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1. Eukaryotic plankton diversity in the sunlit ocean

Author: Jean-Marc Aury, Daniele Iudicone, Hiroyuki Ogata, Stéphane Audic, Frédéric Mahé, Fabrice Not, Johan Decelle, Gabriel Gorsky, Silvia G. Acinas, Pascal Hingamp, Sarah Romac, Noan Le Bescot, Matthieu Mulot, Sébastien Colin, Eleonora Scalco, Michael E. Sieracki, Marc Picheral, Tara Oceans Coordinators, Nicolas Henry, Stephane Pesant, Micah Dunthorn, Adriana Zingone, Sabrina Speich, Margaux Carmichael, Chris Bowler, Sarah Searson, Céline Dimier, Jeroen Raes, Gipsi Lima-Mendez, Shruti Malviya, Aleš Horák, Eric Karsenti, Ramiro Logares, Olga Flegontova, Julius Lukeš, Shinichi Sunagawa, Flora Vincent, Stefanie Kandels-Lewis, Enrique Lara, Raphael Morard, Stefan Engelen, Peer Bork, Patrick Wincker, Colomban de Vargas, Raffaele Siano, Ian Probert, Jean Weissenbach, Lars Stemmann, Cédric Berney, Samuel Chaffron, Olivier Jaillon, Lionel Guidi, Julie Poulain, Lucie Bittner, Nigel Grimsley, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of ecology, Universität Kaiserslautern, Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), 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), Faculty of Informatics [Brno] (FI / MUNI), Masaryk University [Brno] (MUNI), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Département Electronique, Optronique et Signal (DEOS), Institut Supérieur de l'Aéronautique et de l'Espace (ISAE-SUPAERO), Stazione Zoologica Anton Dohrn (SZN), European Molecular Biology Laboratory [Heidelberg] (EMBL), European Molecular Biology Laboratory [Grenoble] (EMBL), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory, 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)-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), Technische Universität Kaiserslautern (TU Kaiserslautern), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), CNRS [GDR3280], EMBL, Agency for Administration of University and Research Grants (AGAUR) [CONES 2010-0036], Veolia Environment Foundation, EBI [PRJEB402, PRJEB6610], Genoscope/CEA, Lorient Agglomeration, Illumina, UNIMIB, Electricite de France Foundation, Fondation pour la Recherche sur la Biodiversite, Tara schooner, Fund for Scientific Research - The French Ministry of Research, French Government [ANR-11-BTBR-0008, ANR-10-INBS-09-08, ANR-10-LABX-54], French Ministry of Foreign Affairs, UPMC, European Research Council [294823], VIB, Stazione Zoologica Anton Dohrn, Rega Institute, Japan Society for the Promotion of Science [26430184], KU Leuven, PSL* Research University [ANR-11-IDEX-0001-02], World Courier, ANR [POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, PHYTBACK/ANR-2010-1709-01, TARA-GIRUS/ANR-09-PCS-GENM-218], EU FP7 [287589, IHMS/HEALTH-F4-2010-261376], Gordon and Betty Moore Foundation [3790], Prince Albert II de Monaco Foundation, Spanish Ministry of Science and Innovation [CGL2011-26848/BOS], Diversité et Interactions au sein du Plancton Océanique ( DIPO ), Adaptation et diversité en milieu marin ( ADMM ), 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 ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), Genoscope - Centre national de séquençage [Evry] ( GENOSCOPE ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Evolution des Protistes et Ecosystèmes Pélagiques ( EPEP ), Institut de biologie de l'ENS Paris (UMR 8197/1024) ( IBENS ), École normale supérieure - Paris ( ENS Paris ) -École normale supérieure - Paris ( ENS Paris ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Génomique métabolique ( UMR 8030 ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université d'Évry-Val-d'Essonne ( UEVE ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), Institut de Biologie Paris-Seine, Institute of Molecular Biology and Swiss Institute of Bioinformatics, University of Zürich [Zürich] ( UZH ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -IFR113-Institut National de la Santé et de la Recherche Médicale ( INSERM ), University of Hawaii at Manoa ( UHM ), Laboratoire d'océanographie de Villefranche ( LOV ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Institut national des sciences de l'Univers ( INSU - CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Faculty of Informatics [Masaryk], Masaryk University, Institut de Génomique, Genoscope, Centre National de Séquençage, MARUM, Universität Bremen Postfach, Dynamiques de l'Environnement Côtier ( DYNECO ), Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ), Département Electronique, Optronique et Signal ( DEOS ), Institut Supérieur de l'Aéronautique et de l'Espace ( ISAE-SUPAERO ), Stazione Zoologica Napoli, European Molecular Biology Laboratory [Heidelberg] ( EMBL ), European Molecular Biology Laboratory ( EMBL ), Biologie intégrative des organismes marins ( BIOM ), Observatoire océanologique de Banyuls ( OOB ), Information génomique et structurale ( IGS ), Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), Kyoto University [Kyoto], Université Catholique de Louvain ( UCL ), Laboratoire de physique des océans ( LPO ), Institut de Recherche pour le Développement ( IRD ) -Institut Français de Recherche pour l'Exploitation de la Mer ( IFREMER ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ), 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 ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut de Recherche pour le Développement ( IRD ) -Université de Brest ( UBO ) -Centre National de la Recherche Scientifique ( CNRS ) -Centre National de la Recherche Scientifique ( CNRS ), Technische Universität Kaiserskautern, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] ( ICM ), Consejo Superior de Investigaciones Científicas [Spain] ( CSIC ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Lausanne (UNIL), 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), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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)-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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Multidisciplinary, biology, [ SDV ] Life Sciences [q-bio], Ecology, Range (biology), [SDV]Life Sciences [q-bio], fungi, Rhizaria, Biodiversity, 15. Life on land, Ribosomal RNA, Plankton, biology.organism_classification, [ SDE ] Environmental Sciences, Phylogenetics, [SDE]Environmental Sciences, natural sciences, 14. Life underwater, Taxonomic rank, Ribosomal DNA
Abstract: Vargas, Colomban de ... et. al.-- 11 pages, 7 figures, supplementary materials www.sciencemag.org/content/348/6237/1261605/suppl/DC1, Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ∼150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ∼11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts. © 2015, American Association for the Advancement of Science. All rights reserved, We thank the following people and sponsors for their commitment: CNRS (in particular, the GDR3280); EMBL; Genoscope/CEA; UPMC; VIB; Stazione Zoologica Anton Dohrn; UNIMIB; Rega Institute; KU Leuven; Fund for Scientific Research – The French Ministry of Research, the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), and MEMO LIFE (ANR-10-LABX-54); PSL* Research University (ANR-11-IDEX-0001-02); ANR (projects POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCSGENM-217, PHYTBACK/ANR-2010-1709-01, and TARA-GIRUS/ANR-09-PCS-GENM-218); EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376); European Research Council Advanced Grant Awards to C. Bowler (Diatomite:294823); Gordon and Betty Moore Foundation grant 3790 to M.B.S.; Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS and TANIT (CONES 2010-0036) grant from the Agency for Administration of University and Research Grants (AGAUR) to S.G.A.; and Japan Society for the Promotion of Science KAKENHI grant 26430184 to H.O. We also thank the following for their support and commitment: A. Bourgois, E. Bourgois, R. Troublé, Région Bretagne, G. Ricono, the Veolia Environment Foundation, Lorient Agglomération, World Courier, Illumina, the Electricité de France Foundation, Fondation pour la Recherche sur la Biodiversité, the Prince Albert II de Monaco Foundation, and the Tara schooner and its captains and crew. We thank MERCATORCORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted sampling permissions. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015
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2. Validation and application of a PCR primer set to quantify fungal communities in the soil environment by real-time quantitative PCR

Author: Samuel Dequiedt, Mélanie Lelievre, Laure Guillou, Claudy Jolivet, Nicolas Chemidlin Prévost-Bouré, Richard Christen, Hamid Reza Shahbazkia, Lionel Ranjard, Christophe Mougel, Dominique Arrouays, AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Microbiologie du Sol et de l'Environnement (MSE), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), Institute of Developmental Biology and Cancer (IBDC), Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), GenoSol (plateforme de l'université de Bourgogne), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité INFOSOL (ORLEANS INFOSOL), Institut National de la Recherche Agronomique (INRA), Universidade do Algarve (UAlg), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), ADEME (French Agency for Energy and Environment), French National Research Agency (ANR), French Ministry for Ecology and Sustainable Development (MEEDDM), French Ministry of Agriculture (MAP), French Institute for Environment (IFEN), French Institute for Research and Development (IRD), National Forest Inventory (IFN), National Institute for Agronomic Research (INRA), FLAveur, VIsion et Comportement du consommateur (FLAVIC), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB), 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 Côte d'Azur (UCA), InfoSol (InfoSol), 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), Microbiologie, Institut de signalisation, biologie du développement et cancer (ISBDC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Université Côte d'Azur (UCA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), Institut National de la Recherche Agronomique (INRA)-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Université de Bourgogne (UB), Microbiologie du Sol et de l'Environnement ( MSE ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ), Institute of Developmental Biology and Cancer ( IBDC ), Centre National de la Recherche Scientifique ( CNRS ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Unité INFOSOL ( ORLEANS INFOSOL ), Institut National de la Recherche Agronomique ( INRA ), Universidade do Algarve, Faro, Diversité et Interactions au sein du Plancton Océanique ( DIPO ), Adaptation et diversité en milieu marin ( ADMM ), 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 )
Subjects: fungal abundance, organic carbon content, real-time Q-PCR, length polymorphism, SYBRGreen method, type de sol, [SDV]Life Sciences [q-bio], lcsh:Medicine, Plant Science, Plant Roots, 18S ribosomal RNA, SYBRGreen method, type de sol, [ SDE ] Environmental Sciences, Soil, Fungal Reproduction, lcsh:Science, DNA, Fungal, Phylogeny, organic carbon content, 2. Zero hunger, 0303 health sciences, Diversity, Multidisciplinary, fungal abundance, Ecology, Reveals, Fungal genetics, Polymerase-chain-reaction, Agriculture, Biodiversity, Amplicon, Soil Ecology, soil texture, amplification enzymatique de l'adn, Bacterial communities, Samples, real-time Q-PCR, Community Ecology, [SDE]Environmental Sciences, Rhizosphere, Research Article, Soil texture, In silico, Molecular Sequence Data, Soil Science, Computational biology, Mycology, Biology, Real-Time Polymerase Chain Reaction, Microbiology, Microbial Ecology, 03 medical and health sciences, Species Specificity, Medicago truncatula, Microbial community, RNA, Ribosomal, 18S, Soil ecology, 030304 developmental biology, DNA Primers, Ribosomal-Rna genes, [ SDV ] Life Sciences [q-bio], 030306 microbiology, lcsh:R, Fungi, Botany, Reproducibility of Results, length polymorphism, soil texture, Sequence Analysis, DNA, Dna, 15. Life on land, amplification enzymatique de l'adn, DNA extraction, lcsh:Q, Primer (molecular biology)
Abstract: Fungi constitute an important group in soil biological diversity and functioning. However, characterization and knowledge of fungal communities is hampered because few primer sets are available to quantify fungal abundance by real-time quantitative PCR (real-time Q-PCR). The aim in this study was to quantify fungal abundance in soils by incorporating, into a real-time Q-PCR using the SYBRGreen (R) method, a primer set already used to study the genetic structure of soil fungal communities. To satisfy the real-time Q-PCR requirements to enhance the accuracy and reproducibility of the detection technique, this study focused on the 18S rRNA gene conserved regions. These regions are little affected by length polymorphism and may provide sufficiently small targets, a crucial criterion for enhancing accuracy and reproducibility of the detection technique. An in silico analysis of 33 primer sets targeting the 18S rRNA gene was performed to select the primer set with the best potential for real-time Q-PCR: short amplicon length; good fungal specificity and coverage. The best consensus between specificity, coverage and amplicon length among the 33 sets tested was the primer set FR1/FF390. This in silico analysis of the specificity of FR1/FF390 also provided additional information to the previously published analysis on this primer set. The specificity of the primer set FR1/FF390 for Fungi was validated in vitro by cloning - sequencing the amplicons obtained from a real time Q-PCR assay performed on five independent soil samples. This assay was also used to evaluate the sensitivity and reproducibility of the method. Finally, fungal abundance in samples from 24 soils with contrasting physico-chemical and environmental characteristics was examined and ranked to determine the importance of soil texture, organic carbon content, C:N ratio and land use in determining fungal abundance in soils. ADEME (French Agency for Energy and Environment); French National Research Agency (ANR); French Ministry for Ecology and Sustainable Development (MEEDDM); French Ministry of Agriculture (MAP); French Institute for Environment (IFEN); French Institute for Research and Development (IRD); National Forest Inventory (IFN); National Institute for Agronomic Research (INRA)
Published: 2011
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3. Green Edge ice camp campaigns: understanding the processes controlling the under-ice Arctic phytoplankton spring bloom

