerman, John M. Dye, Christopher F. Basler, Yong-Zhen Zhang, Kim R. Blasdell, Yanping Fu, Sophie J. Smither, Richard E. Randall, Jens H. Kuhn, Jiǎtāo Xiè, Victoria Wahl-Jensen, Thierry Wetzel, Martin Schwemmle, Michael M. Goodin, John A. Walsh, Thomas Briese, Yīmíng Bào, Peter L. Collins, Dàohóng Jiāng, Sergey V. Netesov, Ron A. M. Fouchier, Szilvia L. Farkas, Claudio L. Afonso, US Department of Agriculture, Washington University School of Medicine (WUSM), University of Washington [Seattle], Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA), National Center for Biotechnology Information (NCBI), Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Instituto Nacional de Tecnología Agropecuaria, Universidad Nacional de la Patagonia Austral (UNPA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Columbia Mailman School of Public Health, The University of Texas Medical Branch (UTMB), Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University System, Albert Einstein College of Medicine [New York], Huazhong Agricultural University, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Queensland Alliance for Agriculture and Food Innovation - Centre for Animal Science, University of Queensland [Brisbane], Philipps University of Marburg, University of Illinois [Chicago] (UIC), University of Illinois System, IDT Biologika, School of Life Sciences, Warwick University, Laboratory of Persistent Viral Diseases, LABOKLIN, Embrapa Cassava and Fruits, Brazilian Agricultural Research Corporation (Embrapa), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Department of Plant Pathology, University of Kentucky, University of Kentucky, Public Health England [Salisbury] (PHE), Kagoshima University, School of Veterinary and Life Sciences [Murdoch], Murdoch University, State Key Laboratory of Agricultural Microbiology, Escola Superior de Agricultura 'Luiz de Queiroz' (ESALQ), Universidade de São Paulo (USP), Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), State Key Laboratory for Infectious Disease prevention and Control, Beijing Institute of Technology (BIT), Wēnzhōu Center for Disease Control and Prevention, Department of Genetics University of Cambridge, University of Cambridge [UK] (CAM), Boston University School of Medicine (BUSM), Boston University [Boston] (BU), Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], College of Veterinary Medicine and Biomedical Sciences, National Institute for Communicable Diseases [Johannesburg] (NICD), Biomedical Sciences Research Complex [St Andrews, Scotland] (BSRC), University of St Andrews [Scotland], Queen's University [Belfast] (QUB), National Center for Immunization and Respiratory Diseases, CDC, Centers for Disease Control and Prevention (CDC), University of Freiburg [Freiburg], Chinese Center for Disease Control and Prevention, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Colorado State University [Fort Collins] (CSU), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Wǔhàn Center for Disease Control and Prevention, Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur [Paris], Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Wageningen University and Research [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Departments of Molecular Microbiology and Pathology & Immunology, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Kansas State University, State Key Laboratory of Emerging Infectious Diseases & Department of Microbiology, The University of Hong Kong (HKU)-Li Ka Shing Faculty of Medicine, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong (HKU), French Agency for Food, Environmental and Occupational Health & Safety (Anses) - Veterinary epidemiology, Albert Einstein College of Medicine, Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Hokkaido University, Istituto Zooprofilattico Sperimentale delle Venezie [Padova], Wageningen University and Research Centre [Wageningen] (WUR), Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Duke NUS Medical School, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], Huazhong Agricultural University [Wuhan] (HZAU), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], University of Kentucky (UK), Universidade de São Paulo = University of São Paulo (USP), Kyoto University, Institut Pasteur [Paris] (IP), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Virology, and Biomedical Sciences Research Complex
Subjects: 0301 basic medicine, 030106 microbiology, Zoology, Genome, Viral, Article, 03 medical and health sciences, Genus, Phylogenetics, Virology, Crustavirus, Life Science, Viral, Mononegavirales, Phylogeny, Order Mononegavirales, QR355, Genome, biology, Entomology & Disease Management, General Medicine, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Pneumoviridae, Subfamily Pneumovirinae, MONONEGAVIRALES, 030104 developmental biology, Evolutionary biology, Wildlife Ecology and Conservation, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Taxonomy (biology), RA, RC
Abstract: International audience; In 2016, the order Mononegavirales was emended through the addition of two new families (Mymonaviridae and Sunviridae), the elevation of the paramyxoviral subfamily Pneumovirinae to family status (Pneumoviridae), the addition of five free-floating genera (Anphevirus, Arlivirus, Chengtivirus, Crustavirus, and Wastrivirus), and several other changes at the genus and species levels. This article presents the updated taxonomy of the order Mononegavirales as now accepted by the International Committee on Taxonomy of Viruses (ICTV).
Published: 2016

23. Do non-native pumpkinseed Lepomis gibbosus affect the growth, diet and trophic niche breadth of native brown trout Salmo trutta?

Author: Jean-Marc Roussel, Zhiqiang Guo, Gordon H. Copp, Julien Cucherousset, Rodolphe E. Gozlan, M. G. Godard, Saulius Stakėnas, Michelle C. Jackson, John Robert Britton, Bournemouth University [Poole] (BU), Centre for Invasion Biology, Department of Zoology and Entomology, University of Pretoria (UPSpace), Salmon & Freshwater Team (SFT), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Chinese Academy of Sciences (CAS), Vilnius University, Muséum national d'Histoire naturelle (MNHN), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and TULIP (ANR -10-LABX-41)
Subjects: 0106 biological sciences, Stable isotope analysis, [SDV]Life Sciences [q-bio], Population, Alien species, Small streams, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, Lepomis, Food chain, Brown trout, Environmental Science(all), Introduced species, Ecological consequences, 14. Life underwater, Salmo, education, Circular statistics, Trophic level, education.field_of_study, biology, Ecology, 010604 marine biology & hydrobiology, Interspecific competition, Environmental impacts, biology.organism_classification, Pollution, Animal ecology
Abstract: International audience; Brown trout Salmo trutta Linnaeus, 1758, is a priority species for conservation and management efforts in many European countries. In its native range, interactions with non-native fishes often adversely affect somatic growth rates and population abundances. Consequences of introduced North American pumpkinseed Lepomis gibbosus (Linnaeus, 1758) for native S. trutta were examined in stream stretches with and without L. gibbosus. Data for somatic growth rates and trophic niche breadth (using stable isotope analyses) provided little evidence of L. gibbosus presence being detrimental for S. trutta. Shifts in S. trutta diet at all sites were associated with increased piscivory with increasing body length, with no evidence to suggest that interspecific resource competition with L. gibbosus structured the food web or affected trophic positions. Three years later, and following L. gibbosus removal, data revealed slight shifts in the food web at each site, but these related to shifts in resources at the bottom of the food chain rather than a response to L. gibbosus removal. Consequently, the ecological consequences of L. gibbosus for S. trutta in the study stream were minimal, with S. trutta populations responding more to natural mechanisms regulating their populations than to the presence of this non-native fish species.
Published: 2016