Author: P. Massicotte, R. Amiraux, M.-P. Amyot, P. Archambault, M. Ardyna, L. Arnaud, L. Artigue, C. Aubry, P. Ayotte, G. Bécu, S. Bélanger, R. Benner, H. C. Bittig, A. Bricaud, É. Brossier, F. Bruyant, L. Chauvaud, D. Christiansen-Stowe, H. Claustre, V. Cornet-Barthaux, P. Coupel, C. Cox, A. Delaforge, T. Dezutter, C. Dimier, F. Domine, F. Dufour, C. Dufresne, D. Dumont, J. Ehn, B. Else, J. Ferland, M.-H. Forget, L. Fortier, M. Galí, V. Galindo, M. Gallinari, N. Garcia, C. Gérikas Ribeiro, M. Gourdal, P. Gourvil, C. Goyens, P.-L. Grondin, P. Guillot, C. Guilmette, M.-N. Houssais, F. Joux, L. Lacour, T. Lacour, A. Lafond, J. Lagunas, C. Lalande, J. Laliberté, S. Lambert-Girard, J. Larivière, J. Lavaud, A. LeBaron, K. Leblanc, F. Le Gall, J. Legras, M. Lemire, M. Levasseur, E. Leymarie, A. Leynaert, A. Lopes dos Santos, A. Lourenço, D. Mah, C. Marec, D. Marie, N. Martin, C. Marty, S. Marty, G. Massé, A. Matsuoka, L. Matthes, B. Moriceau, P.-E. Muller, C.-J. Mundy, G. Neukermans, L. Oziel, C. Panagiotopoulos, J.-J. Pangrazi, G. Picard, M. Picheral, F. Pinczon du Sel, N. Pogorzelec, I. Probert, B. Quéguiner, P. Raimbault, J. Ras, E. Rehm, E. Reimer, J.-F. Rontani, S. Rysgaard, B. Saint-Béat, M. Sampei, J. Sansoulet, C. Schmechtig, S. Schmidt, R. Sempéré, C. Sévigny, Y. Shen, M. Tragin, J.-É. Tremblay, D. Vaulot, G. Verin, F. Vivier, A. Vladoiu, J. Whitehead, M. Babin, Asian School of the Environment, Takuvik Joint ULaval/CNRS Laboratory, Centre National de la Recherche Scientifique (CNRS)-Laval University [Québec], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Université du Québec à Rimouski (UQAR), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Earth System Science [Stanford] (ESS), Stanford University [Stanford], Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), CHU de Québec–Université Laval, Laval University [Québec], Department of Biological Sciences [Columbia], University of South Carolina [Columbia], Institut méditerranéen d'océanologie (MIO), Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences de la MER de Rimouski (ISMER), Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Dept Biologie, Université Laval, Université Laval, Laboratoire d’Océanologie et de Géosciences (LOG) - UMR 8187 (LOG), Université de Lille-Université du Littoral Côte d'Opale-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches Pétrographiques et Géochimiques (CRPG), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Division de la productivité des Océans (Ministère des Pêches et des Océans), Institut Maurice-Lamontagne, Diversité et Interactions au sein du Plancton Océanique (DIPO), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), ECOlogy of MArine Plankton (ECOMAP), Centre National de la Recherche Scientifique (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)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Développement Instrumental et Techniques Marines (DITM), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM), Laboratoire de MicrobiologiE de Géochimie et d'Ecologie Marines (LMGEM), Centre National de la Recherche Scientifique (CNRS)-Université de la Méditerranée - Aix-Marseille 2, Centre d'études spatiales de la biosphère (CESBIO), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-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), Greenland Institute for Natural Resources (GINR), Environnements et Paléoenvironnements OCéaniques (EPOC), Observatoire aquitain des sciences de l'univers (OASU), 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)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie des Plantes (IBP), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Department of Biology [Québec], Processus et interactions de fine échelle océanique (PROTEO), CNES(project#131425)IPEV(project#1164)CSA,FondationTotalArcticNetLEFEFrench Arctic Initiative (GreenEdgeproject), ANR: GreenEdge project,ANR (Contract #111112),Contract #111112, Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Université Laval [Québec] (ULaval), 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 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 Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Stanford EARTH, Stanford University-Stanford University, Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Université Grenoble Alpes (UGA), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut National de Santé Publique du Québec [Canada] (INSPQ), Département de médecine sociale et préventive [ESPUM-Montréal] (ESPUM), Université de Montréal (UdeM), Departement de Biologie, Chimie et Géographie, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Centre for Earth Observation Science [Winnipeg], University of Manitoba [Winnipeg], 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), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Department of Geography [Calgary], University of Calgary, Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), 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), Universidad Mayor [Santiago de Chile], Royal Belgian Institute of Natural Sciences (RBINS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Laboratoire d'Océanographie Microbienne (LOMIC), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Physiologie et biotechnologie des Algues (PBA), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Centre de recherche du CHU de Québec-Université Laval (CRCHUQ), Université Laval [Québec] (ULaval)-Université Laval [Québec] (ULaval), Institut de Biologie Intégrative et des Systèmes [Québec] (IBIS), Asian School of the Environment (ASE), Nanyang Technological University [Singapour], 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), Norwegian Institute for Water Research (NIVA), Faculty of Fisheries Sciences [Hakodate], Hokkaido University [Sapporo, Japan], Observatoire des sciences de l'univers Ecce Terra [Paris] (ECCE TERRA), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-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)-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), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), School of the Earth, Ocean and Environment [Columbia] (SEOE), 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), ANR-14-CE01-0017,Green Edge,Productivité biologique dans l'Océan Arctique: réponse passée, présente et future aux fluctuations climatiques, et impacts sur les flux de carbone, le réseau trophique et les communautés humaines locales(2014), Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), 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 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 Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Centre de Toxicologie du Québec (CTQ), Département de médecine sociale et préventive (DMPS), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Applied Physics Laboratory [Seattle] (APL-UW), University of Washington [Seattle], 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), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP ), Observatoire des sciences de l'univers Ecce Terra (ECCE TERRA), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut polytechnique de Grenoble - Grenoble Institute of Technology [2020-....] (Grenoble INP [2020-....]), Université Grenoble Alpes [2020-....] (UGA [2020-....])-Université Grenoble Alpes [2020-....] (UGA [2020-....])-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Météo France-Centre National de la Recherche Scientifique (CNRS), Université du Littoral Côte d'Opale-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Météo France-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Météo France-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (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)-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), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), 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)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Fédération de recherche de Roscoff (FR2424), Biotechnologies et Ressources Marines (BRM), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Observatoire des sciences de l'univers Ecce Terra [Paris] (OSU ECCE TERRA), 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 Sciences et Technologies - Bordeaux 1 (UB)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France-Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: 0106 biological sciences, PACIFIC, 010504 meteorology & atmospheric sciences, ZONE, 010501 environmental sciences, Zooplankton, 01 natural sciences, CARBON, ALGAE, OCEAN, Ice Camp, Phytoplankton, Sea ice, Ecosystem, 14. Life underwater, lcsh:Environmental sciences, 0105 earth and related environmental sciences, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, lcsh:GE1-350, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, Arctic studies, ACL, lcsh:QE1-996.5, Biology and Life Sciences, Spring bloom, 15. Life on land, CHLOROPHYLL, IRRADIANCE, Environmental engineering [Engineering], lcsh:Geology, Oceanography, Arctic, 13. Climate action, [SDE]Environmental Sciences, VOLUME, General Earth and Planetary Sciences, Environmental science, Phytoplankton Spring Bloom, SEA-ICE, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay
Abstract: The Green Edge initiative was developed to investigate the processes controlling the primary productivity and fate of organic matter produced during the Arctic phytoplankton spring bloom (PSB) and to determine its role in the ecosystem. Two field campaigns were conducted in 2015 and 2016 at an ice camp located on landfast sea ice southeast of Qikiqtarjuaq Island in Baffin Bay (67.4797∘ N, 63.7895∘ W). During both expeditions, a large suite of physical, chemical and biological variables was measured beneath a consolidated sea-ice cover from the surface to the bottom (at 360 m depth) to better understand the factors driving the PSB. Key variables, such as conservative temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured at the ice camp. Meteorological and snow-relevant variables were also monitored. Here, we present the results of a joint effort to tidy and standardize the collected datasets, which will facilitate their reuse in other Arctic studies. The dataset is available at https://doi.org/10.17882/59892 (Massicotte et al., 2019a).
Published: 2020
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4. A global ocean atlas of eukaryotic genes

Author: Carradec, Quentin, Pelletier, Eric, da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel, Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew, Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Weissenbach, Jean, Institut de Biologie François JACOB (JACOB), 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Université Paris-Saclay, Institute for Chemical Research, Kyoto University, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Hasso Plattner Institute [Potsdam, Germany], European Molecular Biology Laboratory [Heidelberg] (EMBL), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Hawai'i [Honolulu] (UH), Ohio State University [Columbus] (OSU), European Molecular Biology Laboratory [Grenoble] (EMBL), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Stazione Zoologica Anton Dohrn (SZN), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Kyoto University, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Savelli, Bruno, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, BLANC - Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton - - PHYTBACK2010 - ANR-10-BLAN-1709 - BLANC - VALID, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Génomique et biotechnologies végétales - Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans. - - PROMETHEUS2009 - ANR-09-GENM-0031 - GENOM-BTV - VALID, Marine Microbial Biodiversity, Bioinformatics and Biotechnology - MICRO B3 - - EC:FP7:KBBE2012-01-01 - 2015-12-31 - 287589 - VALID, and Genome-enabled dissection of marine diatom ecophysiology - DIATOMITE - - EC:FP7:ERC2012-06-01 - 2017-05-31 - 294823 - VALID
Subjects: [SDV] Life Sciences [q-bio], [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Science, [SDV]Life Sciences [q-bio], fungi, lcsh:Q, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, lcsh:Science, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: International audience; While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
Published: 2018
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5. Revision of the Genus Micromonas Manton et Parke (Chlorophyta, Mamiellophyceae), of the Type Species M. pusilla (Butcher) Manton & Parke and of the Species M. commoda van Baren, Bachy and Worden and Description of Two New Species Based on the Genetic and Phenotypic Characterization of Cultured Isolates

Author: Margot Tragin, Christophe Six, Yves Desdevises, Sophie Le Panse, Daniel Vaulot, Evelyne Derelle, Birger Marin, Daphné Grulois, Marie Latimier, Nathalie Simon, Dominique Marie, Elodie Foulon, Aude Houdan, Florence Le Gall, Fabien Jouenne, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Botanisches Institut, Universität zu Köln = University of Cologne, MArine Phototrophic Prokaryotes (MAPP), and Universität zu Köln
Subjects: 0301 basic medicine, Species complex, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, Microbiology, 03 medical and health sciences, Species Specificity, Chlorophyta, Genus, Botany, 14. Life underwater, Internal transcribed spacer, Clade, Phylogeny, Micromonas, Synapomorphy, Genome, Base Sequence, Phylogenetic tree, Pigments, Biological, RNA, Algal, biology.organism_classification, Type species, 030104 developmental biology, RNA, Ribosomal, Evolutionary biology, Sequence Alignment
Abstract: International audience; The green picoalgal genus Micromonas is broadly distributed in estuaries, coastal marine habitats and open oceans, from the equator to the poles. Phylogenetic, ecological and genomic analyses of culture strains and natural populations have suggested that this cosmopolitan genus is composed of several cryptic species corresponding to genetic lineages. We performed a detailed analysis of variations in morphology, pigment content, and sequences of the nuclear-encoded small-subunit rRNA gene and the second internal transcribed spacer (ITS2) from strains isolated worldwide. A new morphological feature of the genus, the presence of tip hairs at the extremity of the hair point, was discovered and subtle differences in hair point length were detected between clades. Clear non-homoplasious synapomorphies were identified in the small-subunit rRNA gene and ITS2 spacer sequences of five genetic lineages. These findings lead us to provide emended descriptions of the genus Micromonas, of the type species M. pusilla, and of the recently described species M. commoda, as well as to describe 2 new species, M. bravo and M. polaris. By clarifying the status of the genetic lineages identified within Micromonas, these formal descriptions will facilitate further interpretations of large-scale analyses investigating ecological trends in time and space for this widespread picoplankter.
Published: 2017
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6. Viral Attachment to Biotic and Abiotic Surfaces in Seawater

Author: Farooq Azam, Yosuke Yamada, Ryan Guillemette, Anne-Claire Baudoux, Nirav Patel, Department of Nutritional Sciences, University of Wisconsin-Madison, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Marine Biology Research Division, University of California [San Diego] (UC San Diego), and University of California-University of California
Subjects: Biogeochemical cycle, [SDV]Life Sciences [q-bio], viruses, Virus Attachment, Applied Microbiology and Biotechnology, Virus, Microbiology, 03 medical and health sciences, Marine bacteriophage, Environmental Microbiology, Bacteriophages, Seawater, 14. Life underwater, Colloids, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Abiotic component, 0303 health sciences, Ecology, biology, 030306 microbiology, Host (biology), Chemistry, Microbiota, fungi, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Microbial population biology, [SDE]Environmental Sciences, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bacteria, Food Science, Biotechnology
Abstract: Viruses influence microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces could influence host viral infection rates; however, the prevalence of such viral attachment is not investigated quantitatively. We used coastal seawater viral assemblages and, as models, marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) to investigate their attachment to probable nonhost marine bacteria. We also studied viral attachment to colloids and other abiotic surfaces in seawater. Centrifugation experiments with bacterium-virus mixtures showed substantial viral loss in the supernatant presumably due to the viral attachment to bacteria. This attachment (0.04 to 24 viruses μm−2 [bacterial surface area]) varied with bacterium-virus combinations. Surprisingly, filtering seawater on 0.2-μm Anodisc or polycarbonate filters retained ∼12 to 84% of viruses presumably attached to ≥0.2-μm-sized particles and/or the filter surface. Enzymatic digestion followed by epifluorescence and atomic force microscopy suggested that 7 to 25% of the total viruses were attached via β-glycosidic linkages. Furthermore, a substantial proportion (7 to 48%) of viruses became attached to model abiotic surfaces (polycarbonate, polypropylene, and glass), and this has significance for laboratory protocols as well as studies of virus ecology in particle-rich marine environments. Substantial attachment of viruses to nonhost surfaces could influence virus-driven biogeochemical cycles and microbial community structure. IMPORTANCE Viruses play important roles in altering microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces can influence host viral infection rates; however, the prevalence of viral attachment to nonhost surfaces and the ratio of attached viruses to total viruses are little known. We used coastal seawater viral assemblages and used marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) as models to investigate their attachment to abiotic and biotic surfaces in seawater. Viral attachment was observed on several surfaces, such as nonhost bacteria, polymers, filters, cover glasses, and tube surfaces. This study cautions against commonly used protocols that require viral incubation and seawater fractionation. More importantly, these results could influence virus-driven biogeochemical cycles and microbial community structure in the ocean.
Published: 2019
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7. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome

Author: Felix Christopher Mark, Betina M. Porcel, Uwe John, Jan Janouškovec, Yameng Lu, Stephan Frickenhaus, Laure Guillou, Marco Groth, Klaus-Ulrich Valentin, Marius Felder, Ahmed A. Moustafa, Sylke Wohlrab, Sarah Farhat, Gurjeet S. Kohli, Ulf Bickmeyer, Patrick J. Keeling, Gernot Glöckner, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Leibniz Association, British Columbia, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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)-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), Department of Biology and Biotechnology Graduate Program, American University in Cairo, American University in Cairo, Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), 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)-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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Singapore Centre for Environmental Life Sciences and Engineering
Subjects: Mitochondrial DNA, DNA, Complementary, [SDV]Life Sciences [q-bio], Mitochondrion, Aerobic Eukaryotic Parasit, Genome, Evolution, Molecular, Engineering::Environmental engineering [DRNTU], 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Cluster Analysis, Genomic library, Plastid, Gene, Phylogeny, Research Articles, Mitochondrial Genome, ComputingMilieux_MISCELLANEOUS, Gene Library, 030304 developmental biology, Cell Nucleus, Genetics, Likelihood Functions, Evolutionary Biology, 0303 health sciences, Microscopy, Confocal, Multidisciplinary, Ecology, biology, fungi, SciAdv r-articles, Sequence Analysis, DNA, biology.organism_classification, Aerobiosis, Mitochondria, Genome, Mitochondrial, [SDE]Environmental Sciences, Dinoflagellida, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery, Research Article, Syndiniales
Abstract: The parasitic marine dinoflagellate Amoebophrya is the first known eukaryote with aerobic mitochondria without a genome., Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
Published: 2019
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8. Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from theChaetoceros neogracilisspecies complex

Author: Raffaele Siano, Diana Sarno, Daniel Vaulot, Dominique Marie, Mélanie Chanoine, Isabella Percopo, Sergio Balzano, Priscillia Gourvil, 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), Stazione Zoologica Anton Dohrn (SZN), Unité Dyneco, Laboratoire Pelagos, Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MArine Phototrophic Prokaryotes (MAPP), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), Royal Netherlands Institute for Sea Research (NIOZ), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), and Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP)
Subjects: 0106 biological sciences, 0301 basic medicine, Canada, Species complex, Nitzschia, Oceans and Seas, Zoology, Plant Science, Aquatic Science, phylogeny, 01 natural sciences, 18S ribosomal RNA, 03 medical and health sciences, ITS2 secondary structure, Microscopy, Electron, Transmission, morphology, Attheya, 14. Life underwater, biogeography, Phylogeny, Diatoms, Cylindrotheca, LSU, Genetic diversity, biology, Arctic Regions, Ecology, 010604 marine biology & hydrobiology, SSU, Genetic Variation, Chaetoceros, Sequence Analysis, DNA, biology.organism_classification, 030104 developmental biology, Diatom, Phytoplankton, Microscopy, Electron, Scanning, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ITS, polar diatoms
Abstract: International audience; Seventy-five diatoms strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM) as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. Chaetoceros neogracilis generally occurred as single cells but can also form short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.
Published: 2016
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9. Zoosporic parasites infecting marine diatoms – A black box that needs to be opened

Author: Sigrid Neuhauser, Bettina Scholz, Ulf Karsten, Frithjof C. Küpper, Frank H. Gleason, Agostina V. Marano, Brooke K. Sullivan, Laure Guillou, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Institute of Biological Sciences, and University of Rostock
Subjects: 0301 basic medicine, Ecology, Primary producers, Host (biology), [SDV]Life Sciences [q-bio], Ecological Modeling, Ecology (disciplines), Aquatic ecosystem, fungi, Plant Science, Biology, biology.organism_classification, Article, 03 medical and health sciences, 030104 developmental biology, Diatom, [SDE]Environmental Sciences, Marine ecosystem, Identification (biology), 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Trophic level
Abstract: International audience; Living organisms in aquatic ecosystems are almost constantly confronted by pathogens. Nevertheless, very little is known about diseases of marine diatoms, the main primary producers of the oceans. Only a few examples of marine diatoms infected by zoosporic parasites are published, yet these studies suggest that diseases may have significant impacts on the ecology of individual diatom hosts and the composition of communities at both the producer and consumer trophic levels of food webs. Here we summarize available ecological and morphological data on chytrids, aphelids, stramenopiles (including oomycetes, labyrinthuloids, and hyphochytrids), parasitic dinoflagellates, cercozoans and phytomyxids, all of which are known zoosporic parasites of marine diatoms. Difficulties in identification of host and pathogen species and possible effects of environmental parameters on the prevalence of zoosporic parasites are discussed. Based on published data, we conclude that zoosporic parasites are much more abundant in marine ecosystems than the available literature reports, and that, at present, both the diversity and the prevalence of such pathogens are underestimated.
Published: 2016
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10. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author: Karp‐Boss, Lee, Wincker, Patrick, Kandels‐Lewis, Stefanie, Jaillon, Olivier, Iudicone, Daniele, Hingamp, Pascal, Grimsley, Nigel, Gorsky, Gabriel, Follows, Michael J., Vargas, Colomban, Bowler, Chris, Boss, Emmanuel, Bork, Peer, Acinas, Silvia G., Karsenti, Eric, Weissenbach, Jean, Velayoudon, Didier, Sunagawa, Shinichi, Sullivan, Matthew B., Stemmann, Lars, Speich, Sabrina, Sieracki, Mike, Sardet, Christian, Reynaud, Emmanuel G., Raes, Jeroen, Pesant, Stéphane, Ogata, Hiroyuki, Not, Fabrice, Krzic, Uros, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Sprovieri, Mario, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Searson, Sarah, Dimier, Céline, Picheral, Marc, Guidi, Lionel, Sordino, Paolo, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, d'Alcalà, Maurizio Ribera, Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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)-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), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Oceanography and Coastal Sciences, Louisiana State University (LSU), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Instituto de Engenharia de Sistemas e Computadores (INESC), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Istituto per l'Ambiente Marino Costiero, Sezione Ecologia Marina Integrata, European Molecular Biology Laboratory [Heidelberg] (EMBL), National Cardiovascular Center, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), 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), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), University of Maine, Department of Earth and Environment [Boston], Boston University [Boston] (BU), Department of Earth Ocean and Ecological Sciences [Liverpool], University of Liverpool, Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, National Science Foundation [Arlington] (NSF), DVIPC, ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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)-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), Université de Lausanne (UNIL), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Consiglio Nazionale delle Ricerche [Roma] (CNR), 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), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Vrije Universiteit Brussel (VUB), Department of Structural Biology, 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), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, and JAMET, Jean-Louis
Subjects: 0106 biological sciences, Atmospheric Science, PROCHLOROCOCCUS, 010504 meteorology & atmospheric sciences, Iron fertilization, species networks, DIVERSITY, PROTEIN, Oceanography, 01 natural sciences, CARBON, Settore BIO/13 - Biologia Applicata, oxidative stress, Meteorology & Atmospheric Sciences, Geosciences, Multidisciplinary, OXIDATIVE STRESS, ComputingMilieux_MISCELLANEOUS, GENE-EXPRESSION, General Environmental Science, Global and Planetary Change, LIMITATION, Ecology, IN-SITU, system biology, Geology, Plankton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], iron response, meta-omics, MARINE-PHYTOPLANKTON, in-situ, limitation, Physical Sciences, Life Sciences & Biomedicine, Biogeochemical cycle, PACIFIC, Environmental Sciences & Ecology, Context (language use), prochlorococcus, Biology, Zooplankton, marine-phytoplankton, diversity, Atmospheric Sciences, Phytoplankton, pacific, Genetics, Environmental Chemistry, Ecosystem, 14. Life underwater, Life Below Water, 0105 earth and related environmental sciences, Science & Technology, 010604 marine biology & hydrobiology, carbon, fungi, Pelagic zone, gene-expression, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, Cardiovascular and Metabolic Diseases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, protein, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 29 pages, 9 figures, supporting information https://doi.org/10.1029/2018GB006022, Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280, the Mission Pour l'Interdisciplinarité – Project MEGALODOM, and the Fédération de Recherche GO‐SEE FR2022), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government “Investissements d'Avenir” programs Oceanomics (ANR‐11‐BTBR‐0008), MEMO LIFE (ANR‐10‐LABX‐54), PSL* Research University (ANR‐11‐IDEX‐0001‐02), and FRANCE GENOMIQUE (ANR‐10‐INBS‐09), Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects “PHYTBACK/ANR‐2010‐1709‐01,” POSEIDON/ANR‐09‐BLAN‐0348, PROMETHEUS/ANR‐09‐PCS‐GENM‐217, TARA‐GIRUS/ANR‐09‐PCS‐GENM‐218, SAMOSA/ANR‐13‐ADAP‐0010, CINNAMON/ANR‐17‐CE02‐0014‐01), EU FP7 (MicroB3/No. 287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to C. B., JSPS/MEXT KAKENHI (26430184, 16H06437, and 16KT0020), The Canon Foundation (203143100025), Gordon and Betty Moore Foundation (award #3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) to MBS, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Fonds Français pour l'Environnement Mondial, the TARA schooner and its captain and crew.
Published: 2019
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11. A review of the characteristics of the dinoflagellate parasite Ichthyodinium chabelardi and its potential effect on fin fish populations

Author: Aurélie Chambouvet, Laure Guillou, Frank H. Gleason, Maitreyi Nagarkar, The University of Sydney, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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)-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), Scripps Institution of Oceanography (SIO - UC San Diego), University of California (UC)-University of California (UC), 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), 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)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), and Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Range (biology), Syndiniophyceae, Amyloodinium ocellatum, Zoology, Aquatic Science, Biology, Saprolegnia parasitica, Oceanography, Generalist and specialist species, 010603 evolutionary biology, 01 natural sciences, Sphaerothecum destruens, X-cell species, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, Ecology, business.industry, 010604 marine biology & hydrobiology, ACL, fungi, Fish fin, Dinoflagellate, biology.organism_classification, Fishing industry, Osteichthyes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Syndiniales
Abstract: International audience; This paper focuses on the biology and ecological impacts of Ichthyodinium chabelardi (phylum Dinophyta, class Syndiniophyceae, order Syndiniales), a virulent endobiotic parasite of yolk sacs and young larvae of many species of marine fin fish. Its infections have been observed in warm and temperate open oceanic environments and crowded marine fish tanks. The prevalence of I. chabelardi and the range of its host fishes is not well studied, and our understanding of its life cycle is incomplete. Here, we describe what is known about I. chabelardi infections in fish and we compare this with several other protistan parasites of fish, including Amyloodium ocellatum, Saprolegnia parasitica, Sphaerothecum destruens and the ‘X-cell’ clades Gadixcellia and Xcellia, all of which are considered emerging generalist parasites infecting a wide variety of fin fish species. Recent findings suggest that rising seawater temperatures might lead to higher infection rates in fishes, and we expect that these changing conditions could also expand the ranges of some of these parasitic species. Thus, it is essential that the fishing industry effectively monitors fish tanks and water in the surrounding environments for the presence of zoosporic parasites, including I. chabelardi, so as to take steps to prevent large losses in these fisheries.
Published: 2019
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12. Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations

Author: Margot Tragin, Stefan Lambert, Jean-Claude Lozano, Daniel Vaulot, François-Yves Bouget, Jean-François Ghiglione, Pierre E. Galand, Adaptation Biologique et Vieillissement = Biological Adaptation and Ageing (B2A), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), ECOlogy of MArine Plankton (ECOMAP), Centre National de la Recherche Scientifique (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)-Centre National de la Recherche Scientifique (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), Laboratoire d'Océanographie Microbienne (LOMIC), Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (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)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Observatoire océanologique de Banyuls (OOB)
Subjects: [SDV]Life Sciences [q-bio], Microbiology, Article, 03 medical and health sciences, Mediterranean sea, Phytoplankton, Mediterranean Sea, Ecosystem, Seawater, 14. Life underwater, Autotroph, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Micromonas, Ecological niche, 0303 health sciences, biology, Bacteria, 030306 microbiology, Ecology, Eukaryota, biology.organism_classification, Archaea, [SDE]Environmental Sciences, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bay
Abstract: International audience; Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.
Published: 2019
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13. First Ultrastructural and Molecular Phylogenetic Evidence from the Blastogregarines, an Early Branching Lineage of Plesiomorphic Apicomplexa

Author: Magdaléna Kováčiková, Vladimir V. Aleoshin, Joseph Schrevel, Gita G. Paskerova, Andrea Bardůnek Valigurová, Andrey A. Dobrovolskij, Laure Guillou, Timur G. Simdyanov, Andrei Diakin, Masaryk University [Brno] (MUNI), Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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: 0301 basic medicine, Lineage (evolution), [SDV]Life Sciences [q-bio], [SDV.BID]Life Sciences [q-bio]/Biodiversity, Lymphocyte Activation, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Apicomplexa, 03 medical and health sciences, Phylogenetics, parasitic diseases, Phylogeny, ComputingMilieux_MISCELLANEOUS, biology, Phylogenetic tree, DNA, Protozoan, biology.organism_classification, Basal Bodies, Microscopy, Electron, 030104 developmental biology, Germ Cells, Evolutionary biology, Molecular phylogenetics, Morphological analysis, Ultrastructure, Apical complex
Abstract: Blastogregarines are poorly studied parasites of polychaetes superficially resembling gregarines, but lacking syzygy and gametocyst stages in the life cycle. Furthermore, their permanent multinuclearity and gametogenesis by means of budding considerably distinguish them from other parasitic Apicomplexa such as coccidians and hematozoans. The affiliation of blastogregarines has been uncertain: different authors considered them highly modified gregarines, an intermediate apicomplexan lineage between gregarines and coccidians, or an isolated group of eukaryotes altogether. Here, we report the ultrastructure of two blastogregarine species, Siedleckia nematoides and Chattonaria mesnili, and provide the first molecular data on their phylogeny based on SSU, 5.8S, and LSU rDNA sequences. Morphological analysis reveals that blastogregarines possess both gregarine and coccidian features. Several traits shared with archigregarines likely represent the ancestral states of the corresponding cell structures for parasitic apicomplexans: a distinctive tegument structure and myzocytotic feeding with a well-developed apical complex. Unlike gregarines but similar to coccidians however, the nuclei of male blastogregarine gametes are associated with two kinetosomes. Molecular phylogenetic analyses reveal that blastogregarines are an independent, early diverging lineage of apicomplexans. Overall, the morphological and molecular evidence congruently suggests that blastogregarines represent a separate class of Apicomplexa.
Published: 2018
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14. Comparative Time-Scale Gene Expression Analysis Highlights the Infection Processes of Two Amoebophrya Strains

Author: Farhat, Sarah, Florent, Isabelle, Noel, Benjamin, Kayal, Ehsan, Da Silva, Corinne, Bigeard, Estelle, Adriana Alberti, Labadie, Karine, Corre, Erwan, Aury, Jean-Marc, Rombauts, Stephane, Wincker, Patrick, Guillou, Laure, Porcel, Betina M., Molécules de Communication et Adaptation des Micro-Organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), Consiglio Nazionale delle Ricerche (CNR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Systems Biology, Universiteit Gent = Ghent University [Belgium] (UGENT), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), 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)-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)-Université Paris-Saclay, Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universiteit Gent = Ghent University (UGENT), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Microbiology (medical), [SDV]Life Sciences [q-bio], plankton, amoebophrya, syndiniales, lcsh:QR1-502, oxidative stress response, Microbiology, infection, lcsh:Microbiology, parasite, gene expression, dinoflagellates, ComputingMilieux_MISCELLANEOUS, Original Research
Abstract: Understanding factors that generate, maintain, and constrain host-parasite associations is of major interest to biologists. Although little studied, many extremely virulent micro-eukaryotic parasites infecting microalgae have been reported in the marine plankton. This is the case for Amoebophrya, a diverse and highly widespread group of Syndiniales infecting and potentially controlling dinoflagellate populations. Here, we analyzed the time-scale gene expression of a complete infection cycle of two Amoebophrya strains infecting the same host (the dinoflagellate Scrippsiella acuminata), but diverging by their host range (one infecting a single host, the other infecting more than one species). Over two-thirds of genes showed two-fold differences in expression between at least two sampled stages of the Amoebophrya life cycle. Genes related to carbohydrate metabolism as well as signaling pathways involving proteases and transporters were overexpressed during the free-living stage of the parasitoid. Once inside the host, all genes related to transcription and translation pathways were actively expressed, suggesting the rapid and extensive protein translation needed following host-cell invasion. Finally, genes related to cellular division and components of the flagellum organization were overexpressed during the sporont stage. In order to gain a deeper understanding of the biological basis of the host-parasitoid interaction, we screened proteins involved in host-cell recognition, invasion, and protection against host-defense identified in model apicomplexan parasites. Very few of the genes encoding critical components of the parasitic lifestyle of apicomplexans could be unambiguously identified as highly expressed in Amoebophrya. Genes related to the oxidative stress response were identified as highly expressed in both parasitoid strains. Among them, the correlated expression of superoxide dismutase/ascorbate peroxidase in the specialist parasite was consistent with previous studies on Perkinsus marinus defense. However, this defense process could not be identified in the generalist Amoebophrya strain, suggesting the establishment of different strategies for parasite protection related to host specificity.
Published: 2018
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15. Blastodinium spp. infect copepods in the ultra-oligotrophic marine waters of the Mediterranean Sea