24. First evidence of European eels exiting the Mediterranean Sea during their spawning migration

Author: Kim Aarestrup, Elisabeth Faliex, David Righton, Håkan Westerberg, Gaël Simon, Elsa Amilhat, Centre de Formation et de Recherche sur les Environnements Méditérranéens (CEFREM), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), Institute of Freshwater Research, Department of Aquatic Resources, Swedish University of Agricultural Sciences (SLU)-Swedish University of Agricultural Sciences (SLU), and Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS)
Subjects: 0106 biological sciences, Mediterranean climate, Multidisciplinary, Behavioural ecology, Mesopelagic zone, [SDV.BA]Life Sciences [q-bio]/Animal biology, 010604 marine biology & hydrobiology, Animal migration, 010603 evolutionary biology, 01 natural sciences, Article, Spawning site, Predation, Deep water, Fishery, Geography, Mediterranean sea, Diel vertical migration, Escapement
Abstract: International audience; The migration route and the spawning site of the European eel Anguilla anguilla are still uncertain. It has been suggested that the Mediterranean eel stock does not contribute to spawning because there is no evidence of eels leaving the Mediterranean Sea. To test this hypothesis, we equipped eight female silver eels from the south of France with pop-up satellite tags during escapement from coastal waters. Once in deeper water, the eels quickly established diel vertical migration (DVM) between the upper and lower mesopelagic zone. Five tagged eels were taken by predators within the Mediterranean, but two eels reached the Atlantic Ocean after six months and at distances greater than 2000 km from release. These eels ceased their DVM while they negotiated the Gibraltar Strait, and remained in deep water until they reached the Atlantic Ocean, when they recommenced DVM. Our results are the first to show that eels from Mediterranean can cross the Strait of Gibraltar and continue their migration into the Atlantic Ocean. This finding suggests that Mediterranean countries, as for other EU states, have an important role to play in contributing to conservation efforts for the recovery of the European eel stock. Although European eels are found in fresh and brackish waters throughout Europe and North Africa, they escape to sea to spawn towards the end of their lives. European eels, like American eels, are presumed to spawn in the Sargasso Sea, where eel larvae of both species are found in the greatest abundance 1–3. The evidence for a single spawning area is strong and modern genetic studies indicate a panmictic species 4,5. European eels therefore need to undertake a spawning migration of at least 5000 km from the western margin of the continental habitat in Europe; this distance is much greater for eels escaping from more easterly locations, including those in the Baltic and Mediterranean Seas. However, despite the advent of marine remote sensing, genetic and otolith analyses, electronic tagging, and investigative computer modelling in the century since Schmidt 3
Published: 2016

25. The Large Subunit rDNA Sequence of Plasmodiophora brassicae Does not Contain Intra-species Polymorphism

Author: Schwelm, Arne, Berney, Cédric, Dixelius, Christina, Bass, David, Neuhauser, Sigrid, Swedish University of Agricultural Sciences (SLU), University of Innsbruck, The Natural History Museum [London] (NHM), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and Leopold Franzens Universität Innsbruck - University of Innsbruck
Subjects: pathotyping, plas- modiophorids, Clubroot, LSU rDNA, fungi, FISH (fluorescence in-situ hybridisation), food and beverages, phytomyxea, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, plasmodiophorids, Microbiology
Abstract: International audience; Clubroot disease caused by Plasmodiophora brassicae is one of the most important diseases of cultivated brassicas. P. brassicae occurs in pathotypes which differ in the aggressiveness towards their Brassica host plants. To date no DNA based method to distinguish these pathotypes has been described. In 2011 polymorphism within the 28S rDNA of P. brassicae was reported which potentially could allow to distinguish pathotypes without the need of time-consuming bioassays. However, isolates of P. brassicae from around the world analysed in this study do not show polymorphism in their LSU rDNA sequences. The previously described polymorphism most likely derived from soil inhabiting Cer-cozoa more specifically Neoheteromita-like glissomonads. Here we correct the LSU rDNA sequence of P. brassicae. By using FISH we demonstrate that our newly generated sequence belongs to the causal agent of clubroot disease.
Published: 2016

26. Benthic protists: the under-charted majority

Author: Diana Sarno, Nathalie Simon, John R. Dolan, Adriana Zingone, Patrick Wincker, Jan Pawlowski, Wiebe H. C. F. Kooistra, Bente Edvardsen, Marina Montresor, Fabrice Not, Colomban de Vargas, Thorsten Stoeck, Ramiro Logares, Elianne Egge, Sarah Romac, Stéphane Audic, Thomas A. Richards, Micah Dunthorn, Wenche Eikrem, Ramon Massana, Johan Decelle, Richard Christen, Hiroyuki Ogata, Dominik Forster, Kamran Shalchian-Tabrizi, Massimo C. Pernice, Raffaele Siano, Lucie Bittner, Jean-Michel Claverie, Frédéric Mahé, Daniel Vaulot, Angélique Gobet, David Bass, Christophe Boutte, Sébastien Santini, University of Kaiserslautern [Kaiserslautern], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), The Natural History Museum [London] (NHM), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (Cefas), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), Symbiose Marine (SM), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), University of Oslo (UiO), Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), Stazione Zoologica Anton Dohrn (SZN), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Diversité et Interactions au sein du Plancton Océanique (DIPO), Kyoto University [Kyoto], Department of Genetics and Evolution [Genève], University of Geneva [Switzerland], University of Exeter, Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Stipendienstiftung Rheinland-Pfalz, European Commission, German Research Foundation, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Université de Genève = University of Geneva (UNIGE), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Microbial Ecology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie virtuelle, COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015 - 2019) (COMUE UCA), Max Planck Institute for Biological Cybernetics, Max-Planck-Gesellschaft, Marine Botany, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Department of genetics and evolution, School of Geography and Environmental, Monash University, Monash University [Clayton], Dynamiques de l'Environnement Côtier (DYNECO), Commissariat à l'Energie Atomique, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0106 biological sciences, 0301 basic medicine, Aquatic Organisms, Geologic Sediments, Foraminifera, medicine.disease_cause, 01 natural sciences, Applied Microbiology and Biotechnology, 18S ribosomal RNA, Benthic microbial communities, Sequence Read Archive, Phylogeny, High-throughput sequencing, Ecology, Protist, high-throughput sequencing, Biodiversity, Plankton, respiratory system, protist diversity, Benthic zone, geographic locations, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Hydrothermal Vents, benthic microbial communities, coastal environments, parasitic diseases, RNA, Ribosomal, 18S, medicine, 14. Life underwater, Ecosystem, Diatoms, Base Sequence, 010604 marine biology & hydrobiology, fungi, DNA, Sequence Analysis, DNA, 030104 developmental biology, Taxon, Protist diversity, Reference database, Coastal environments, Species richness, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities
Abstract: Forster, Dominik ... et al.-- 11 pages, 6 figures, 1 table, supplementary data http://femsec.oxfordjournals.org/content/suppl/2016/06/05/fiw120.DC1, Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbor greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and benthic communities, as well as between separate benthic communities. We argue that these patterns reflect the heterogeneity and diversity of benthic habitats. A comparison of all OTUs against the Protist Ribosomal Reference database showed that a higher proportion of benthic than planktonic protist diversity is missing from public databases; similar results were obtained by comparing all OTUs against environmental references from NCBI's Short Read Archive. We suggest that the benthic realm may therefore be the world's largest reservoir of marine protist diversity, with most taxa at present undescribed, This work was supported by the European Commission and is part of the EU-FP7 ERA-net program BiodivERsA, under the project BioMarKs [2008-6530]. Dominik Forster was supported by a graduate scholarship of Stipendienstiftung Rheinland-Pfalz. Micah Dunthorn and Frédéric Mahé were supported by the Deutsche Forschungsgemeinschaft [grant #DU1319/1-1]. Thorsten Stoeck was supported by the Deutsche Forschungsgemeinschaft [grant #STO414/11-1]. Daniel Vaulot was supported by the European Union [grants MicroB3/FP7-287589, MaCuMBA/FP7-KBBE-2012-6-311975]
Published: 2016

27. Biomarker responses in wild three-spined stickleback (Gasterosteus aculeatus L.) as a useful tool for freshwater biomonitoring: A multiparametric approach