Author: Alves-De-Souza, C., Cornet, C., Nowaczyk, A., Gasparini, S., Skovgaard, A., Guillou, Laure, 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), Universidad Austral de Chile, 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), Laboratoire d'Océanographie Physique et Biogéochimique (LOPB), Université de la Méditerranée - Aix-Marseille 2-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Veterinary Disease Biology [Copenhagen], Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Conicyt (Chilean government), French ANR, 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), and University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)
Subjects: lcsh:Geology, lcsh:QH501-531, lcsh:QH540-549.5, [SDV]Life Sciences [q-bio], lcsh:QE1-996.5, [SDE]Environmental Sciences, lcsh:Life, lcsh:Ecology
Abstract: Blastodinium are chloroplast-containing dinoflagellates which infect a wide range of copepods. They develop inside the gut of their host, where they produce successive generations of sporocytes that are eventually expelled through the anus of the copepod. Here, we report on copepod infections in the oligotrophic to ultra-oligotrophic waters of the Mediterranean Sea sampled during the BOUM cruise. Based on a DNA-stain screening of gut contents, 16 % of copepods were possibly infected in samples from the Eastern Mediterranean infected, with up to 51 % of Corycaeidae, 33 % of Calanoida, but less than 2 % of Oithonidae and Oncaeidae. Parasites were classified into distinct morphotypes, with some tentatively assigned to species B. mangini, B. contortum, and B. cf. spinulosum. Based upon the SSU rDNA gene sequence analyses of 15 individuals, the genus Blastodinium was found to be polyphyletic, containing at least three independent clusters. The first cluster grouped all sequences retrieved from parasites of Corycaeidae and Oncaeidae during this study, and included sequences of Blastodinium mangini (the "mangini" cluster). Sequences from cells infecting Calanoida belonged to two different clusters, one including B. contortum (the "contortum" cluster), and the other uniting all B. spinulosum-like morphotypes (the "spinulosum" cluster). Cluster-specific oligonucleotidic probes were designed and tested by fluorescence in situ hybridization (FISH) in order to assess the distribution of dinospores, the Blastodinium dispersal and infecting stage. Probe-positive cells were all small thecate dinoflagellates, with lengths ranging from 7 to 18 μm. Maximal abundances of Blastodinium dinospores were detected at the Deep Chlorophyll Maximum (DCM) or slightly below. This was in contrast to distributions of autotrophic pico- and nanoplankton, microplanktonic dinoflagellates, and nauplii which showed maximal concentrations above the DCM. The distinct distribution of dinospores and nauplii argues against infection during the naupliar stage. Dinospores, described as autotrophic in the literature, may escape the severe nutrient limitation of ultra-oligotrophic ecosystems by living inside copepods.
Published: 2018
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16. A New Freshwater Cyanosiphovirus Harboring Integrase

Author: Zhong, Kevin, Zhong, Kevin Xu, Suttle, Curtis, Baudoux, Anne-Claire, Derelle, Evelyne, Colombet, Jonathan, Cho, Anna, Caleta, Jessica, Six, Christophe, Jacquet, Stéphan, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), MArine Phototrophic Prokaryotes (MAPP), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: Synechococcus, genome sequencing, lakes, [SDE]Environmental Sciences, cyanosiphovirus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, freshwater
Abstract: International audience; Pelagic cyanobacteria are key players in the functioning of aquatic ecosystems, and their viruses (cyanophages) potentially affect the abundance and composition of cyanobacterial communities. Yet, there are few well-described freshwater cyanophages relative to their marine counterparts, and in general, few cyanosiphoviruses (family Siphoviridae) have been characterized, limiting our understanding of the biology and the ecology of this prominent group of viruses. Here, we characterize S-LBS1, a freshwater siphovirus lytic to a phycoerythrin-rich Synechococcus isolate (Strain TCC793). S-LBS1 has a narrow host range, a burst size of ∼400 and a relatively long infecting step before cell lysis occurs. It has a dsDNA 34,641 bp genome with putative genes for structure, DNA packing, lysis, replication, host interactions, DNA repair and metabolism. S-LBS1 is similar in genome size, genome architecture, and gene content, to previously described marine siphoviruses also infecting PE-rich Synechococcus, e.g., S-CBS1 and S-CBS3. However, unlike other Synechococcus phages, S-LBS1 encodes an integrase, suggesting its ability to establish lysogenic relationships with its host. Sequence recruitment from viral metagenomic data showed that S-LBS1-like viruses are diversely present in a wide range of aquatic environments, emphasizing their potential importance in controlling and structuring Synechococcus populations. A comparative analysis with 16 available sequenced cyanosiphoviruses reveals the absence of core genes within the genomes, suggesting high degree of genetic variability in siphoviruses infecting cyanobacteria. It is likely that cyanosiphoviruses have evolved as distinct evolutionary lineages and that adaptive co-evolution occurred between these viruses and their hosts (i.e., Synechococcus, Prochlorococcus, Nodularia, and Acaryochloris), constituting an important driving force for such phage diversification.
Published: 2018
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17. Protists Within Corals: The Hidden Diversity

Author: Eve Toulza, Jeremie Vidal-Dupiol, Mehdi Adjeroud, Laure Guillou, Pierre Lepage, Jean-Michel Escoubas, Camille Clerissi, Sébastien Brunet, 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), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (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), McGill University and Genome Quebec Innovation Centre, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Station biologique de Roscoff (SBR), and 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Microbiology (medical), Coral, lcsh:QR1-502, Scleractinia, Pocillopora damicornis, medicine.disease_cause, 01 natural sciences, Microbiology, lcsh:Microbiology, Montastraea, 03 medical and health sciences, Symbiodinium, parasitic diseases, medicine, 14. Life underwater, holobiont, Favia, protists, geography, blocking primer, geography.geographical_feature_category, biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 010604 marine biology & hydrobiology, fungi, Protist, Coral reef, biology.organism_classification, symbiosis, 030104 developmental biology, Evolutionary biology, metabarcoding
Abstract: International audience; Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.
Published: 2018
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18. Rhizaria : An unexpected role in the carbon biological pump, and in the silica cycle

Author: Leynaert, Aude, Llopis-Monferrer, Natalia, Mendez-Sandin, Miguel, Not, Fabrice, Tréguer, Paul, 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), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Institut Universitaire Européen de la Mer (IUEM), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience
Published: 2018

19. Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria)

Author: Camille Poirier, Noritoshi Suzuki, Tristan Biard, Fabrice Not, Loic Pillet, Johan Decelle, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), University of Geneva [Switzerland], Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Institute of Geology and Paleontology, Tohoku University [Sendai], ``DESIR' Project Emergence-UPMC from Universite Pierre et Marie Curie, JST-CNRS exchange program, Swiss National Science Foundation [P2GEP3\₁48800], ``Bibliotheque du Vivant' network - CNRS, Museum National d'Histoire Naturelle, INRA, CEA (Centre National de Sequencage), and Université de Genève = University of Geneva (UNIGE)
Subjects: polycystine, [SDV]Life Sciences [q-bio], Zoology, DNA, Ribosomal, Microbiology, Monophyly, 14. Life underwater, Clade, Ribosomal DNA, Phylogeny, integrative taxonomy, molecular phylogeny, Radiolaria, biology, Phylogenetic tree, Rhizaria, Biodiversity, Collodaria, single-cell, biology.organism_classification, Taxon, [SDE]Environmental Sciences, Molecular phylogenetics, Microscopy, Electron, Scanning
Abstract: International audience; Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists. They occur as either large colonies or solitary specimens, and, unlike most radiolarians, some taxa lack silicified structures. Collodarians are known to play an important role in oceanic food webs as both active predators and hosts of symbiotic microalgae, yet very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Here we investigated collodarian diversity using phylogenetic analyses of both nuclear small (18S) and large (28S) subunits of the ribosomal DNA, including 124 new sequences from 75 collodarians sampled worldwide. The resulting molecular phylogeny was compared to morphology-based classification. Our analyses distinguished the monophyletic clade of skeleton-less and spicule-bearing Sphaerozoidae from the sister clades Collosphaeridae (skeleton-bearing) and Collophidiidae (skeleton-less), while the Thalassicollidae was not retrieved as a monophyletic clade. Detailed morphological examination with electron microscopy combined with molecular analyses revealed many discrepancies, such as a mix between solitary and colonial species, co-existence of skeleton-less and skeleton-bearing specimens within the Collosphaeridae, as well as complex intraspecific variability in silicified structures. Such observations challenge a morphology-based classification and highlight the pertinence of an integrative taxonomic approach to study collodarian diversity. (C) 2015 Elsevier GmbH. All rights reserved.
Published: 2015
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20. Potential roles for recently discovered chytrid parasites in the dynamics of harmful algal blooms

Author: Laure Guillou, Télesphore Sime-Ngando, Thomas G. Jephcott, Mélanie Gerphagnon, Sergey Karpov, Frank H. Gleason, Floris van Ogtrop, Frithjof C. Küpper, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), French ANR, European Project MaCuMBa [FP7-KBBE-2012-6-311975], program ``Problems of life origin and biosphere development', USA Sydney University Foundation, Mary M. Collins Trust, Boston MA, and Australian Postgraduate Award
Subjects: education.field_of_study, biology, Ecology, Host, [SDV]Life Sciences [q-bio], Aquatic ecosystem, fungi, Population, Effective management, Phylum Chytridiomycota, biology.organism_classification, Microbiology, Algal bloom, Chytrid, Parasite, Algae, 13. Climate action, Phytoplankton, [SDE]Environmental Sciences, Bloom, 14. Life underwater, Toxin, education
Abstract: International audience; Zoosporic true fungi belonging to the phylum Chytridiomycota, commonly referred to as chytrids, are ubiquitous in aquatic environments, however their role in phytoplankton population and eco-physiological dynamics is not fully understood. With the rising occurrence of harmful algal blooms (HABs) of phytoplankton worldwide, there is a growing need to investigate the factors affecting toxicity in algae, with a view to determining the significance of these factors in light of the current trends in global climate change. In this review we present current knowledge regarding the parasitism of phytoplankton by chytrids, including incidence of chytrid epidemics, methodologies used in their isolation and classification, their life cycles and infection strategies, and their potential role in toxin production in algae. We outline key areas in phytoplankton host parasite dynamics that are poorly understood, discuss the potential roles of chytrids in these areas, and highlight future research directions for the furthering of our knowledge regarding algal ecophysiology. The synthesis of current knowledge in these fields will help researchers develop new hypotheses to further our understanding of primary production in aquatic ecology, and thus enhance our understanding of aquatic ecology, for more effective management of aquatic ecosystems. Crown Copyright (C) 2015 Published by Elsevier Ltd on behalf of The British Mycological Society. All rights reserved.
Published: 2015
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21. The Ocean Gene Atlas: exploring the biogeography of plankton genes online

Author: Villar, Emilie, Vannier, Thomas, Vernette, Caroline, Lescot, Magali, Cuenca, Miguelangel, Alexandre, Aurélien, Bachelerie, Paul, Rosnet, Thomas, Pelletier, Eric, Sunagawa, Shinichi, Hingamp, Pascal, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Centre National de la Recherche Scientifique (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)-Centre National de la Recherche Scientifique (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), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut de Biologie François JACOB (JACOB), 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), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), 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)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Aquatic Organisms, Internet, [SDV.GEN]Life Sciences [q-bio]/Genetics, [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], Oceans and Seas, [SDV]Life Sciences [q-bio], [INFO.INFO-WB]Computer Science [cs]/Web, fungi, Biodiversity, Plankton, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Phylogeography, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Web Server Issue, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Ecosystem, Software, ComputingMilieux_MISCELLANEOUS, geographic locations, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/. ISSN:1362-4962 ISSN:0301-5610
Published: 2018
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22. Impact de la température sur les interactions entre la microalgue marine Micromonas et les virus qui l’infectent

Author: Demory, David, Arsenieff, Laure, Simon, Nathalie, Six, Christophe, Rigaut-Jalabert, Fabienne, Marie, Dominique, Ge, Pei, Bigeard, Estelle, Sciandra, Antoine, Bernard, Olivier, Rabouille, Sophie, Baudoux, A. C., Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), 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), Biological control of artificial ecosystems (BIOCORE), 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)-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)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), MArine Phototrophic Prokaryotes (MAPP), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), 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 National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), 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), 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), 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), 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)-Observatoire océanologique de Villefranche-sur-mer (OOVM), and 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)-Inria Sophia Antipolis - Méditerranée (CRISAM)
Subjects: [SDE.MCG]Environmental Sciences/Global Changes, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017

23. Redescription and phylogenetic analyses of Durchoniella spp. (Ciliophora, Astomatida) associated with the polychaete Cirriformia tentaculata (Montagu, 1808)

Author: Erwan Roussel, Laure Guillou, Anne-Laure Sauvadet, Sophie Le Panse, Denis H. Lynn, Joseph Schrével, Estelle Bigeard, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), University of Guelph, School of Earth and Ocean Sciences [Cardiff], Cardiff University, Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Phophorylation de protéines et Pathologies Humaines (P3H), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Lineage (evolution), Zoology, Astome, Molecular phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, Oligohymenophorea, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Microscopy, Electron, Transmission, Genus, Astomatida, RNA, Ribosomal, 18S, Animals, 14. Life underwater, Ciliophora, Phylogeny, Polychaete, Microscopy, Cirratulidae, biology, Phylogenetic tree, Ecology, Endocytoplasmic bacteria, Polychaeta, Ribosomal RNA, biology.organism_classification, Type species, 030104 developmental biology
Abstract: International audience; Microscopic and phylogenetic analyses were performed on endocommensal astome ciliates retrieved from the middle intestine of a marine cirratulid polychaete, Cirriformia tentaculata, collected in the bay of Roscoff (English Channel, Northwest French coast) and on the Southwest English coast. Three morphotypes of the astome genus Durchoniella were identified, two corresponding to described species (the type species Durchoniella brasili (Léger and Duboscq, 1904) De Puytorac, 1954 and Durchoniella legeriduboscqui De Puytorac, 1954) while a third morphotype remains undescribed. Their small subunit (SSU) rRNA gene sequences showed at least 97.2% identity and phylogenetic analyses grouped them at the base of the subclass Scuticociliatia (Oligohymenophorea), as a sister lineage to all astomes from terrestrial oligochaete annelids. Ultrastructural examination by transmission electron microscopy and fluorescence in situ hybridization analyses revealed the presence of endocytoplasmic cocci and rod-shaped bacteria surrounded by a very thin membrane. These endocytoplasmic bacteria may play a role in the association between endocommensal astome ciliates and cirratulid polychaetes inhabiting in anoxic coastal sediments.
Published: 2017
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24. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author: Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Guy, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Bazire, Pascal, Beluche, Odette, Bertrand, Laurie, Besnard-Gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Espérance, Aiach, Nathalie, Guerin, Thomas, Hamon, Chadia, Brun, Élodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Céline, Payen, Emilie, Perroud, Peggy, Petit, Emmanuel, Robert, Dominique, Ronsin, Murielle, Vacherie, Benoit, Acinas, Silvia, Royo-Llonch, Marta, Cornejo-Castillo, Francisco, Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, de Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael, Stepanauskas, Ramunas, Sullivan, Matthew, Brum, Jennifer, Duhaime, Melissa, Poulos, Bonnie, Hurwitz, Bonnie, Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Pesant, Stéphane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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), 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), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Centre National de Génotypage (CNG), Universidad Politécnica de Madrid (UPM), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Toulon - Faculté de Droit de Toulon (UTLN UFR Droit), Université de Toulon (UTLN), Actilia Multimedia, Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Grande Rue, Auteur indépendant, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Informatics Department, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), European Molecular Biology Laboratory [Heidelberg] (EMBL), Bigelow Laboratory for Ocean Sciences, University of Arizona, Ecology and Evolutionary Biology [Tucson] (EEB), European Molecular Biology Laboratory, School of Marine Sciences, University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), 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), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Groupe de Biologie Marine du CEA, Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), EA 3900 BIOPI Laboratoire de Phytotechnologie, Université de Picardie Jules Verne (UPJV), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), 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), 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 Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn, Vrije Universiteit [Brussels] (VUB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and 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)
Subjects: [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017
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25. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network

Author: Fabrice Not, Arnaud Meng, Adriana Alberti, Anita Annamale, Andrés Gutiérrez-Rodríguez, Ian Probert, Patrick Wincker, Stéphane Le Crom, Corinne Da Silva, Lucie Bittner, Erwan Corre, Raffaele Siano, Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, 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), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (ABIMS), Fédération de recherche de Roscoff (FR2424), 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)-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), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), 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), 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), CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), and Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0301 basic medicine, 0106 biological sciences, Proteome, Protein domain, Datasets as Topic, Genomics, Computational biology, 010603 evolutionary biology, 01 natural sciences, Transcriptome, 03 medical and health sciences, Annotation, transcriptomics, MESH: Gene Expression Profiling, proteomics, genomics/proteomics, Molecular evolution, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, genomics, MESH: Datasets as Topic, MESH: Genome, Symbiosis, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Sequence (medicine), protists, 0303 health sciences, MESH: Symbiosis, Genome, biology, microbial biology, molecular evolution, MESH: Transcriptome, Gene Expression Profiling, Dinoflagellate, biology.organism_classification, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], MESH: Proteome, 030104 developmental biology, MESH: Dinoflagellida, Dinoflagellida, Identification (biology)
Abstract: Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
Published: 2017
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26. A new view on the morphology and phylogeny of eugregarines suggested by the evidence from the gregarine Ancora sagittata (Leuckart, 1860) Labbé, 1899 (Apicomplexa: Eugregarinida)

Author: Andrei Diakin, Joseph Schrevel, Timur G. Simdyanov, Kirill V. Mikhailov, Laure Guillou, Vladimir V. Aleoshin, Lomonosov Moscow State University (MSU), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Department of Botany and Zoology, Masaryk University [Brno] (MUNI), Institute for Information Transmission Problems, Russian Academy of Sciences [Moscow] (RAS), Molécules de Communication et Adaptation des Micro-organismes (MCAM), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Species complex, Zoology, Marine gregarines, lcsh:Medicine, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Environmental DNA sequences, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Monophyly, Phylogenetics, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, 14. Life underwater, Phylogeny, Taxonomy, Synapomorphy, Phylogenetic tree, General Neuroscience, lcsh:R, Mucron, Cell Biology, General Medicine, SSU and LSU rDNA, Ribosomal RNA, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Phylogenesis, Ultrastructure, Parasitology, General Agricultural and Biological Sciences, Apicomplexa
Abstract: Background Gregarines are a group of early branching Apicomplexa parasitizing invertebrate animals. Despite their wide distribution and relevance to the understanding the phylogenesis of apicomplexans, gregarines remain understudied: light microscopy data are insufficient for classification, and electron microscopy and molecular data are fragmentary and overlap only partially. Methods Scanning and transmission electron microscopy, PCR, DNA cloning and sequencing (Sanger and NGS), molecular phylogenetic analyses using ribosomal RNA genes (18S (SSU), 5.8S, and 28S (LSU) ribosomal DNAs (rDNAs)). Results and Discussion We present the results of an ultrastructural and molecular phylogenetic study on the marine gregarine Ancora sagittata from the polychaete Capitella capitata followed by evolutionary and taxonomic synthesis of the morphological and molecular phylogenetic evidence on eugregarines. The ultrastructure of Ancora sagittata generally corresponds to that of other eugregarines, but reveals some differences in epicytic folds (crests) and attachment apparatus to gregarines in the family Lecudinidae, where Ancora sagittata has been classified. Molecular phylogenetic trees based on SSU (18S) rDNA reveal several robust clades (superfamilies) of eugregarines, including Ancoroidea superfam. nov., which comprises two families (Ancoridae fam. nov. and Polyplicariidae) and branches separately from the Lecudinidae; thus, all representatives of Ancoroidea are here officially removed from the Lecudinidae. Analysis of sequence data also points to possible cryptic species within Ancora sagittata and the inclusion of numerous environmental sequences from anoxic habitats within the Ancoroidea. LSU (28S) rDNA phylogenies, unlike the analysis of SSU rDNA alone, recover a well-supported monophyly of the gregarines involved (eugregarines), although this conclusion is currently limited by sparse taxon sampling and the presence of fast-evolving sequences in some species. Comparative morphological analyses of gregarine teguments and attachment organelles lead us to revise their terminology. The terms “longitudinal folds” and “mucron” are restricted to archigregarines, whereas the terms “epicystic crests” and “epimerite” are proposed to describe the candidate synapomorphies of eugregarines, which, consequently, are considered as a monophyletic group. Abolishing the suborders Aseptata and Septata, incorporating neogregarines into the Eugregarinida, and treating the major molecular phylogenetic lineages of eugregarines as superfamilies appear as the best way of reconciling recent morphological and molecular evidence. Accordingly, the diagnosis of the order Eugregarinida Léger, 1900 is updated.
Published: 2017
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27. Mixotrophy everywhere on land and in water: the grand écart hypothesis

Author: Marie Charpin, Marc-André Selosse, Fabrice Not, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Laboratoire Microorganismes : Génome et Environnement - Clermont Auvergne (LMGE), Université Clermont Auvergne (UCA)-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), Department of Zoology, Oklahoma State University [Stillwater], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), 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), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-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 de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-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 la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA)
Subjects: 0106 biological sciences, 0301 basic medicine, ved/biology.organism_classification_rank.species, Heterotroph, Biological pump, Kleptoplastidy, Biology, 01 natural sciences, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Botany, Terrestrial plant, Photosymbiosis, Ecosystem, 14. Life underwater, Autotroph, Osmotrophy, Ecology, Evolution, Behavior and Systematics, Phylogeny, ComputingMilieux_MISCELLANEOUS, Autotrophic Processes, Ecology, ved/biology, Aquatic ecosystem, Hemiparasitism, Carnivorous plants, Eukaryota, Heterotrophic Processes, Protists, 15. Life on land, Biological Evolution, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Mycoheterotrophy, 030104 developmental biology, Phagotrophy, 13. Climate action, Carbohydrate Metabolism, Mycorrhiza, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Kleptoplasty, Mixotroph, 010606 plant biology & botany, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; There is increasing awareness that many terrestrial and aquatic organisms are not strictly heterotrophic or autotrophic but rather mixotrophic. Mixotrophy is an intermediate nutritional strategy, merging autotrophy and heterotrophy to acquire organic carbon and/or other elements, mainly N, P or Fe. We show that both terrestrial and aquatic mixotrophs fall into three categories, namely necrotrophic (where autotrophs prey on other organisms), biotrophic (where heterotrophs gain autotrophy by symbiosis), and absorbotrophic (where autotrophs take up environmental organic molecules). Here we discuss their physiological and ecological relevance since mixotrophy is found in virtually every ecosystem and occurs across the whole eukaryotic phylogeny, suggesting an evolutionary pressure towards mixotrophy. Ecosystem dynamics tend to separate light from non-carbon nutrients (N and P resources): the biological pump and water stratification in aquatic ecosystems deplete non-carbon nutrients from the photic zone, while terrestrial plant successions create a canopy layer with light but devoid of non-carbon soil nutrients. In both aquatic and terrestrial environments organisms, face a grand-écart (dancer’s splits, i.e. i.e. the need to reconcile two opposing needs) between optimal conditions for photosynthesis versus gain of non-C elements. We suggest that mixotrophy allows adaptationof organisms to such environmental gradients, ultimately explaining why mixotrophic behaviors are widespread
Published: 2017
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28. Biogeography and diversity of Collodaria (Radiolaria) in the global ocean

Author: Julie Poulain, Stephane Pesant, Fabrice Not, Stéphane Audic, Andrés Gutiérrez-Rodríguez, Estelle Bigeard, Lars Stemmann, Tristan Biard, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and 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)
Subjects: 0301 basic medicine, Biogeography, Oceans and Seas, Biome, Microbiology, DNA, Ribosomal, 03 medical and health sciences, RNA, Ribosomal, 18S, Animals, 14. Life underwater, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics, Phylogeny, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Trophic level, biology, Ecology, fungi, Rhizaria, Genetic Variation, Plankton, biology.organism_classification, 030104 developmental biology, Environmental biotechnology, Original Article, Animal Distribution, human activities, Radiolaria
Abstract: Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770 +/- 1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474 +/- 17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.
Published: 2017
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29. Temperature is a key factor in Micromonas-virus interactions

Author: Olivier Bernard, Fabienne Rigaut-Jalabert, Christophe Six, Stéphan Jacquet, Pei Ge, Anne-Claire Baudoux, Dominique Marie, Antoine Sciandra, Laure Arsenieff, Nathalie Simon, Estelle Bigeard, David Demory, Sophie Rabouille, 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), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), MArine Phototrophic Prokaryotes (MAPP), 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), Biological control of artificial ecosystems (BIOCORE), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA)-Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), 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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-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)-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)-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)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de la Recherche Agronomique (INRA), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), ANR funding agency REVIREC12-BSV7-0006-01, ANR-14-CE04-0011,Phycover,Durabilité des productions microalgales par recyclage du phosphore et de l'azote des eaux résiduaires : vers la station d'épuration du futur(2014), Institut National de la Recherche Agronomique (INRA)-Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'océanographie de Villefranche (LOV), 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)-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), 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), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-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)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA), 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)-Inria Sophia Antipolis - Méditerranée (CRISAM), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Modeling and control of renewable resources (COMORE), and Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)
Subjects: 0301 basic medicine, Ecophysiology, Lysis, Microorganism, [SDV]Life Sciences [q-bio], Microbiology, Virus, 03 medical and health sciences, [SPI]Engineering Sciences [physics], Microbial ecology, Chlorophyta, [INFO.INFO-AU]Computer Science [cs]/Automatic Control Engineering, Phycodnaviridae, Seawater, 14. Life underwater, [MATH]Mathematics [math], Ecology, Evolution, Behavior and Systematics, Ecosystem, Micromonas, biology, Geomicrobiology, Temperature, Virion, biology.organism_classification, 030104 developmental biology, Lytic cycle, Host-Pathogen Interactions, Phytoplankton, [SDE]Environmental Sciences, Original Article, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4-32.5°C. Similar growth temperature optima (T opt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below T opt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above T opt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochem-istry and evolution.
Published: 2017
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30. Comparison of coastal phytoplankton composition estimated from the V4 and V9 regions of 18S rRNA gene with a focus on photosynthetic groups and especially Chlorophyta

Author: Tragin, Margot, Zingone, Adriana, Vaulot, Daniel, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), and Stazione Zoologica Anton Dohrn (SZN)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; We compared the composition of eukaryotic communities using two genetic markers (18S rRNA V4 and V9 regions) at 27 sites sampled during Ocean Sampling Day 2014, with a focus on photosynthetic groups and, more specifically green algae (Chlorophyta). Globally, the V4 and V9 regions of the 18S rRNA gene provided similar images of alpha diversity and ecological patterns. However, V9 provided 20% more OTUs built at 97% identity than V4 and 39% and 56% of the genera were found only in one dataset, respectively V4 and V9. For photosynthetic groups, V4 and V9 performed equally well to describe global communities at different taxonomic levels from the division to the genus and provided similar Chlorophyta distribution patterns. However, at lower taxonomic level, the V9 dataset failed for example to describe the diversity of Dolichomastigales (Chlorophyta, Mamiellophyceae) emphasizing the lack of V9 sequences for this group and the importance of the reference database for metabarcode analysis. We conclude that in order to address specific questions regarding specific groups (e.g. a given genus), it is necessary to choose the marker based not only on the genetic divergence within this group but also on the existence of reference sequences in databases.
Published: 2017
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31. Estimating microbial populations by flow cytometry: Comparison between instruments

Author: Gérikas Ribeiro, Catherine, Marie, Dominique, Lopes dos Santos, Adriana, Pereira Brandini, Frederico, Vaulot, Daniel, Departamento de Oceanografia Biologica, Instituto Oceanografico, Universidade de Sao Paulo, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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: [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; For almost three decades, flow cytometry has allowed researchers to investigate ocean planktonic communities using size and cell fluorescence properties. However, oceanographic applications must face two constraints. First, when dealing with marine microbes, instruments must be sensitive because these organisms are very small and with low fluorescence. Second, instruments must be portable to be used on board ships. We compared the performance of two instruments, the BD FACSCanto™ and BD Accuri™ C6. The former is an expensive laboratory-based instrument which has a very good sensitivity, whilst the latter is less sensitive but presents critical advantages for field studies (easy handling and transportation, relatively low cost). We have analyzed 102 samples from the South Atlantic Ocean from three transects off Brazil, within the euphotic zone. We compared cell abundance of heterotrophic bacteria, Prochlorococcus and Synechococcus, as well as photosynthetic pico- and nano-eukaryotes. Heterotrophic bacteria, pico- and nano-eukaryotes could be easily detected with both cytometers. Prochlorococcus and Synechococcus populations were severely under-estimated with the BD Accuri™ C6, particularly for samples from the well-lit layers of the water column. Correction of abundance data using previously suggested approaches was not sufficient to fully compensate for the low sensibility. Our data suggest that the BD Accuri™ C6 is suitable for counting marine bacteria and photosynthetic eukaryotes, but not Prochlorococcus and Synechococcus.
Published: 2017
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32. Micromonas versus virus: New experimental insights challenge viral impact