Author: Ioanna Katsiadaki, Wilfried Sanchez, Benjamin Piccini, Jean-Marc Porcher, Jean-Maxence Ditche, Institut National de l'Environnement Industriel et des Risques (INERIS), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Délégation Inter-Régionale Nord Ouest, and Office National de l'eau et des milieux aquatiques
Subjects: Three-spined stickleback, Endocrine System, Fresh Water, Gasterosteus, 010501 environmental sciences, FIELD STUDY, Nervous System, 01 natural sciences, Xenobiotics, 03 medical and health sciences, chemistry.chemical_compound, FISH, Biomonitoring, ENDOCRINE DISRUPTION, Water Pollution, Chemical, Animals, Ecotoxicology, 14. Life underwater, Population dynamics of fisheries, lcsh:Environmental sciences, Biotransformation, 030304 developmental biology, 0105 earth and related environmental sciences, General Environmental Science, lcsh:GE1-350, 0303 health sciences, biology, Ecology, Aquatic ecosystem, Stickleback, biology.organism_classification, Smegmamorpha, Oxidative Stress, THREE-SPINED STICKLEBACK, chemistry, NEUROTOXICITY, [SDE]Environmental Sciences, BIOTRANSFORMATION ENZYMES, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, France, Xenobiotic, Biomarkers, Environmental Monitoring
Abstract: The biochemical response of wild sticklebacks collected in Autumn 2005 at seven stations in the North of France was studied using a set of complementary biomarkers. Here, data on biotransformation of xenobiotics, oxidative stress exposure and damages, neurotoxicity and endocrine disruption are provided. All the sites are characterized by a specific response pattern that allows distinguishing sampling locations. Moreover, these responses are in accordance with data on existing environmental pressures and the chemical analysis of metals performed in surface water. The assessment of individual responses is completed by fish population disturbance monitoring. Based on these measurements, the investigated sites are characterized by different levels of disturbance. This study argues for a multi-parametric approach of aquatic ecosystem contamination based on association between chemical, biochemical and ecological endpoints and provides a testimony of the usefulness of stickleback for this purpose. Keywords: Three-spined stickleback, Biomarkers, Fish, Biotransformation enzymes, Oxidative stress, Neurotoxicity, Endocrine disruption
Published: 2008

28. The Ocean Sampling Day Consortium

Author: Oleksandra Bobrova, Petra ten Hoopen, Rodrigo Costa, Rania Siam, Rehab Z. Abdallah, Jorge A. Herrera Silveira, Catarina Magalhães, Nedime Serakinci, Marie E. DeLorenzo, Riccardo Rosselli, Paul Malthouse, Lise Øvreås, Eyjólfur Reynisson, Susan Gebbels, Francesca Malfatti, Frank Oliver Glöckner, Federico M. Lauro, Hans Erik Karlsen, David Wallom, Christian Jeanthon, Mark J. Costello, Fergal O'Gara, Nadezhda Todorova, Ana C. Costa, Monia El Bour, Paul D. van Ruth, Ivaylo Kostadinov, Martin Ostrowski, Jed A. Fuhrman, Viggo Marteinsson, Thierry Cariou, Hiroyuki Ogata, Maria Luiza Pedrotti, Emilie Villar, Federico Baltar, Sandi Orlić, Valentina Turk, Katja Lehmann, Dawn Field, Renzo Kottmann, Florence Jude-Lemeilleur, Daniel Vaulot, Alessandro Vezzi, Neil M Davies, Mahrous M. Kandil, Véronique Berteaux-Lecellier, Christopher D. Sinigalliano, Timothy W. Davis, Peter N. Golyshin, Stéphane L'Haridon, Jonathan A. Martinez, Sandra Ramos, Pascal Conan, Ma. Leopoldina Aguirre-Macedo, Antonio Fernandez-Guerra, Soumya Essayeh, Clara Loureiro, Edvardsen Bente, Noureddine Boukhatem, Rachelle M. Jensen, Sophie Pitois, Bouchra Chaouni, Kate Munnik, Anke Kremp, Stephane Pesant, Roberto Danovaro, Cecilia Alonso, Said Barrijal, Jodie van de Kamp, Michail M. Yakimov, Nicole J. Poulton, Zackary I. Johnson, Adriana Zingone, Bernardo Duarte, Ilkay Salihoglu, Paraskevi N. Polymenakou, Jack A. Gilbert, Melody S. Clark, Ian Salter, Hassan Ghazal, Julie LaRoche, J. Mortelmans, Ranjith Edirisinghe, Grazia Marina Quero, Dion Matthew Frederick Frampton, Isabel Caçador, Georgios Tsiamis, Declan C. Schroeder, Jamie Hinks, Ana Martins, Noga Stambler, Rachel Collin, João Canning-Clode, Tinkara Tinta, Mesude Bicak, Scott Jones, Valentina Amaral, Matthias S. Ullrich, Gunnar Gerdts, Klaas Deneudt, Michael Steinke, Mohamed Bennani, Rafael Santana, Fabio De Pascale, Jennifer Tolman, Juan Iriberri, Levente Bodrossy, Abderrahim Bouali, Antonella Penna, Bruno Cataletto, Josep M. Gasol, Florencia Biancalana, Maribeth L. Gidley, Stephen A. Jackson, Mahmut Cerkez Ergoren, Carolin R. Löscher, Antje Wichels, Ventzislav Karamfilov, R. Eric Collins, Sara Ettamimi, Riccardo Schiavon, Mohammed Timinouni, Christina Bienhold, Julia Schnetzer, Marc E. Frischer, Wayne J. Fuller, Simon Claus, Ibon Cancio, Guy Cochrane, Patrick Martin, Gian Marco Luna, Snejana Moncheva, Linda A. Amaral-Zettler, Eva C. Sonnenschein, Paul Anders Fronth Nyhus, Shiao Y. Wang, Antonina Dos Santos, Eyal Rahav, Eileen Bresnan, Anna Kopf, Barker Katherine, Michèle Barbier, Naiara Rodríguez-Ezpeleta, Kemal Can Bizsel, Tim Ingleton, Patricia Wecker, Julia A. Busch, Kelly D. Goodwin, El Houcine Zaid, Rajaa Chahboune, Takashi Yoshida, Fatima El Otmani, Marianna Mea, Nina Dzhembekova, Anne-Lise Ducluzeau, Christopher P. Meyer, Georgios Kotoulas, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Jacobs University [Bremen], University of Oxford, Centre for Ecology & Hydrology, Oxfordshire UK, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Israel Oceanographic and Limnological Research (IOLR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Hellenic Centre for Marine Research (HCMR), American University in Cairo, Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University College Cork (UCC), Curtin University [Perth], Planning and Transport Research Centre (PATREC), Institut Ruder Boskovic, Institut Ruđer Bošković (IRB), University of Essex, Carl Von Ossietzky Universität Oldenburg = Carl von Ossietzky University of Oldenburg (OFFIS), Universidade de Lisboa = University of Lisbon (ULISBOA), Smithonian Environmental Research Center, Research Center, Odessa National I.I.Mechnikov University, Matis Ltd, Universidade dos Açores, Istituto di Science Marine (ISMAR ), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Finnish Environment Institute (SYKE), National Oceanic and Atmospheric Administration (NOAA), University of Bergen (UiB), Dalhousie University [Halifax], Università di Urbino, Skidaway Institute of Oceanography, Smithsonian Institution, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mississippi State University [Mississippi], Bigelow Laboratory for Ocean Sciences, Smithsonian Marine Station, Smithsonian Tropical Research Institute, University of Southern California (USC), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Universidad de la República [Montevideo] (UDELAR), Bar-Ilan University [Israël], The Interuniversity Institute for marine Science in Eilat, IAMC-CNR, Istituto per l'Ambiente Marino Costiero &ndash, University of