Author: Ruiz, Eliana, Baudoux, Anne-Claire, Simon, Nathalie, Sandaa, Ruth-Anne, Thingstad, T. Frede, Pagarete, António, University of Bergen (UiB), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, viruses, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Viruses have recurrently been hypothesized as instrumental in driving microbial population diversity. Nonetheless, viral mediated coexistence of r/k-strategists, predicted in the Killing-the-Winner (KtW) hypothesis, remains controversial and demands empirical evidence. Therefore, we measured the life strategy parameters that characterize the relevant system Micromonas-Micromonas Virus (MicV). A large number of host and viral strains (37 and 17, respectively) were used in a total of 629 cross-infectivity tests. Algal and viral abundances were monitored by flow cytometry and used to calculate values of growth rate, resistance capacity, and viral production. Two main assumptions of the KtW model , namely (1) a resistance-associated cost on growth and (2) a negative correlation between resistance and viral production capacity, were mildly observed and lacked statistical significance. Micro-monas strains infected by more MicV strains presented higher lysis and viral production rates as the number of infectious virus strains increased, suggesting a 'one-gate' regulation of infection in this system. MicV strains demonstrated a vast range of virion production capacity, which unexpectedly grew with increasing host-range. Overall, the significant trends observed in here demonstrate strong co-interactions at different levels between Micromonas and MicV populations, however, the role of viruses as major driving force in phytoplankton fitness wasn't explicitly observed.
Published: 2017
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33. Improvement of phytoplankton culture isolation using single cell sorting by flow cytometry

Author: Daniel Vaulot, Priscillia Gourvil, Florence Le Gall, Dominique Marie, Roseline Edern, MArine Phototrophic Prokaryotes (MAPP), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), and Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP)
Subjects: 0106 biological sciences, 0301 basic medicine, Algal cells, Plant Science, Penicillins, Aquatic Science, Bacterial growth, Biology, 01 natural sciences, Flow cytometry, Microbiology, 03 medical and health sciences, Phytoplankton, medicine, Bovine serum albumin, Laser beams, medicine.diagnostic_test, 010604 marine biology & hydrobiology, Neomycin, Cell sorting, Flow Cytometry, Anti-Bacterial Agents, 030104 developmental biology, Biochemistry, biology.protein, Streptomycin, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, medicine.drug
Abstract: International audience; Flow cytometry provides a tool to physically sort single algal cells in order to obtain clonal cultures. During sorting, cells are submitted to physical stress factors such as high fluidic pressure, exposure to the laser beam, electrostatic charges, deflection through high voltage fields and collisions with container surfaces. All of these can damage the cells of interest and success rates for initiation of cultures from flow-sorted cells are generally very low. We found that the addition of Bovine Serum Albumin (BSA) in the culture medium into which cells are sorted drastically improved the success of initiation of pico- and nano-eukaryotic phytoplankton strains. Adding a mixture of antibiotics (PNS: Penicillin, Neomycin, Streptomycin) to the medium in order to slow down bacterial growth further improved culture development. This approach was successfully used to isolate taxonomically diverse strains, including novel taxa, from a fresh sample obtained in the English Channel and from enrichment cultures established during an Atlantic Meridional Transect (AMT) cruise. We anticipate that these improvements will be useful to clone or purify existing cultures and to isolate novel cultures from oceanic samples.
Published: 2017
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34. Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P)

Author: Gutiérrez-Rodríguez, Andrés, Pillet, Loic, Biard, Tristan, Said-Ahmad, Ward, Amrani, Alon, Simó, Rafel, Not, Fabrice, United States-Israel Binational Science Foundation, Ministerio de Ciencia e Innovación (España), National Institution for Water and Atmospheric (New Zealand), Swiss National Science Foundation, Région Bretagne, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), National Institute of Water and Atmospheric Research [Wellington] (NIWA), University of Geneva [Switzerland], The Hebrew University of Jerusalem (HUJ), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), and Université de Genève = University of Geneva (UNIGE)
Subjects: DMS(P), fungi, Symbiosis, Radiolaria, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: 16 pages, 5 figures, 1 table, supporting information https://dx.doi.org/10.1002/lno.10491, Symbiosis with micro-algae (photosymbiosis) is a common feature among marine planktonic protists, but very little is known about the physiology and ecological significance of these associations. High concentrations of dimethylsulfoniopropionate (DMSP), a metabolite produced by marine microalgae, are commonly observed in coral-microalgae symbiosis, where DMS(P) is involved in multiple physiological functions. Knowledge on concentration and role of DMSP in analogous photosymbiosis in plankton is lacking. Here, we assess the total DMSP (DMSPt = DMSP + DMS) concentration and natural stable isotopes of sulfur across ecologically relevant symbiotic plankton groups, the Radiolaria and Foraminifera. We found that intracellular DMSPt concentrations in microalgal symbionts were among the highest recorded (range = 170–702 mmol L), while lower concentrations (range = 0.1–23 mmol L) were characteristic of the holobiont (i.e., host-microalgae). The contribution of symbiotic Radiolaria to the water column particulate DMSPt concentration ranged 0.1–8%. Sulfur isotopic composition (S) of DMSPt in the Collodaria holobionts was significantly higher than their symbiotic microalgae isolated in culture. Despite their high intracellular DMSPt content, SO uptake in these holobionts throughout 3-d incubations was not detected. We observed a systematic S depletion (∼ 1.5‰) of DMS relative to DMSP in experimental incubations containing filtered seawater, which we hypothesize is related to the bacterial preference for the uptake of S-depleted DMS. Overall, the results indicate that plankton symbiosis can, at times, represent a potentially important source of DMS(P). Specific differences in S provided new insights into sulfur isotopic fractionation associated with DMS(P) biotransformation processes, with potential implications for current interpretations of isotopically tracked biogenic sources of marine aerosols., A.A. thanks the Binational Science Foundation Grant 2010407 for partial funding of this work. R.S. acknowledges support from the Spanish Ministry of Science and Innovation through the SUMMER project (CTM2008-03309). A.G.R. was supported by a Region Bretagne postdoctoral fellowship SYMBIOX and by the National Institution for Water and Atmospheric research (NIWA, New Zealand). T.B. was supported by the UMPC Emergence program and L.P. by the SNF Seastar project. LP was supported by the Swiss National Science Foundation postdoctoral grant P2GEP3_148800
Published: 2017
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35. Development of Axial Pile Load Transfer Curves Based on Instrumented Load Tests

Author: Roger Frank, Cécilia Bohn, Alexandre Lopes dos Santos, Laboratoire Navier (navier umr 8205), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), California Institute of Technology (CALTECH), Mathematisches Institut [München] (LMU), Ludwig-Maximilians-Universität München (LMU), and École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)
Subjects: International level, Engineering, business.industry, Hyperbolic function, 0211 other engineering and technologies, Modulus, 020101 civil engineering, 02 engineering and technology, Structural engineering, Geotechnical Engineering and Engineering Geology, Dynamic load testing, 0201 civil engineering, Set (abstract data type), [SPI]Engineering Sciences [physics], Transfer (computing), Development (differential geometry), Geotechnical engineering, business, Pile, 021101 geological & geomatics engineering, General Environmental Science
Abstract: International audience; The load transfer method is an efficient and practical tool for the analysis of single piles and combined systems such as pile-raft foundations and rigid inclusions. The existing transfer curves rely either on the measurement of the pressuremeter modulus, which is not widespread at the international level, or they have been developed only for specific pile and ground types. In order to develop new transfer curves valid for all pile and ground types without the need of pressuremeter tests, a database of 50 instrumented pile load tests was examined. The existing curves were first compared to the measurements at the pile shaft and at the tip. Then the parameters of the most appropriate curve types, the cubic root and the hyperbolic curve, were calibrated in order to best match the measurements. A single set of parameters for each proposed curve type is suitable enough for most pile and ground types. The good agreement of the proposed curves was confirmed by applying them to assess the overall load-settlement curve of 72 other pile load tests.
Published: 2017
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36. The Evolution of Silicon Transport in Eukaryotes

Author: Marron, Alan O., Ratcliffe, Sarah, Wheeler, Glen L., Goldstein, Raymond E., King, Nicole, Not, Fabrice, de Vargas, Colomban, Richter, Daniel J., Goldstein, Raymond [0000-0003-2645-0598], Apollo - University of Cambridge Repository, Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), Department of Applied Mathematics and Theoretical Physics (DAMTP), University of Bristol [Bristol], Marine Biological Association, Department of Molecular & Cell Biology [Berkeley], University of California [Berkeley], University of California-University of California, Howard Hughes Medical Institute (HHMI), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of California [Berkeley] (UC Berkeley), and University of California (UC)-University of California (UC)
Subjects: Silicon, Evolution, Sequence Homology, transporter, Evolution, Molecular, eukaryotes, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, convergent evolution, Discoveries, Choanoflagellata, Phylogeny, Diatoms, Sequence Homology, Amino Acid, Molecular, Eukaryota, Membrane Transport Proteins, Biological Transport, DNA, Sequence Analysis, DNA, Biological Evolution, Lsi2, Amino Acid, SIT, Carrier Proteins, Sequence Analysis
Abstract: International audience; Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, including major silicified lineages (radiolarians and chrysophytes) and also bacterial SIT-Ls. Our evidence suggests that the symmetrical 10-transmembrane-domain SIT structure has independently evolved multiple times via duplication and fusion of 5-transmembrane-domain SIT-Ls. We also identify a second gene family, similar to the active Si transporter Lsi2, that is broadly distributed amongst siliceous and nonsiliceous eukaryotes. Our analyses resolve a distinct group of Lsi2-like genes, including plant and diatom Si-responsive genes, and sequences unique to siliceous sponges and choanoflagellates. The SIT/SIT-L and Lsi2 transporter families likely contribute to biosilicification in diverse lineages, indicating an ancient role for Si transport in eukaryotes. We propose that these Si transporters may have arisen initially to prevent Si toxicity in the high Si Precambrian oceans, with subsequent biologically induced reductions in Si concentrations of Phanerozoic seas leading to widespread losses of SIT, SIT-L, and Lsi2-like genes in diverse lineages. Thus, the origin and diversification of two independent Si transporter families both drove and were driven by ancient ocean Si levels.
Published: 2016
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37. Survey of the green picoalga Bathycoccus genomes in the global ocean

Author: Yoann Seeleuthner, Patrick Wincker, Samuel Mondy, Jean-Marc Aury, Daniele Iudicone, Jade Leconte, Olivier Jaillon, Michael E. Sieracki, Thomas Vannier, Daniel Vaulot, Eric Pelletier, Colomban de Vargas, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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), Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-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), National Science Foundation [Arlington] (NSF), Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Oceans and Seas, 030106 microbiology, Sequence assembly, Genomics, comparative genomics, Genome, Article, 18S ribosomal RNA, Bathycoccus, 03 medical and health sciences, Chlorophyta, Phylogenetics, Surveys and Questionnaires, Microalgae, RNA, Ribosomal, 18S, Seawater, biogeography, metagenomics, 14. Life underwater, Phylogeny, Ecotype, Comparative genomics, Genetics, Multidisciplinary, biology, biology.organism_classification, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Metagenomics, Phytoplankton, Metagenome
Abstract: Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region. Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes. Bathycoccus is relatively abundant and widely distributed in nutrient rich waters. The two genomes rarely co-occur and occupy distinct oceanic niches in particular with respect to depth. Metatranscriptomic data provide evidence for gain or loss of highly expressed genes in some samples, suggesting that the gene repertoire is modulated by environmental conditions.
Published: 2016
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38. Ultrastructure of Selenidium pendula, the Type Species of Archigregarines, and Phylogenetic Relations to Other Marine Apicomplexa

Author: Gerard Prensier, Isabelle Florent, Aurélie Chambouvet, Andrea Bardůnek Valigurová, Joseph Schrevel, Laure Guillou, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Masaryk University [Brno] (MUNI), Université de Tours (UT), 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 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), ANR-11-IDEX-0004,SUPER,Sorbonne Universités à Paris pour l'Enseignement et la Recherche(2011), ANR-14-CE02-0007,HAPAR,Le paradoxe de la spécialisation chez un parasite de microalgues responsables de marées rouges(2014), Université de Tours, 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), Institut Universitaire Européen de la Mer (IUEM), 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)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: 0301 basic medicine, Myzocytosis, food.ingredient, Subpellicular microtubule, Selenidium pendula, Cirratulidae, phylogeny, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, DNA, Ribosomal, Microbiology, [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, 03 medical and health sciences, Archigregarines, food, Microscopy, Electron, Transmission, Phylogenetics, Botany, sporozoite, 14. Life underwater, Inner membrane complex, Rhoptry, biology, ACL, DNA, Protozoan, biology.organism_classification, ultrastructure, 030104 developmental biology, Evolutionary biology, Microscopy, Electron, Scanning, Selenidium, Apical complex, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Apicomplexa
Abstract: International audience; Archigregarines, an early branching lineage within Apicomplexa, are a poorly-known group of invertebrate parasites. By their phylogenetic position, archigregarines are an important lineage to understand the functional transition that occurred between free-living flagellated predators to obligatory parasites in Apicomplexa. In this study, we provide new ultrastructural data and phylogenies based on SSU rDNA sequences using the type species of archigregarines, the Selenidiidae Selenidium pendula Giard, 1884. We describe for the first time the syzygy and early gamogony at the ultrastructural level, revealing a characteristic nuclear multiplication with centrocones, cryptomitosis, filamentous network of chromatin, a cyst wall secretion and a 9 + 0 flagellar axoneme of the male gamete. S. pendula belongs to a monophyletic lineage that includes several other related species, all infecting Sedentaria Polychaeta (Spionidae, Sabellaridae, Sabellidae and Cirratulidae). All of these Selenidium species exhibit similar biological characters: a cell cortex with the plasma membrane - inner membrane complex - subpellicular microtubule sets, an apical complex with the conoid, numerous rhoptries and micronemes, a myzocytosis with large food vacuoles, a nuclear multiplication during syzygy and young gamonts. Two other distantly related Selenidium-like lineages infect Terebellidae and Sipunculida, underlying the ability of archigregarines to parasite a wide range of marine hosts.
Published: 2016
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39. Defining planktonic protist functional groups on mechanisms for energy and nutrient acquisition: Incorporation of diverse mixotrophic strategies