Otago [Dunedin, Nouvelle-Zélande], Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Macquarie University, South Australian Research and Development Institute (SARDI), South Australian Research and Development Institute, Flanders Marine Institute, VLIZ, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), University of Algarve [Portugal], Marine Biological Association of the UK, Department of Chemistry, Alexandria University [Alexandrie], Argentine Institute of Oceanography, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of Tasmania [Hobart, Australia] (UTAS), Waters, wetlands & coasts Sydney, Lwande technologies Cape Town, AZTI (AZTI), AZTI, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU), Université Mohammed Premier [Oujda], Université Mohammed V de Rabat [Agdal] (UM5), Université Sidi Mohamed Ben Abdellah (USMBA), Université Abdelmalek Essaâdi (UAE), Institut Pasteur du Maroc, Réseau International des Instituts Pasteur (RIIP), Faculty of Sciences, Rabat, Morocco., Bulgarian Academy of Sciences (BAS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Université de Brest (UBO), Dokuz Eylül Üniversitesi = Dokuz Eylül University [Izmir] (DEÜ), Università degli Studi di Padova = University of Padua (Unipd), Singapore centre for environmental life sciences engineering, Nanyang Technological University [Singapour], Indigo V Expeditions, Newcastle University [Newcastle], Instituto Português de Investigação do Mar e da Atmosfera (IPMA), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Universität Bremen, Istituto Nazionale di Geofisica e di Oceanografia Sperimentale (OGS), Rajarata University of Sri-Lanka (RUSL), University of Southern Mississippi (USM), Mediterranean Science Commission, National institute of biology Fornace, Near East University, Marine Scotland Marine Laboratory, Kind of Blue Project ABS, University of Oslo (UiO), Marine biology research station, Bangor University, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Fridtjof Nansen Institute of oceanology, Duke University [Durham], Miami University, Miami University [Ohio] (MU), Stazione Zoologica Anton Dohrn (SZN), Polytechnic University of Marche, University of Patras, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), INSTIM, University of Alaska [Fairbanks] (UAF), University of Hawaii, University of Auckland [Auckland], Marine Biological Laboratory (MBL), University of Chicago, Brown University, Zhejiang University, Argonne National Laboratory [Lemont] (ANL), Department of Mathematics [Berkeley], University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), Repositório da Universidade de Lisboa, Kopf, A, Bicak, M, Kottmann, R, Schnetzer, J, Kostadinov, I, Lehmann, K, Fernandez-Guerra, A, Jeanthon, C, Rahav, E, Ullrich, M, Wichels, A, Gerdts, G, Polymenakou, P, Kotoulas, G, Siam, R, Abdallah, Rz, Sonnenschein, Ec, Cariou, T, O'Gara, F, Jackson, S, Orlic, S, Steinke, M, Busch, J, Duarte, B, Cacador, I, Canning-Clode, J, Bobrova, O, Marteinsson, V, Reynisson, E, Loureiro, Cm, Luna, Gm, Quero, Gm, Loscher, Cr, Kremp, A, Delorenzo, Me, Ovreas, L, Tolman, J, Laroche, J, Penna, A, Frischer, M, Davis, T, Katherine, B, Meyer, Cp, Ramos, S, Magalhaes, C, Jude-Lemeilleur, F, Aguirre-Macedo, Ml, Wang, S, Poulton, N, Jones, S, Collin, R, Fuhrman, Ja, Conan, P, Alonso, C, Stambler, N, Goodwin, K, Yakimov, Mm, Baltar, F, Bodrossy, L, Van De Kamp, J, Frampton, Dmf, Ostrowski, M, Van Ruth, P, Malthouse, P, Claus, S, Deneudt, K, Mortelmans, J, Pitois, S, Wallom, D, Salter, I, Costa, R, Schroeder, Dc, Kandil, Mm, Amaral, V, Biancalana, F, Santana, R, Pedrotti, Ml, Yoshida, T, Ogata, H, Ingleton, T, Munnik, K, Rodriguez-Ezpeleta, N, Berteaux-Lecellier, V, Wecker, P, Cancio, I, Vaulot, D, Bienhold, C, Ghazal, H, Chaouni, B, Essayeh, S, Ettamimi, S, Zaid, E, Boukhatem, N, Bouali, A, Chahboune, R, Barrijal, S, Timinouni, M, El Otmani, F, Bennani, M, Mea, M, Todorova, N, Karamfilov, V, ten Hoopen, P, Cochrane, G, L'Haridon, S, Bizsel, Kc, Vezzi, A, Lauro, Fm, Martin, P, Jensen, Rm, Hinks, J, Gebbels, S, Rosselli, R, De Pascale, F, Schiavon, R, dos Santos, A, Villar, E, Pesant, S, Cataletto, B, Malfatti, F, Edirisinghe, R, Silveira, Jah, Barbier, M, Turk, V, Tinta, T, Fuller, Wj, Salihoglu, I, Serakinci, N, Ergoren, Mc, Bresnan, E, Iriberri, J, Nyhus, Paf, Bente, E, Karlsen, He, Golyshin, Pn, Gasol, Jm, Moncheva, S, Dzhembekova, N, Johnson, Z, Sinigalliano, Cd, Gidley, Ml, Zingone, A, Danovaro, R, Tsiamis, G, Clark, M, Costa, Ac, El Bour, M, Martins, Am, Collins, Re, Ducluzeau, Al, Martinez, J, Costello, Mj, Amaral-Zettler, La, Gilbert, Ja, Davies, N, Field, D, Glockner, Fo, European Commission, University of Oxford [Oxford], Israel Oceanographic and Limnological Research - IOLR (ISRAEL), Danmarks Tekniske Universitet (DTU), Carl Von Ossietzky Universität Oldenburg, Universidade de Lisboa (ULISBOA), Consiglio Nazionale delle Ricerche (CNR), Universidade do Porto, UMR 5805 Environnements et Paléoenvironnements Océaniques et Continentaux (EPOC), Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Sciences et Technologies - Bordeaux 1-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE), Universidad de la República [Montevideo] (UCUR), Kyoto University [Kyoto], Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), University of Mohammed V, Sidi Mohammed Ben Abdellah University, Universita degli Studi di Padova, Rajarata University of Sri-Lanka, University of Patras [Patras], University of California [Berkeley], and University of California-University of California
Subjects: 0106 biological sciences, Biodiversity, Marine life, 01 natural sciences, Bacteria, Genomics, Health Index, Marine, Metagenomics, Micro B3, Microorganism, OSD, Ocean sampling day, Standards, 11. Sustainability, Data and Information, Ocean Sampling Day, biodiversity, genomics, health index, bacteria, microorganism, metagenomics, marine, standards, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Ecology, Environmental resource management, Geology, Computer Science Applications, Interdisciplinary Natural Sciences, Microbial biodiversity, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Ocean sampling day, OSD, Biodiversity, Genomics, Health Index, Bacteria, Microorganism, Metagenomics,Marine, Micro B3, Standards, Oceans and Seas, Microorganisms, Marine Biology, Health Informatics, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Ecology and Environment, Metagenomic, 03 medical and health sciences, Health index, Medisinske Fag: 700 [VDP], SDG 14 - Life Below Water, 14. Life underwater, 030304 developmental biology, business.industry, 010604 marine biology & hydrobiology, Ocean sampling, 13. Climate action, Commentary, Genomic, Database Management Systems, Global Ocean, business
Abstract: Kopf, Anna ... et. al.-- 5 pages, 1 figure.-- This manuscript is NOAA-GLERL contribution number 1763, Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits, This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589
Published: 2015

29. Protocol for assessing antifouling activities of macroalgal extracts

Author: Rozenn Trepos, Claudia J. Hernández-Guerrero, R. Noemí Aguila-Ramírez, Claire Hellio, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Portsmouth, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Stengel Dagmar B., Connan Solène, European Project: 314697,EC:FP7:TPT,FP7-SST-2012-RTD-1,LEAF(2012), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Bacteria, Marine extracts, OS, Antifouling, Environmentally friendly, Biofouling, Macroalgae, Microalgae, Environmental science, Mussels, Bioassay, Biochemical engineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Barnacles
Abstract: International audience; The development of novel environmentally friendly antifouling (AF) solutions is a very active field in fundamental and applied research. An attractive option in producing such material resides in biomimetic studies: living organisms have evolved well-adapted structures and materials over geological times through natural selection. In this chapter, we explain the experimental procedure to be followed for the preparation of macroalgal extracts and to assess their AF efficiency towards key species. All bioassays described here have the advantage of being fast, reliable, and standardized.
Published: 2015

30. Embedding stock assessment within an integrated hierarchical Bayesian life cycle modelling framework : an application to Atlantic salmon in the Northeast Atlantic

Author: Ted Potter, Gérald Chaput, Félix Massiot-Granier, Samu Mäntyniemi, Jonathan White, Etienne Prévost, Etienne Rivot, Gordon W. Smith, Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Fisheries and Oceans Canada (DFO), Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Inchbraoch House, Marine Scotland, Fisheries Science Services, Marine Institute, Fisheries and Environmental Management Group, and The research leading to these results has received funding from the European Union’s Seventh Framework Programme (FP7/2007– 2013) under grant agreement No. 244706/ECOKNOWS project
Subjects: Stock assessment, north atlantic, post-smolt growth, complex of populations, hierarchical bayesian model, mixed stock fishery, Aquatic Science, Oceanography, survival, salar l, 14. Life underwater, stock assessment, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Ecology, pre-fishery abundance, time-series, prefishery abundance, population-dynamics, integrated life cycle, northwest atlantic, Archaeology, Fishery, atlantic salmon, fisheries, climate-change, history variation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, measurement error
Abstract: We developed a hierarchical Bayesian integrated life cycle model for Atlantic salmon that improves on the stock assessment approach currently used by ICES and provides some interesting insights about the population dynamics of a stock assemblage. The model is applied to the salmon stocks in eastern Scotland. It assimilates a 40-year (1971–2010) time-series of data compiled by ICES, including the catches in the distant water fisheries at Faroes and West Greenland and estimates of returning fish abundance. Our model offers major improvements in terms of statistical methodology for A. salmon stock assessment. Uncertainty about inferences is readily quantified in the form of Bayesian posterior distributions for parameters and abundance at all life stages, and the model could be adapted to provide projections based on the uncertainty derived from the estimation phase. The approach offers flexibility to improve the ecological realism of the model. It allows the introduction of density dependence in the egg-to-smolt transition, which is not considered in the current ICES assessment method. The results show that this modifies the inferences on the temporal dynamics of the post-smolt marine survival. In particular, the overall decrease in the marine survival between 1971 and 2010 and the sharp decline around 1988–1990 are dampened when density dependence is considered. The return rates of smolts as two-sea-winter (2SW) fish has declined in a higher proportion than return rates as one-sea-winter (1SW) fish. Our results indicate that this can be explained either by an increase in the proportion maturing as 1SW fish or by an increase in the mortality rate at sea of 2SW fish, but the data used in our analyses do not allow the likelihood of these two hypotheses to be gauged.
Published: 2014

31. Salmonids have an extraordinary complex type I IFN system: characterization of the IFN locus in Rainbow trout [i]Oncorhynchus mykiss[/i] reveals two novel IFN subgroups

Author: Tzong-Yueh Chen, Carine Genet, Jun Zou, Akshaya Panigrahi, Christopher J. Secombes, Young Mao Chen, Mahmood Ul Hassan, Sharif M. Mughal, Po Tsang Lee, Thitiya Summathed, Pierre Boudinot, Bartolomeo Gorgoglione, Nick G.H. Taylor, Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institute of Biotechnology, National Cheng Kung University (NCKU), Zoology Department, Government College University, Faculty of Fisheries and Wild Life, University of Veterinary and Animal Sciences, Unité de recherche Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892))
Subjects: Fish Proteins, endocrine system, animal structures, animal diseases, [SDV]Life Sciences [q-bio], Immunology, Molecular Sequence Data, Stimulation, Spleen, Biology, Brown trout, chemistry.chemical_compound, medicine, Immunology and Allergy, Animals, Salmo, Innate immune system, Base Sequence, urogenital system, biology.organism_classification, Molecular biology, 3. Good health, medicine.anatomical_structure, chemistry, Cell culture, Genetic Loci, Organ Specificity, Oncorhynchus mykiss, Interferon Type I, Rainbow trout, Resiquimod
Abstract: Fish type I IFNs are classified into two groups with two (group I) or four (group II) cysteines in the mature peptide and can be further divided into four subgroups, termed IFN-a, -b, -c, and -d. Salmonids possess all four subgroups, whereas other teleost species have one or more but not all groups. In this study, we have discovered two further subgroups (IFN-e and -f) in rainbow trout Oncorhynchus mykiss and analyzed the expression of all six subgroups in rainbow trout and brown trout Salmo trutta. In rainbow trout RTG-2 and RTS-11 cells, polyinosinic-polycytidylic acid stimulation resulted in early activation of IFN-d, whereas the IFN-e subgroup containing the highest number of members showed weak induction. In contrast with the cell lines, remarkable induction of IFN-a, -b, and -c was detected in primary head kidney leukocytes after polyinosinic-polycytidylic acid treatment, whereas a moderate increase of IFNs was observed after stimulation with resiquimod. Infection of brown trout with hemorrhagic septicemia virus resulted in early induction of IFN-d, -e, and -f and a marked increase of IFN-b and IFN-c expression in kidney and spleen. IFN transcripts were found to be strongly correlated with the viral burden and with marker genes of the IFN antiviral cascade. The results demonstrate that the IFN system of salmonids is far more complex than previously realized, and in-depth research is required to fully understand its regulation and function.
Published: 2014

32. Demographic response of Atlantic salmon populations to multiple stressors : a Bayesian hierarchical modelling approach at broad ocean scale

Author: Massiot-Granier, Félix, Prévost, Etienne, Chaput, Gerald, Smith, Gordon, White, Jonathan, Potter, Ted, Rivot, Etienne, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Fisheries and Oceans Canada (DFO), FRS FL Field Station, Marine Scotland, Marine Institute, Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and International Council for the Exploration of the Sea (ICES). DNK.
Subjects: changement climatique, Biodiversité et Ecologie, [SDE.MCG]Environmental Sciences/Global Changes, analyse demographique, modèle bayésien, Biodiversity and Ecology, salmo salar, scale, climate change, atlantic salmon, bayesian hierarchical model, life cycle, cycle de vie, réponse au stress, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Milieux et Changements globaux
Abstract: Résumé; International audience
Published: 2013

33. Réponse démographique des populations de saumon atlantique à de multiples facteurs de pression : une approche par modélisation hiérarchique Bayésienne à l'échelle de son aire de distribution

Author: Massiot-Granier, Félix, Prévost, Etienne, Chaput, G., Smith, G., White, J., Potter, T., Rivot, Etienne, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Ecologie Comportementale et Biologie des Populations de Poissons (ECOBIOP), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Fisheries and Oceans Canada (DFO), FRS FL Field Station, Marine Scotland, Marine Institute, Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), and Association Française d'Halieutique (AFH). FRA.
Subjects: démographie de population, Biodiversité et Ecologie, pression anthropique, modèle bayésien, Biodiversity and Ecology, salmo salar, écosystème aquatique, survie, poisson, modèle hiérarchique, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, écologie des populations, ComputingMilieux_MISCELLANEOUS, modélisation
Abstract: National audience
Published: 2013

34. Advanced diagnostics applied to fish liver tumours: relating pathology to underlying molecular aetiology

Author: John P. Bignell, Jeanette M. Rotchell, Brett P. Lyons, Stephen W. Feist, Adélaïde Lerebours, Grant D. Stentiford, University of Portsmouth, LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Weymouth Laboratory, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), School of Biological, Biomedical and Environmental Sciences, and University of Hull [United Kingdom]
Subjects: medicine.medical_specialty, Pathology, Disease, Aquatic Science, Oceanography, 03 medical and health sciences, Fish Diseases, 0302 clinical medicine, Fish liver, medicine, Biomarkers, Tumor, Animals, Limanda, 14. Life underwater, 030304 developmental biology, Laser capture microdissection, 0303 health sciences, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, biology, Liver Neoplasms, Cancer, retinoblastoma gene, medicine.disease, biology.organism_classification, Pollution, fish cancer, Liver, 030220 oncology & carcinogenesis, frozen sections, tumourigenesis, Flatfishes, Histopathology, Retinoblastoma gene, Sample collection, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, Laser microdissection, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Environmental Monitoring
Abstract: International audience; Liver tumours in flatfish have been diagnosed using histopathology for decades in order to monitor the impacts of marine pollution in coastal and estuarine environments. This traditional method has been coupled with molecular analyses of tumours in the liver of the dab, Limanda limanda, in order to elucidate underpinning molecular level aetiology of such disease. A laser capture microdissection technique for molecular investigation of cancer has been applied in fish. The present study provides optimized steps for environmental sample utilisation: a procedure for field sample collection and handling; a method allowing reliable identification of lesions on frozen tissue sections; and, downstream molecular analyses of tumourigenesis markers (retinoblastoma gene) in laser microdissected samples. This approach facilitates the use of wild flatfish as a model of environmentally-induced tumourigenesis, and has wide applicability to any disease pathology for which the underpinning molecular aetiology is required.
Published: 2013