Author: Mitra, Aditee, Flynn, Kevin J., Tillmann, Urban, Raven, John A., Caron, David, Stoecker, Diane K., Not, Fabrice, Hansen, Per J., Hallegraeff, Gustaaf, Sanders, Robert, Wilken, Susanne, McManus, George, Johnson, Mathew, Pitta, Paraskevi, Våge, Selina, Berge, Terje, Calbet, Albert, Thingstad, Frede, Jeong, Hae Jin, Burkholder, JoAnn, Glibert, Patricia M., Granéli, Edna, Lundgren, Veronica, Swansea University, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Division of Plant Sciences, College of Life Sciences, University of Dundee, Department of Biological Sciences, University of Southern California (USC), University of Maryland Center for Environmental Science, Horn Point Laboratory, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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 Ocean Life, University of Copenhagen = Københavns Universitet (KU), Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), Department of Biology, Temple University [Philadelphia], Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Marine Sciences, University of Connecticut (UCONN), Woods Hole Oceanographic Institution (WHOI), Hellenic Centre for Marine Research (HCMR), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB), School of Earth and Environmental Sciences [Seoul] (SEES), Seoul National University [Seoul] (SNU), Center for Applied Aquatic Ecology, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Lund University, Department of Biology and Environmental Sciences, Linnaeus University, University of Copenhagen = Københavns Universitet (UCPH), Institute for Marine and Antarctic Studies [Hobart] (IMAS), and Lund University [Lund]
Subjects: phagotroph, phototroph, Food Chain, Plankton functional types (PFTs), Eukaryota, Microbiology, Zooplankton, Phototrophic Processes, mixotroph, microzooplankton, Phytoplankton, Animals, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Energy Metabolism, Phylogeny
Abstract: International audience; Arranging organisms into functional groups aids ecological research by grouping organisms (irrespective of phylogenetic origin) that interact with environmental factors in similar ways. Planktonic protists traditionally have been split between photoautotrophic “phytoplankton” and phagotrophic “microzooplankton”. However, there is a growing recognition of the importance of mixotrophy in euphotic aquatic systems, where many protists often combine photoautotrophic and phagotrophic modes of nutrition. Such organisms do not align with the traditional dichotomy of phytoplankton and microzooplankton. To reflect this understanding, we propose a new functional grouping of planktonic protists in an eco-physiological context: (i) phagoheterotrophs lacking phototrophic capacity, (ii) photoautotrophs lacking phagotrophic capacity, (iii) constitutive mixotrophs (CMs) as phagotrophs with an inherent capacity for phototrophy, and (iv) non-constitutive mixotrophs (NCMs) that acquire their phototrophic capacity by ingesting specific (SNCM) or general non-specific (GNCM) prey. For the first time, we incorporate these functional groups within a foodweb structure and show, using model outputs, that there is scope for significant changes in trophic dynamics depending on the protist functional type description. Accordingly, to better reflect the role of mixotrophy, we recommend that as important tools for explanatory and predictive research, aquatic food-web and biogeochemical models need to redefine the protist groups within their frameworks.
Published: 2016
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40. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to diatoms

Author: Colomban de Vargas, Daniel Vaulot, Stéphane Audic, Shinya Yoshikawa, Mary-Hélène Noël, Akira Kuwata, Mitsunobu Kamiya, Priscillia Gourvil, Adriana Lopes dos Santos, Kaori Ohki, Mutsuo Ichinomiya, Prefectural University of Kumamoto, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Fukui Prefectural University, University of Fukui, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), National Institute for Environmental Studies (NIES), Tohoku National Fisheries Research Institute, and National Fisheries Research Institute
Subjects: 0301 basic medicine, Operational taxonomic unit, Bolidomonas, Oceans and Seas, Molecular Sequence Data, Antarctic Regions, DNA, Ribosomal, Microbiology, rail, 03 medical and health sciences, Monophyly, Mediterranean sea, Algae, Mediterranean Sea, Seawater, 14. Life underwater, Clade, Phylogeny, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Diatoms, biology, Ecology, rail.locomotive_class, Biodiversity, biology.organism_classification, 030104 developmental biology, Phytoplankton, Bolidophyceae, Original Article, Taxonomy (biology)
Abstract: International audience; Bolidomonas is a genus of picoplanktonic flagellated algae that is closely related to diatoms. Triparma laevis, a species belonging to the Parmales, which are small cells with a siliceous covering, has been shown to form a monophyletic group with Bolidomonas. We isolated several novel strains of Bolidophyceae that have permitted further exploration of the diversity of this group using nuclear, plastidial and mitochondrial genes. The resulting phylogenetic data led us to formally emend the taxonomy of this group to include the Parmales within the Bolidophyceae, to combine Bolidomonas within Triparma and to define a novel species, Triparma eleuthera sp. nov. The global distribution of Bolidophyceae was then assessed using environmental sequences available in public databases, as well as a large 18S rRNA V9 metabarcode data set from the Tara Oceans expedition. Bolidophyceans appear ubiquitous throughout the sampled oceans but always constitute a minor component of the phytoplankton community, corresponding to at most ~ 4% of the metabarcodes from photosynthetic groups (excluding dinoflagellates). They are ~ 10 times more abundant in the small size fraction (0.8– 5 μm) than in larger size fractions. T. eleuthera sp. nov. constitutes the most abundant and most widespread operational taxonomic unit (OTU) followed by T. pacifica, T. mediterranea and the T. laevis clade. The T. mediterranea OTU is characteristic of Mediterranean Sea surface waters and the T. laevis clade OTU is most prevalent in colder waters, in particular off Antarctica.
Published: 2016
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41. Plankton networks driving carbon export in the oligotrophic ocean

Author: Guidi, Lionel, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Chaffron, Samuel, Tara Oceans Consortium Coordinators, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Bittner, Lucie, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Eveillard, Damien, Gorsky, Gabriel, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, 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), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), Department of Applied Biological Sciences (DBIT), Department of Microbiology and Immunology, Rega Institute, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), 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), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Biological Oceanography Division, CSIR National Institute of Oceanography [India] (NIO), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Ohio State University [Columbus] (OSU), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), 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), Structural and Computational Biology, European Molecular Biology Laboratory [Heidelberg] (EMBL), Directors’ Research European Molecular Biology, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), 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)-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), Diversité et Interactions au sein du Plancton Océanique (DIPO), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), School of Marine Sciences, University of Maine, Institute for Chemical Research, Kyoto University, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Génomique métabolique (UMR 8030), 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)-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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Max Delbrück Centre for Molecular Medicine, Stazione Zoologica Anton Dohrn (SZN), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Department of Bio-engineering Sciences, 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), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), Department of Ecology and Evolutionary Biology, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École polytechnique (X)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Kyoto University [Kyoto], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0301 basic medicine, Chlorophyll, Aquatic Organisms, 010504 meteorology & atmospheric sciences, Genes, Viral, General Science & Technology, Oceans and Seas, chemistry.chemical_element, Biology, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 01 natural sciences, Deep sea, Article, 03 medical and health sciences, Ecosystem, Seawater, Viral, 14. Life underwater, Photosynthesis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Total organic carbon, Marine biology, Synechococcus, Deep chlorophyll maximum, Multidisciplinary, Geography, Ecology, Tara Oceans coordinators, fungi, Bacterial, 15. Life on land, Plankton, Carbon, 030104 developmental biology, Oceanography, Genes, chemistry, 13. Climate action, Ocean color, Genes, Bacterial, Dinoflagellida, Expeditions
Abstract: Guidi, Lionel ... et al.-- 16 pages, 4 figures, supplementary information https://dx.doi.org/10.1038/nature16942 .-- This article is contribution number 34 of Tara Oceans, The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions, We thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research – Flanders, Rega Institute, KU Leuven, The French Ministry of Research, the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ANR (projects POSEIDON/ANR-09-BLAN-0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218, SAMOSA, ANR-13-ADAP-0010), European Union FP7 (MicroB3/No.287589, ERC Advanced Grant Award to C.B. (Diatomite: 294823), Gordon and Betty Moore Foundation grant (#3790 and #2631) and the UA Technology and Research Initiative Fund and the Water, Environmental, and Energy Solutions Initiative to M.B.S., the Italian Flagship Program RITMARE to D.I., the Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d'Ajusts Universitaris i Reserca to S.G.A., JSPS KAKENHI grant number 26430184 to H.O., and FWO, BIO5, Biosphere 2 to M.B.S. We also thank the support and commitment of Agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, the Tara schooner and its captains and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions
Published: 2016
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42. Picophytoplankton biomass distribution in the global ocean

Author: Diego Macías, Lisa Campbell, Osvaldo Ulloa, Stéphan Jacquet, Michael W. Lomas, George B. McManus, François Lantoine, Francisco P. Chavez, Michael R. Landry, William K. W. Li, Michel Gosselin, Erik T. Buitenhuis, David M. Karl, Frédéric Partensky, Daniel Vaulot, Tyndall Centre for Climate Change Research and School of Environmental Sciences, University of East Anglia [Norwich] (UEA), Fisheries and Oceans Canada, Bedford Institute of Oceanography, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Bermuda Institute of Ocean Sciences (BIOS), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Procaryotes Phototrophes Marins = MArine Phototrophic Prokaryotes (MAPP), Department of Oceanography, University of Hawaii, Departmento de Oceanografía & Centro de Investigación Oceanográfica en el Pacífico Sur-Oriental, Universidad de Concepción - University of Concepcion [Chile], Department of Oceanography [College Station], Texas A&M University [College Station], Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Institut National de la Recherche Agronomique (INRA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, Department of Coastal Ecology and Management, Institute of Marine Sciences of Andalusia, Institut des Sciences de la MER de Rimouski (ISMER), Université du Québec à Rimouski (UQAR), Department of Marine sciences, University of Connecticut (UCONN), U (CarboChange) 264879, Networks of Centres of Excellence of Canada-ArcticNet, Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-Centre National de la Recherche Scientifique (CNRS), Scripps Institution of Oceanography (SIO), University of California-University of California, MArine Phototrophic Prokaryotes (MAPP), Universidad de Concepción [Chile], and Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Biodiversité et Ecologie, Distribution (economics), picophytoplancton, 01 natural sciences, Cell size, Biodiversity and Ecology, Abundance (ecology), Phytoplankton, 14. Life underwater, biomasse microbienne, lcsh:Environmental sciences, 0105 earth and related environmental sciences, lcsh:GE1-350, Biomass (ecology), océan, biology, business.industry, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Synechococcus, biology.organism_classification, Biomass carbon, lcsh:Geology, analyse par flux cytométrique, Oceanography, General Earth and Planetary Sciences, Environmental science, Prochlorococcus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business
Abstract: Buitenhuis, Erik et al., The smallest marine phytoplankton, collectively termed picophytoplankton, have been routinely enumerated by flow cytometry since the late 1980s during cruises throughout most of the world ocean. We compiled a database of 40 946 data points, with separate abundance entries for Prochlorococcus, Synechococcus and picoeukaryotes. We use average conversion factors for each of the three groups to convert the abundance data to carbon biomass. After gridding with 1° spacing, the database covers 2.4% of the ocean surface area, with the best data coverage in the North Atlantic, the South Pacific and North Indian basins, and at least some data in all other basins. The average picophytoplankton biomass is 12 ± 22 μg C l−1 or 1.9 g C m−2. We estimate a total global picophytoplankton biomass of 0.53–1.32 Pg C (17–39% Prochlorococcus, 12–15% Synechococcus and 49–69% picoeukaryotes), with an intermediate/best estimate of 0.74 Pg C. Future efforts in this area of research should focus on reporting calibrated cell size and collecting data in undersampled regions., We thank Claude Belzile, Jacques Neveux and Genevieve Tremblay for their comments on a draft manuscript, the EU (CarboChange, contract 264879) for financial support to ETB, and the Networks of Centres of Excellence of Canada-ArcticNet for financial support to MG.
Published: 2012
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43. Lotharella reticulosa sp. nov.: A Highly Reticulated Network Forming Chlorarachniophyte from the Mediterranean Sea

Author: Shuhei Ota, Daniel Vaulot, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Contrat de Projet Etat-Region ``Souchotheque de Bretagne', EU [EU-RI-227799, 2008-29765-62739-34], and French embassy in Japan
Subjects: 0106 biological sciences, Cell division, [SDV]Life Sciences [q-bio], Molecular Sequence Data, DNA, Ribosomal, 01 natural sciences, Microbiology, 18S ribosomal RNA, Pyrenoid, Chlorarachniophyte, taxonomy, 03 medical and health sciences, Botany, Mediterranean Sea, Seawater, 14. Life underwater, Flagellate, Cercozoa, Nucleomorph, Phylogeny, 030304 developmental biology, 0303 health sciences, biology, 010604 marine biology & hydrobiology, chlorarachniophytes, DNA, Protozoan, Lotharella, biology.organism_classification, Chloroplast, [SDE]Environmental Sciences, Ultrastructure, RCC375, RCC376
Abstract: International audience; A new chlorarachniophyte Lotharella reticulosa sp. nov. is described from a culture isolated from the Mediterranean Sea. This strain is maintained as strain RCC375 at the Roscoff Culture Collection, France. This species presents a multiphasic life cycle: vegetative cells of this species were observed to be coccoid, but amoeboid cells with filopodia and globular suspended cells were also present in the life cycle, both of which were not dominant phases. Flagellate cells were also observed but remained very rare in culture. The vegetative cells were 9-16 mu m in diameter and highly vacuolated, containing several green chloroplasts with a projecting pyrenoid, mitochondria, and a nucleus. The chloroplast was surrounded by four membranes possessing a nucleomorph in the periplastidial compartment near the pyrenoid base. According to ultrastructural observations of the pyrenoid and nucleomorph, the present species belongs to the genus Lotharella in the phylum Chlorarachniophyta. This taxonomic placement is consistent with the molecular phylogenetic trees of the 18S rRNA gene and ITS sequences. This species showed a unique colonization pattern. Clusters of cells extended cytoplasmic strands radially. Then, amoeboid cells being born proximately moved distally along the cytoplasmic strand like on a ``railway track''. Subsequently the amoeboid cell became coccoid near the strand. In this way, daughter cells were dispersed evenly on the substratum. We also observed that the present species regularly formed a structure of filopodial nodes in mid- stage and later-stage cultures, which is a novel phenotype in chlorarachniophytes. The unique colonization pattern and other unique features demonstrate that RCC375 is a new chlorarachniophyte belonging to genus Lotharella, which we describe as Lotharella reticulosa sp. nov. (C) 2011 Elsevier GmbH. All rights reserved.
Published: 2012
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44. Occurrence of the toxic dinoflagellate Ostreopsis cf. ovata in relation with environmental factors in Monaco (NW Mediterranean)

Author: J.M. Cottalorda, Aurelie Blanfuné, Rodolphe Lemée, Nathalie Simon, S. Cohu, Luisa Mangialajo, O. Passafiume, Thierry Thibaut, Jean-Philippe Labat, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), and Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)
Subjects: 0106 biological sciences, Mediterranean climate, Population Dynamics, 010501 environmental sciences, Aquatic Science, Biology, Oceanography, Polymerase Chain Reaction, 01 natural sciences, Mediterranean sea, Mediterranean Sea, 14. Life underwater, Weather, 0105 earth and related environmental sciences, HAB, Ecology, 010604 marine biology & hydrobiology, Monaco, fungi, Temperature, Dinoflagellate, Eutrophication, Plankton, biology.organism_classification, Dinoflagellates, Pollution, 13. Climate action, Benthic zone, Benthic microalgae, Dinoflagellida, Biological dispersal, Seasons, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Bloom, Ostreopsis
Abstract: To study environment characteristics favoring the toxic benthic dinoflagellate Ostreopsis cf. ovata, a survey was conducted in Monaco (NW Mediterranean Sea), in summers 2007 and 2008. Epiphytic and planktonic blooms occurred almost simultaneously and a high variation of abundances at low spatial scales was observed. An early and very marked bloom occurred in 2007, compared to a later and less abundant development in 2008. These distinct patterns in bloom timing corresponded with very different hydroclimatic scenarios in 2007 (hot spring and relatively cold summer) and 2008 (standard year compared to the median year profile estimated with data from 1995 to 2008). No clear impacts of summer seawater temperature, rainfall or nutrient concentrations were evident. Strong wind may favor the dispersal of benthic and planktonic cells. Our study suggests that further investigations are needed to examine the potential role of Ostreopsis nutritional mode (i.e. autotrophy vs. mixotrophy).
Published: 2011
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45. Distribution and host diversity of Amoebophryidae parasites across oligotrophic waters of the Mediterranean Sea