35. Réseaux d’experts et prise de décisions : l’exemple du Royaume-Uni

Author: Booy, O., Copp, G.H., Mazaubert, E., NNSS, Food and Environment Research Agency, Salmon and Freshwater team, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Réseaux épuration et qualité des eaux (UR REBX), and Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)
Subjects: lcsh:GE1-350, GESTION, GRANDE BRETAGNE, ROYAUME-UNIS, ESPECE EXOTIQUE, INVASION BIOLOGIQUE, lcsh:TD1-1066, EXOTIQUE, ESPECES, ROYAUME-UNI, [SDE]Environmental Sciences, RESEAUX, INVASIONS BIOLOGIQUES, lcsh:Environmental technology. Sanitary engineering, ESPECE ENVAHISSANTE, lcsh:Environmental sciences
Abstract: Minimiser le risque posé et réduire les impacts négatifs causés par les espèces invasives sur le territoire britannique sont les objectifs du " GB Mechanism ", collectif d'experts mis en place au Royaume-Uni afin de coordonner les recherches et les actions dans le domaine de la gestion des espèces exotiques envahissantes.
Published: 2012

36. Shedding Light on Fish Otolith Biomineralization Using a Bioenergetic Approach

Author: Ronan Fablet, Hans Høie, Richard S. Millner, Henrik Mosegaard, Laure Pecquerie, Sebastiaan A.L.M. Kooijman, Hélène de Pontual, Lab-STICC_TB_CID_TOMS, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-Télécom Bretagne-Institut Brestois du Numérique et des Mathématiques (IBNM), Université de Brest (UBO)-Université européenne de Bretagne - European University of Brittany (UEB)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS), Département Signal et Communications (SC), Université européenne de Bretagne - European University of Brittany (UEB)-Télécom Bretagne-Institut Mines-Télécom [Paris] (IMT), University of California [Santa Barbara] (UCSB), University of California, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), University of Bergen (UiB), Danish Technical University (.), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Vrije Universiteit Amsterdam [Amsterdam] (VU), and Theoretical Life Sciences
Subjects: 0106 biological sciences, Biomineralization, Atmospheric Science, Anatomy and Physiology, Marine and Aquatic Sciences, lcsh:Medicine, 01 natural sciences, Biochemistry, VDP::Mathematics and natural science: 400::Zoology and botany: 480::Marine biology: 497, lcsh:Science, Otolith, Climatology, Multidisciplinary, Ecology, Gadiformes, Marine Ecology, Chemical Reactions, Temperature, Ocean acidification, otolitter, Molecular Imaging, Chemistry, medicine.anatomical_structure, otoliths, Mathematics and natural science: 400::Zoology and botany: 480::Marine biology: 497 [VDP], Calibration, Fisheries management, Seasons, [SPI.SIGNAL]Engineering Sciences [physics]/Signal and Image processing, Ichthyology, Algorithms, Research Article, Ecology (disciplines), Climate Change, Marine Biology, Biology, Bioenergetics, Agriculture and fishery disciplines: 900::Fisheries science: 920 [VDP], 010603 evolutionary biology, Ecosystems, Calcification, Inorganic Chemistry, Otolithic Membrane, Fish physiology, Calcification, Physiologic, Otolith formation, medicine, Animals, Ecosystem, 14. Life underwater, Inorganic Reactions, SDG 14 - Life Below Water, 010604 marine biology & hydrobiology, lcsh:R, Computational Biology, Fisheries Science, biology.organism_classification, Animal Feed, 13. Climate action, Earth Sciences, lcsh:Q, Physiological Processes, Energy Metabolism, Ecosystem Modeling, Zoology
Abstract: International audience; Otoliths are biocalcified bodies connected to the sensory system in the inner ears of fish. Their layered, biorhythm-following formation provides individual records of the age, the individual history and the natural environment of extinct and living fish species. Such data are critical for ecosystem and fisheries monitoring. They however often lack validation and the poor understanding of biomineralization mechanisms has led to striking examples of misinterpretations and subsequent erroneous conclusions in fish ecology and fisheries management. Here we develop and validate a numerical model of otolith biomineralization. Based on a general bioenergetic theory, it disentangles the complex interplay between metabolic and temperature effects on biomineralization. This model resolves controversial issues and explains poorly understood observations of otolith formation. It represents a unique simulation tool to improve otolith interpretation and applications, and, beyond, to address the effects of both climate change and ocean acidification on other biomineralizing organisms such as corals and bivalves.
Published: 2011

37. The Application of Variable Chlorophyll Fluorescenceto Microphytobenthic Biofilms

Author: Bruno Jesus, Rupert Gordon Perkins, João Serôdio, Johann Lavaud, Jean-Luc Mouget, Jacco C. Kromkamp, Rodney M. Forster, Sébastien Lefebvre, School of Earth and Ocean Sciences [Cardiff], Cardiff University, Centre for Estuarine and Marine Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Universidade de Aveiro, LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Mer, molécules et santé EA 2160 (MMS), Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN), Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Nord]), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes - UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes (UN)-Université de Nantes (UN)-Le Mans Université (UM)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut national des sciences de l'Univers (INSU - CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut national des sciences de l'Univers (INSU - CNRS)
Subjects: 0106 biological sciences, Ecology, 010604 marine biology & hydrobiology, Coastal fish, Sediment, Intertidal zone, 15. Life on land, Biology, 01 natural sciences, Rocky shore, Oceanography, Productivity (ecology), 13. Climate action, Benthic zone, [SDU]Sciences of the Universe [physics], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecosystem, 14. Life underwater, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 010606 plant biology & botany, Trophic level
Abstract: Community assemblages of diatoms, green algae and cyanobacteria comprise the microphytobenthos (MPB), which inhabit benthic sediment ecosystems (Admiraal 1984; Underwood and Kromkamp 1999; Consalvey et al. 2004). Particular attention has been paid to the analysis of intertidal soft sediment systems, e.g. cohesive mudflat and sandy substrata typical of estuarine habitats. Variable chlorophyll fluorescence has been applied to these systems since the 1990s, in an attempt to investigate the primary productivity and photophysiology of the integrated biofilms, when viewed as a “black box system”, and also at the species level (Sections 5, 6 and 7). These transient (i.e. temporary) biofilms are not confined to such soft sediment habitats however, and more recently application of fluorescence methodologies has been applied to biofilms inhabiting rocky shores and stromatolite systems (Kromkamp et al. 2007; Perkins et al. 2007). However the large majority of published work has centred upon benthic soft-sediment biofilms, due to their important ecosystem functions of carbon flow and sediment stability (Underwood and Kromkamp 1999). In the former their high magnitude of productivity fuels carbon flow through invertebrate and bacterial food webs to support important trophic levels of anthropogenically exploited taxa, including coastal fish and shell fisheries and coastal avifauna. In the case of sediment stability, biogenic exopolymers, usually referred to as extracellular polymeric substances (EPS), produced by the MPB in part to facilitate mobility, may contribute significantly to sediment stability, hence increasing the sediment resistance to hydrodynamic stresses and thus resistance to coastal erosion (e.g. Underwood and Kromkamp 1999 and citations there-in). Finally, the photosynthetic production of oxygen can be regarded as an important ecosystem function.
Published: 2010

38. Bioaccumulation of persistent organic pollutants in female common dolphins (Delphinus delphis) and harbour porpoises (Phocoena phocoena) from western European seas: Geographical trends, causal factors and effects on reproduction and mortality