Author: Nathalie Simon, Elodie Foulon, Fabrice Not, Raffaele Siano, El Mahdi Bendif, Laure Guillou, Catharina Alves-de-Souza, 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), Universidad Austral de Chile, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Universite Pierre et Marie Curie (UPMC) [09036], CAS (Chilean government), French ANR AQUAPARADOX, and project SYMFORAD from the Region Bretagne
Subjects: 0106 biological sciences, Range (biology), [SDV]Life Sciences [q-bio], lcsh:Life, 01 natural sciences, Alveolate, 03 medical and health sciences, Mediterranean sea, Water column, lcsh:QH540-549.5, Marine ecosystem, 14. Life underwater, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Earth-Surface Processes, 0303 health sciences, Microbial food web, biology, Ecology, 010604 marine biology & hydrobiology, lcsh:QE1-996.5, Dinoflagellate, biology.organism_classification, lcsh:Geology, lcsh:QH501-531, [SDE]Environmental Sciences, lcsh:Ecology, Syndiniales
Abstract: Sequences affiliated to Syndiniales (Marine alveolate, MALV) regularly dominate 18S rDNA genetic libraries of nearly all marine ecosystems investigated so far. Among them, Amoebophryidae (MALV group II) is composed of numerous and genetically distant environmental sequences, where Amoebophrya is the only known and formally described genus. Amoebophrya species include virulent pathogens for a wide range of dinoflagellate species. Beside their regular occurrence in marine ecosystems, their quantitative distribution and the environmental factors triggering host infection have barely been studied in open oligotrophic waters. In order to understand the functional role of these parasites in natural environments, we studied the distribution and contribution to the eukaryotic community of the small free-living stage of Amoebophryidae (the dinospores) along a transect in the Mediterranean Sea, as well as their host diversity at three oligotrophic stations. Dinospores were more abundant at a coastal station (max. 1.5 × 103 cells ml−1) than in oligotrophic waters (max. 51 ± 16.3 cells ml−1), where they represented 10.3 to 34.9% of the total eukaryotic community at 40 and 30 m depth, respectively and 21.2% on average along the water column. Positive correlation was found between dinospore occurrence and higher concentration of NO3 + NO2 at the coastal station. At selected stations, out of 38 different dinoflagellates taxa identified, 15 were infected, among which a majority were not recognized as Amoebophryidae host so far. Prevalences (percentage of infected cells) generally varied between 1% and 10%, with a notable exception for Blepharocysta paulsenii for which 25% of cells were infected at the most oligotrophic station. The present study shows that dinospores are able to thrive and infect dinoflagellates both in coastal and ultra-oligotrophic open waters. Our results emphasize the role of parasitism in microbial food web dynamics and ultimately on biogeochemical cycles.
Published: 2011
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46. Effects of salinity on the growth rate and morphology of ten Skeletonema strains

Author: Wiebe H. C. F. Kooistra, Sergio Balzano, Diana Sarno, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Marine Botany, and Stazione Zoologica Anton Dohrn (SZN)
Subjects: 0106 biological sciences, Ecology, Brackish water, 010604 marine biology & hydrobiology, fungi, Life Sciences, Euryhaline, Aquatic Science, Biology, Plankton, biology.organism_classification, Cell morphology, 010603 evolutionary biology, 01 natural sciences, 6. Clean water, Salinity, Skeletonema marinoi, Algae, Genus, Botany, 14. Life underwater, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; Skeletonema comprises a planktonic genus of centric diatoms occurring in coastal and brackish waters worldwide. The most commonly reported species, S. costatum, was believed to be ubiquitous, morphologically plastic and euryhaline. Yet, recent studies showed that this perceived taxon consists of a series of species, including a more narrowly defined S. costatum sensu stricto. Here we investigated the effect of salinity on growth rate and cell morphology. Ten strains belonging to six Skeletonema species were incubated at salinities between zero and 35, their growth response was measured and their cell morphology observed in light and electron microscopy. All strains grew well between salinities of 10 and 35, whereas the lowest salinity at which growth was observed differed among species and even within the same species: Skeletonema marinoi strains deriving from distinct environments (Baltic and North Sea) showed different lower tolerance limits. Two species, Skeletonema costatum and S. subsalsum, showed growth between salinities of zero and 35 and exhibited very short intercellular processes when cultured in freshwater. Skeletonema subsalsum went through cell enlargement when exposed to a salinity of 35.
Published: 2010
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47. Photosynthetic picoeukaryote community structure in the South East Pacific Ocean encompassing the most oligotrophic waters on Earth

Author: Cécile Lepère, David J. Scanlan, Daniel Vaulot, 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), BIOSOPE cruise (CNRS-INSU LEFE), and PICOFUNPAC [06-BDIV-013]
Subjects: Chlorophyll, 0106 biological sciences, Food Chain, Range (biology), [SDV]Life Sciences [q-bio], Immunoblotting, Biodiversity, Biology, 01 natural sciences, Microbiology, 03 medical and health sciences, Food chain, Seawater, 14. Life underwater, Photosynthesis, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, South Pacific Gyre, Trophic level, Abiotic component, 0303 health sciences, Pacific Ocean, Picoeukaryote, Geography, Ecology, Chlorophyll A, 010604 marine biology & hydrobiology, Community structure, Eukaryota, biology.organism_classification, [SDE]Environmental Sciences
Abstract: International audience; P>Photosynthetic picoeukaryotes (PPEs), comprising organisms < 3 mu m in size, are important primary producers in marine food webs and include representatives from all known algal lineages. Little is known, however, regarding the composition and distribution of PPE communities, particularly at large spatial scales, or in relation to the underlying biotic and abiotic factors that influence this structure. Here, we analysed PPE community structure along a transect in the South East Pacific Ocean (BIOSOPE cruise) that encompassed a large trophic gradient, including hyper-oligotrophic waters in the South Pacific Gyre (SPG), considered to be some of the `clearest' natural waters on Earth. Using dot blot hybridizations with 16S rRNA oligonucleotide probes, we established that the PPE community was dominated by members of the classes Prymnesiophyceae and Chrysophyceae throughout the transect. Moreover, clone library construction followed by phylogenetic analysis of sequenced clones revealed several novel 16S rRNA gene lineages, including new clades of prymnesiophytes (designated Prym 16S-III) and prasinophytes (Pras 16S-VIII). Pras 16S-VIII was found at all five stations at which clone libraries were constructed, representing a range of trophic conditions, including the South Pacific Gyre, suggesting members of this clade have a broad distribution in this part of the South East Pacific at least. In contrast, Prym 16S-III sequences were largely restricted to oligotrophic stations of the SPG. Subsequent multivariate statistical analyses showed that, within the measured factors, chemical and biological factors seem to influence PPE community structure more than physical parameters. However, more than 50% of the variation in distribution of PPE classes remained unexplained.
Published: 2009
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48. In situ evidence for pre-capture qualitative selection in the tropical bivalve Lithophaga simplex

Author: Shiri Eckstein, Gitai Yahel, Amatzia Genin, Dominique Marie, Peter G. Beninger, The Interuniversity Institute for Marine Sciences of Eilat and the Department of Evolution, The School of Marine Sciences and Marine Environment, Ruppin Academic Center, Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), ISOMer, Rieger Foundation, US-Israel Binational Science Foundations, Israel Science Foundation, German Ministry of Science, Technology and Education (BMBF), Red Sea Program, French program PROSOPE, and European program PROMOLEC
Subjects: 0106 biological sciences, In situ, Coral reefs, [SDV]Life Sciences [q-bio], Population, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Algae, Botany, Dominance (ecology), Selectivity, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, Nutrition, education.field_of_study, Ecology, biology, Suspension feeding, 010604 marine biology & hydrobiology, Plankton, biology.organism_classification, Synechococcus, [SDE]Environmental Sciences, Prochlorococcus, Bacteria
Abstract: International audience; Few feeding studies have been performed on tropical bivalves, and in situ feeding studies are lacking altogether. We investigated retention efficiencies for natural particles in the coral-boring tropical mytilid Lithophaga simplex. Using the in situ InEx technique (Yahel et at. 2005; Limnol Oceanogr Methods 3:46-58) SCUBA divers collected samples from the water inhaled and exhaled by undisturbed bivalves at the coral reef of Eilat (Gulf of Aqaba). Particle retention efficiencies were determined using flow cytometry analysis of the paired water samples. The photosynthetic bacterium Synechococcus (0.9 +/- 0.1 mu m) and larger eukaryotic algae (1 to 10 mu m) were preferentially retained by the bivalve with removal efficiencies of up to 90 % (1996 to 2000: averages of 69 +/- 14 % and 60 +/- 17 %, respectively, n = 74 individual bivalves). The minute photosynthetic bacterium Prochlorococcus (0.4 +/- 0.1 mu m) was also moderately retained (41 +/- 19%). Only a small proportion of the non-photosynthetic bacteria (0.3 +/- 0.1 mu m) were retained (5 +/- 18%, median of 9%), despite their numerical dominance in the plankton and considerable size overlap with Prochlorococcus. Size-independent preferential retention was also observed within particle types: (1) L. simplex more efficiently retained Prochlorococcus and picoeukaryotic algal cells with higher chlorophyll content and (2) the small fraction of non-photo synthetic bacteria retained did not differ in size, but bad higher nucleic acid content (compared to the inhaled population) an indicator for viable and active bacteria. We conclude that particle retention is not strictly size-dependent in L. simplex, and probably involves other cell attributes such as cell surface properties and/or motility.
Published: 2009
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49. Heterogeneous distribution in sediments and dispersal in waters of Alexandrium minutum in a semi-enclosed coastal ecosystem

Author: Florian Caradec, Martin Plus, Lucia Pineau-Guillou, Julien Quere, Annie Chapelle, Raffaele Siano, Z.K. Klouch, T. Hernández-Fariñas, Laure Guillou, Sophie Schmitt, Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Unité Dyneco, Laboratoire Pelagos, Dynamiques de l'Environnement Côtier (DYNECO), and Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Geologic Sediments, 010504 meteorology & atmospheric sciences, Population dynamics, Species distribution, Intertidal zone, Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Aquatic Science, Biology, Real-Time Polymerase Chain Reaction, Spatial distribution, DNA, Ribosomal, 01 natural sciences, Molecular ecology, Lagrangian model, Ecosystem, 14. Life underwater, Dinoflagellate cyst, 0105 earth and related environmental sciences, Ecology, 010604 marine biology & hydrobiology, Sediment, Oceanography, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Bays, Dinoflagellida, Biological dispersal, France, Bay, Water Pollutants, Chemical, Environmental Monitoring, Real-time PCR
Abstract: International audience; Within the framework of research aimed at using genetic methods to evaluate harmful species distribution and their impact on coastal ecosystems, a portion of the ITS1rDNA of Alexandrium minutum was amplified by real-time PCR from DNA extracts of superficial (1–3 cm) sediments of 30 subtidal and intertidal stations of the Bay of Brest (Brittany, France), during the winters of 2013 and 2015. Cell germinations and rDNA amplifications of A. minutum were obtained for sediments of all sampled stations, demonstrating that the whole bay is currently contaminated by this toxic species. Coherent estimations of ITS1rDNA copy numbers were obtained for the two sampling cruises, supporting the hypothesis of regular accumulation of A. minutum resting stages in the south-eastern, more confined embayments of the study area, where fine-muddy sediments are also more abundant. Higher ITS1rDNA copy numbers were detected in sediments of areas where blooms have been seasonally detected since 2012. This result suggests that specific genetic material estimations in superficial sediments of the bay may be a proxy of the cyst banks of A. minutum. The simulation of particle trajectory analyses by a Lagrangian physical model showed that blooms occurring in the south-eastern part of the bay are disconnected from those of the north-eastern zone. The heterogeneous distribution of A. minutum inferred from both water and sediment suggests the existence of potential barriers for the dispersal of this species in the Bay of Brest and encourages finer analyses at the population level for this species within semi-enclosed coastal ecosystems.
Published: 2016
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50. Pseudo-nitzschia arctica sp. nov., a new cold-water cryptic Pseudo-nitzschia species within the P. pseudodelicatissima complex

Author: Diana Sarno, Nina Lundholm, Raffaele Siano, Sergio Balzano, Daniel Vaulot, Priscillia Gourvil, Anna Tammilehto, Isabella Percopo, Maria Valeria Ruggiero, Stazione Zoologica Anton Dohrn (SZN), 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), Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Dynamiques de l'Environnement Côtier (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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), University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), Laboratoire d'Ecologie Pélagique (PELAGOS), Dynamiques des Écosystèmes Côtiers (DYNECO), and Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: 0106 biological sciences, 0301 basic medicine, Species complex, media_common.quotation_subject, rbcL, nov, Morphology (biology), P. arctica sp. nov, Plant Science, Aquatic Science, Biology, phylogeny, 01 natural sciences, 03 medical and health sciences, Arctic, Species Specificity, ITS2 secondary structure, Molecular evolution, Phylogenetics, Genus, Toxicity Tests, morphology, cryptic, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, media_common, Diatoms, Likelihood Functions, Phylogenetic tree, Base Sequence, Ecology, 010604 marine biology & hydrobiology, Water, biology.organism_classification, Cold Temperature, Speciation, 030104 developmental biology, Evolutionary biology, Pseudo-nitzschia, Nucleic Acid Conformation, ITS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, arctica sp, LSU rRNA
Abstract: International audience; A new nontoxic Pseudo-nitzschia species belonging to the P. pseudodelicatissima complex, P. arctica, was isolated from different areas of the Arctic. The erection of P. arctica is mainly supported by molecular data, since the species shares identical ultrastructure with another species in the complex, P. fryxelliana, and represents a new case of crypticity within the genus. Despite their morphological similarity, the two species are not closely related in phylogenies based on LSU, ITS and rbcL. Interestingly, P. arctica is phylogenetically most closely related to P. granii and P. subcurvata, from which the species is, however, morphologically different. P. granii and P. subcurvata lack the central larger interspace which is one of the defining features of the P. pseudodelicatissima complex. The close genetic relationship between P. arctica and the two species P. granii and P. subcurvata is demonstrated by analysis of the secondary structure of ITS2 which revealed no compensatory base changes, two hemi-compensatory base changes, and two deletions in P. arctica with respect to the other two species. These findings emphasize that rates of morphological differentiation, molecular evolution and speciation are often incongruent for Pseudo-nitzschia species, resulting in a restricted phylogenetic value for taxonomic characters used to discriminate species. The description of a new cryptic species, widely distributed in the Arctic and potentially representing an endemic component of the Arctic diatom flora, reinforces the idea of the existence of noncosmopolitan Pseudo-nitzschia species and highlights the need for combined morphological and molecular analyses to assess the distributional patterns of phytoplankton species.
Published: 2016
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