Author: Pierce, Graham, Santos, Maria, Murphy, Sinead, Learmonth, Jennifer, Zuur, Alan, Rogan, Emer, Bustamante, Paco, Caurant, Florence, Lahaye, Virginie, Ridoux, Vincent, Zegers, B., Mets, A., Addink, Marian, Smeenk, C., Jauniaux, Thierry, Law, Robin, Dabin, Willy, Lopez, Alfredo, Alonso Farré, J.M., Gonzalez, Angel, Guerra, Angel, García-Hartmann, Manuel, Reid, R.J., Moffat, Colin, Lockyer, Christina, School of Biological Sciences, University of Aberdeen, Centro Oceanográfico de Vigo, Instituto Espagňol de Oceanografia (IEO), Department of Zoology, Ecology and Plant Sciences (AFDC), University College Cork (UCC), Sea Mammal Research Unit [University of St Andrews] (SMRU), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland]-Natural Environment Research Council (NERC), Highland Statistics, Centre de Recherche sur les Ecosystèmes Littoraux Anthropisés (CRELA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Royal Netherlands Institute for Sea Research (NIOZ), Nationaal Natuurhistorisch Museum, Faculté de Médecine Vétérinaire [Liège], Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Centre de Recherche sur les Mammifères Marins (CRMM), Université de La Rochelle (ULR), Coordinadora para o Estudo dos Mamiferos Mariños (CEMMA), CEMMA, Coordinadora para o Estudo dos Mamíferos Mariños (CEMMA), Instituto de Investigaciones Marinas (ECOBIOMAR), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Instituto de Investigaciones Marinas (CSIC) (ECOBIOMAR), Institute de Investigaciones Marinas (CSIC), Elephant house, Veterinary Science Division (SAC), Veterinary Science Division, FRS Marine Laboratory, and Age Dynamics
Subjects: Reproduction, Persistent organic pollutants, Delphinus delphis, [SDV.TOX.ECO]Life Sciences [q-bio]/Toxicology/Ecotoxicology, human activities, Diet, Phocoena phocoena
Abstract: International audience; Concentrations of polychlorinated biphenyls (PCBs) in blubber of female common dolphins and harbour porpoises from the Atlantic coast of Europe were frequently above the threshold at which effects on reproduction could be expected, in 40% and 47% of cases respectively. This rose to 74% for porpoises from the southern North Sea. PCB concentrations were also high in southern North Sea fish. The average pregnancy rate recorded in porpoises (42%) in the study area was lower than in the western Atlantic but that in common dolphins (25%) was similar to that of the western Atlantic population. Porpoises that died from disease or parasitic infection had higher concentrations of persistent organic pollutants (POPs) than animals dying from other causes. Few of the common dolphins sampled had died from disease or parasitic infection. POP profiles in common dolphin blubber were related to individual feeding history while those in porpoises were more strongly related to condition.
Published: 2008

39. Distribution and microhabitats of native and non-native gammarids (Amphipoda, Crustacea) in Brittany, with particular reference to the endangered endemic sub-species Gammarus duebeni celticus

Author: Gordon H. Copp, Alain Manach, Pierre Marmonier, Christophe Piscart, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Salmon & Freshwater Team (SFT), Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Ecologie, Evolution, Ecosystèmes Souterrains, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), and Lyvet, Nathalie
Subjects: 0106 biological sciences, Amphipoda, Fauna, Biogeography, freshwater fauna, Endangered species, Introduced species, 010603 evolutionary biology, 01 natural sciences, 14. Life underwater, Endemism, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, Ecology, Evolution, Behavior and Systematics, Gammaridae, biogeography, Ecology, biology, historical biogeography, 010604 marine biology & hydrobiology, Biodiversity, endangered species, 15. Life on land, biology.organism_classification, species replacement, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Pulex, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Aim To assess temporal changes in gammarid distribution in Brittany and microhabitat-use overlap between the endangered endemic Gammarus duebeni celticus Stock & Pinkster, 1970, the expanding natives G. pulex (Linnaeus, 1758) and Echinogammarus berilloni (Catta, 1878), and the introduced G. tigrinus Sexton, 1939. Location Brittany and adjacent regions in western France. Methods The spatial and temporal patterns in distribution of gammarids at the scale of Brittany were studied using 351 sites. Longitudinal distributions (from the source to the estuary of the river) and microhabitat-use (substratum type and water velocity) were also considered in selected rivers. Results At the regional scale, all species occurred together less often than expected statistically, with significant deviations from expected for G. pulex vs. both G. duebeni celticus and G. tigrinus, and for E. berilloni vs. both G. duebeni celticus and G. tigrinus. However, at the microhabitat scale, E. berilloni occurred significantly more often than expected with the endemic G. duebeni celticus, and this appears to be due to similar substratum and water velocity preferences, although at both the regional and microhabitat scales E. berilloni prefers wider streams than G. duebeni celticus. This study reveals a decline in the endangered G. duebeni celticus since 1970. Main conclusions The longitudinal and local distributions of G. duebeni celticus, and the higher-than-expected co-occurrence of the species with G. pulex, suggest that the decline of the endemic species may be due to changes in the environment and/or interference from native G. pulex, which is expanding its range in Brittany. The results are discussed as regards to the consequences for regional biodiversity.
Published: 2007

40. Synergistic patterns of threat and the challenges facing global anguillid eel conservation

Author: Hyojin Ahn, Kenzo Kaifu, Vicki Crook, David M. P. Jacoby, Matthew Gollock, Kevin G. Smith, Kazuo Uchida, Pierre Sasal, Anders M.C. Silfvergrip, Alan Walker, John M. Casselman, Mari-Beth Delucia, Tagried Kurwie, Zoological Society of London - ZSL (UNITED KINGDOM), Department of Biology [kingston], Queen's University [Kingston, Canada], TRAFFIC, The Nature Conservancy, Fisheries Laboratory, Kinki University, Faculty of Law, Chuo University, Mahurangi Technical Institute, Laboratoire d'excellence 'CORAIL', Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), International Union for Conservation of Nature (IUCN), Japan Fisheries Research and Education Agency (FRA), and Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS)
Subjects: Data deficient, Anguillidae, Near-threatened species, Ecology, Red List, Endangered species, Vulnerability, Conservation-dependent species, Biology, Red List Index, Critically endangered, Freshwater eels, Population trends, lcsh:QH540-549.5, Threatened species, IUCN Red List, lcsh:Ecology, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Threats, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract: International audience; With broad distributions, diadromous fishes can be exposed to multiple threats at different stages of development. For the primarily catadromous eels of the family Anguillidae, there is growing international concern for the population abundance and escapement trends of some of these species and yet incomplete knowledge of their remarkable life-histories hampers management and conservation. Anguillids experience a suite of pressures that include habitat loss/modification, migration barriers, pollution, parasitism, exploitation, and fluctuating oceanic conditions that likely have synergistic and regionally variable impacts, even within species. In beginning to redress this rather fragmented picture, we evaluated the extinction risk of these species using the IUCN Red List of Threatened Species Categories and Criteria to infer population-wide trends from catch and monitoring data. Here we consolidate and build upon these species assessments by presenting an overview of the current state of global eel data and conservation, categorising the knowledge gaps and geographic regions where resources are needed and discussing future recommendations to improve our understanding of anguillids. We find stark disparity between the quality and length of data available to assess population trends and conservation priorities in temperate and tropical anguillids. Of the 13 species assessed, four were listed as ‘Threatened’ (Vulnerable, Endangered or Critically Endangered); four were Near Threatened, three were Data Deficient and two were deemed Least Concern. Comparing with other diadromous species, we examine the multiple threats that impact eels during their different life-history stages, highlighting the challenges of applying the Red List Categories and Criteria to geographically-expansive, catadromous and panmictic groups of species.
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41. Possibility and Challenges of Conversion of Current Virus Species Names to Linnaean Binomials

Author: Sbina Bavari, Susan Payne, Alexander Bukreyev, Arvind Varsani, Víctor Romanowski, Kartik Chandran, Ralf G. Dietzgen, Mark D. Stenglein, Anna N. Clawson, Sead Sabanadzovic, Gael Kurath, Andrea Maisner, Peter J. Walker, Ralf Dürrwald, Juan Carlos de la Torre, Eric M. Leroy, Mária Benko, Keizo Tomonaga, Gary P. Kobinger, Robert A. Lamb, Hideki Kondo, F. Murilo Zerbini, Martin Schwemmle, Robert B. Tesh, Gaya K. Amarasinghe, Andrew J. Easton, Michael J. Buchmeier, Jean-Paul Gonzalez, Anna E. Whitfield, Nikos Vasilakis, Jonathan S. Towner, Pierre Formenty, Jens H. Kuhn, Norbert Nowotny, Roger Hewson, Ayato Takada, Mart Krupovic, Igor S. Lukashevich, David M. Stone, Clarence J. Peters, Sheli R. Radoshitzky, Bertus K. Rima, Janusz T. Paweska, Masayuki Horie, Christopher S. Clegg, Victoria Wahl-Jensen, Christopher F. Basler, Sébastian Emonet, Charles H. Calisher, Lin-Fa Wang, Rémi N. Charrel, Jean L. Patterson, Elodie Ghedin, Dennis Rubbenstroth, Dàohóng Jiāng, Sergey V. Netesov, Hélène Sanfaçon, Thomas S. Postler, Ron A. M. Fouchier, Peter L. Collins, Noël Tordo, Maria S. Salvato, John M. Dye, Arcady Mushegian, Sophie J. Smither, Joseph L. DeRisi, Olga Dolnik, Kim R. Blasdell, Balázs Harrach, Viktor E. Volchkov, Thomas Briese, Andrew M. Kropinski, Columbia University College of Physicians and Surgeons, Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Washington University School of Medicine (WUSM), University of Washington [Seattle], Georgia State University, University System of Georgia (USG), Army Medical Research Institute of Infectious Diseases [USA] (USAMRIID), Institute for Soil Sciences and Agricultural Chemistry (ATK TAKI), Centre for Agricultural Research [Budapest] (ATK), Hungarian Academy of Sciences (MTA)-Hungarian Academy of Sciences (MTA), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), Columbia Mailman School of Public Health, University of California [Irvine] (UCI), University of California, The University of Texas Medical Branch (UTMB), College of Veterinary Medicine and Biomedical Sciences, Colorado State University [Fort Collins] (CSU), Albert Einstein College of Medicine [New York], Emergence des Pathologies Virales (EPV), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM), Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille), Les Mandinaux, National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Immunology and Microbial Science, Scripps Research Institute, Department of Medicine [San Francisco], University of California [San Francisco] (UCSF), University of California-University of California, Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland [Brisbane], Philipps University of Marburg, IDT Biologika, School of Life Sciences, Warwick University, Unité de Virologie, Institut de Recherche Biomédicale des Armées (IRBA), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Department of Viroscience [Rotterdam, The Netherlands], Erasmus University Medical Center [Rotterdam] (Erasmus MC), Center for Genomics and Systems Biology, Department of Biology [New York], New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU)-New York University [New York] (NYU), NYU System (NYU)-NYU System (NYU), Health for Development, Public Health England [Salisbury] (PHE), Kagoshima University, State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Research Centre in Infectious Diseases, CHUL Research Centre and Department of Microbiology and Immunology, Université Laval [Québec] (ULaval)-Faculty of Medicine, Institute of Plant Science and Resources, Okayama University, University of Guelph, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], US Geological Survey [Seattle], United States Geological Survey [Reston] (USGS), Northwestern University [Evanston], Centre International de Recherches Médicales de Franceville (CIRMF), Department of Pharmacology and Toxicology, University of Louisville, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Infectious Disease, University of Texas at Austin [Austin], Novosibirsk State University (NSU), University of Veterinary Medicine [Vienna] (Vetmeduni), Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Texas Biomedical Research Institute [San Antonio, TX], Texas A&M University System, National Institute for Communicable Diseases [Johannesburg] (NICD), Queen's University [Belfast] (QUB), Instituto de Biotecnología y Biología Molecular [La Plata] (IBBM), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Facultad de Ciencias Exactas [La Plata], Universidad Nacional de la Plata [Argentine] (UNLP)-Universidad Nacional de la Plata [Argentine] (UNLP), University of Freiburg [Freiburg], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology [Mstate, USA] (BCH-EPP), Mississippi State University [Mississippi], Summerland Research and Development Centre, Agriculture and Agri-Food [Ottawa] (AAFC), University of Maryland School of Medicine, University of Maryland System, Defence Science and Technology Laboratory (Dstl), Ministry of Defence (UK) (MOD), Department of Microbiology, Immunology and Pathology, Centre for Environment, Fisheries and Aquaculture Science [Weymouth] (CEFAS), Hokkaido University [Sapporo, Japan], Institute for Virus Research, Kyoto University [Kyoto], Stratégies antivirales, Institut Pasteur de Guinée, Réseau International des Instituts Pasteur (RIIP), Viral Special Pathogens Branch, Centers for Disease Control and Prevention-WHO Collaborative Centre for Viral Hemorrhagic Fevers, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity (BMPV), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), National Biodefense Analysis and Countermeasures Center [Frederick], U.S. Social Security Administration, CSIRO Health & Biosecurity, Department of Agriculture, Fisheries and Forestry, Ecoscience Precinct, GPO Box 267, Brisbane, Duke-NUS Medical School [Singapore], Center for Fundamental and Applied Microbiomics, Arizona State University [Tempe] (ASU)-Biodesign Institute, Kansas State University, Departamento de Fitopatologia [Viçosa, Brazil] (BIOAGRO), Universidade Federal de Vicosa (UFV), This work was supported in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This work was also funded in part under National Institutes of Health (NIH) contract HHSN272201000040I/HHSN27200004/D04 and R24AI120942 (N.V., R.B.T.), and the National Science Foundation (NSF) Individual Research and Development (IR/D) program (A.R.M.)., We thank Laura Bollinger (NIH/NIAID Integrated Research Facility at Fort Detrick, Frederick, MD, USA) for critically editing the manuscript, Andrew J. Davison (MRC – University of Glasgow Centre for Virus Research, Glasgow, UK) and Michael J. Adams (Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Herts, UK) of the ICTV Executive Committee for suggestions on manuscript improvement, and Arya Ariël Kuhn for sustained vocal support and (dia)critical remarks, Albert Einstein College of Medicine, Institut Hospitalier Universitaire Méditerranée Infection (IHU AMU), Queensland Alliance for Agriculture and Food Innovation, University of Queensland (UQ), Public Health England [Porton Down, Salisbury], Faculty of Medicine-Laval University [Québec], Okayama University [Okayama], Centre International de Recherches Médicales de Franceville, Texas Biomedical Research Institute [San Antonio, Texas], A&M University, National Institute for Communicable Diseases (NICD), Centre for Experimental Medicine [Queen’s University of Belfast], Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Hokkaido University, Bases moléculaires de la pathogénicité virale – Molecular Basis of Viral Pathogenicity, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Duke NUS Medical School, Departamento de Fitopatologia/BIOAGRO, Virology, U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Columbia University [New York], University of California [Irvine] (UC Irvine), University of California (UC), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Assistance Publique - Hôpitaux de Marseille (APHM)-Institut National de la Santé et de la Recherche Médicale (INSERM), The Scripps Research Institute [La Jolla, San Diego], University of California [San Francisco] (UC San Francisco), University of California (UC)-University of California (UC), Philipps Universität Marburg = Philipps University of Marburg, University of Warwick [Coventry], Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA), Huazhong Agricultural University [Wuhan] (HZAU), Institut Pasteur [Paris] (IP), Agriculture and Agri-Food (AAFC), Kyoto University, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Viçosa = Federal University of Viçosa (UFV)
Subjects: 0301 basic medicine, MESH: Terminology as Topic, media_common.quotation_subject, Biología, 030106 microbiology, Binomials, Zoology, Biology, Points of View, 03 medical and health sciences, Genus, Terminology as Topic, Genetics, MESH: Classification, Epithet, Arenaviridae, Ecology, Evolution, Behavior and Systematics, Virus classification, media_common, Order Mononegavirales, Evolutionary Biology, Virus taxonomy, Classification, MESH: Viruses, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Virus nomenclature, Genealogy, Ictv, International committee on taxonomy of viruses, 030104 developmental biology, Homo sapiens, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDV.IMM]Life Sciences [q-bio]/Immunology, Mononegavirales
Abstract: Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and, even when binomial, are not Linnaean in style. In this thought exercise, we attempted toconvert all currently official names ofspecies included in the viru sfamily Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment., La lista completa de autores que integran el documento puede consultarse en el archivo, Instituto de Biotecnologia y Biologia Molecular

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