Author: "Johan Decelle" / Topic: 03 medical and health sciences - Searchworks@Jio Institute Digital Library Search Results

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28 results on '"Johan Decelle"'

1. Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism

Author: Andreas P.M. Weber, Phillip Westhoff, Marianne Tardif, Denis Falconet, Erika Guglielmino, Dagmar Lyska, Benoit Gallet, Giovanni Finazzi, Gilles Curien, Clément Hallopeau, Michele Carone, Davide Dal Bo, Claire Remacle, Johan Decelle, Sabine Brugière, Myriam Ferro, Janina Janetzko, Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ)-Universität zu Köln = University of Cologne, Etude de la dynamique des protéomes (EDyP), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Photosymbiose, Institut de biologie structurale (IBS - UMR 5075), LIPID, Université de Liège, ARC grant (DARKMET proposal) for Concerted Research Actions (17/21-08), financed by the French Community of Belgium (Wallonia-Brussels Federation)., Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany´s Excellence Strategy – EXC-2048/1 – project ID 390686111, ANR-17-CE05-0029,MoMix,Modélisation de la Mixotrophie chez l'algue extrêmophile Galdieria sulphuraria(2017), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), European Project: 833184, ChloroMito, Martin-Laffon, Jacqueline, Modélisation de la Mixotrophie chez l'algue extrêmophile Galdieria sulphuraria - - MoMix2017 - ANR-17-CE05-0029 - AAPG2017 - VALID, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, Chloroplast and Mitochondria interactions for microalgal acclimation - ChloroMito - 833184 - INCOMING, Universität zu Köln-Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]-Max Planck Institute for Plant Breeding Research (MPIPZ), and InBios/Phytosystems Research Unit, University of Liege
Subjects: Proteomics, 0106 biological sciences, 0301 basic medicine, photorespiration, Physiology, Heterotroph, Plant Science, Photosynthesis, 7. Clean energy, 01 natural sciences, Galdieria sulphuraria, Extremophiles, 03 medical and health sciences, mixotrophy, Total inorganic carbon, Botany, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, red algae, photosynthesis, biology, Chemistry, Research, RuBisCO, Heterotrophic Processes, Carbon Dioxide, Full Papers, 15. Life on land, Carbon, 030104 developmental biology, Rhodophyta, biology.protein, Photorespiration, Energy source, Mixotroph, 010606 plant biology & botany
Abstract: Summary Galdieria sulphuraria is a cosmopolitan microalga found in volcanic hot springs and calderas. It grows at low pH in photoautotrophic (use of light as a source of energy) or heterotrophic (respiration as a source of energy) conditions, using an unusually broad range of organic carbon sources. Previous data suggested that G. sulphuraria cannot grow mixotrophically (simultaneously exploiting light and organic carbon as energy sources), its photosynthetic machinery being repressed by organic carbon.Here, we show that G. sulphuraria SAG21.92 thrives in photoautotrophy, heterotrophy and mixotrophy. By comparing growth, biomass production, photosynthetic and respiratory performances in these three trophic modes, we show that addition of organic carbon to cultures (mixotrophy) relieves inorganic carbon limitation of photosynthesis thanks to increased CO2 supply through respiration. This synergistic effect is lost when inorganic carbon limitation is artificially overcome by saturating photosynthesis with added external CO2.Proteomic and metabolic profiling corroborates this conclusion suggesting that mixotrophy is an opportunistic mechanism to increase intracellular CO2 concentration under physiological conditions, boosting photosynthesis by enhancing the carboxylation activity of Ribulose‐1,5‐bisphosphate carboxylase‐oxygenase (Rubisco) and decreasing photorespiration.We discuss possible implications of these findings for the ecological success of Galdieria in extreme environments and for biotechnological applications.
Published: 2021
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2. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae

Author: Niculina Musat, Yannick Schwab, Rémi Tucoulou, Hryhoriy Stryhanyuk, Johan Decelle, Sophie Marro, Fabien Chevalier, Charlotte LeKieffre, Nicole L. Schieber, Stéphane Ravanel, Giovanni Finazzi, Benoit Gallet, Giulia Veronesi, Department of Isotope Biogeochemistry, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Photosymbiose, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Chimie computationnelle, modélisation et rayons X (COMX), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), European Synchroton Radiation Facility [Grenoble] (ESRF), Institut de biologie structurale (IBS - UMR 5075), 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), Plantes, Stress & Métaux (MetalStress), European Molecular Biology Laboratory (EMBL), Light Photosynthesis & Metabolism (Photosynthesis), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), and ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)
Subjects: 0106 biological sciences, Stable-isotope probing, Biology, Photosynthesis, 01 natural sciences, Microbiology, Pyrenoid, 03 medical and health sciences, symbols.namesake, Symbiosis, Microalgae, Plastid, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, 0303 health sciences, Chemistry, Host (biology), 010604 marine biology & hydrobiology, fungi, Dinoflagellate, Metabolism, Golgi apparatus, biology.organism_classification, Plankton, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Biochemistry, 13. Climate action, symbols, Dinoflagellida, Intracellular, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the “greenhouse-like” colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low13C and15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.
Published: 2021
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3. Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

Author: Guy Schoehn, Clarisse Uwizeye, Gilles Curien, Rachel Templin, Samuel C. Zeeman, Yannick Schwab, Davide Dal Bo, Denis Falconet, Fabien Chevalier, Serena Flori, Christine Moriscot, Florence Courtois, Claire Seydoux, Jean-Baptiste Keck, Benoit Gallet, Johan Decelle, Nicole L. Schieber, Pierre-Henri Jouneau, Giovanni Finazzi, Guillaume Allorent, LIPID, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Photosymbiose, Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Institut de biologie structurale (IBS - UMR 5075), Calcul des Variations, Géométrie, Image (CVGI), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Cell Biology and Cell Biophysics Unit, European Molecular Biology Laboratory, European Molecular Biology Laboratory [Grenoble] (EMBL), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Défi X-Life grant from CNRS, CEA DRFimpulsion FIB-Bioprogram, Auvergne-Rhône-Alpes Region, Fondation Recherche Medicale (FRM), FEDER and the GIS-Infrastructures en Biologie Santé et Agronomie (IBiSA), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-17-CE05-0029,MoMix,Modélisation de la Mixotrophie chez l'algue extrêmophile Galdieria sulphuraria(2017), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), European Project: 833184, ChloroMito, and European Project: 654248,H2020,H2020-INFRADEV-1-2014-1,CORBEL(2015)
Subjects: 0106 biological sciences, 0301 basic medicine, Cell biology, Light, Bioenergetics, MESH: Mitochondria, Acclimatization, Science, General Physics and Astronomy, MESH: Acclimatization, MESH: Imaging, Three-Dimensional, Cellular imaging, Photosynthesis, 01 natural sciences, Article, General Biochemistry, Genetics and Molecular Biology, Pyrenoid, MESH: Microalgae, 03 medical and health sciences, Imaging, Three-Dimensional, Phytoplankton, Microalgae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastids, Plastid, Cellular microbiology, Trophic level, Biomass (ecology), Multidisciplinary, biology, Ecology, MESH: Energy Metabolism, fungi, MESH: Plastids, General Chemistry, biology.organism_classification, MESH: Light, Mitochondria, 030104 developmental biology, Diatom, MESH: Subcellular Fractions, Energy Metabolism, Subcellular Fractions, MESH: Phytoplankton, 010606 plant biology & botany
Abstract: Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales., Nature Communications, 12 (1), ISSN:2041-1723
Published: 2021
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4. A community perspective on the concept of marine holobionts: current status, challenges, and future directions

Author: Laura Núñez Pons, Alexey Vorobev, Ezequiel M. Marzinelli, Derek J. Skillings, Ehsan Kayal, François H. Lallier, Enora Briand, Eve Toulza, Tilmann Harder, Paco Cárdenas, Willem Stock, Fabrice Not, José Pintado, Johan Decelle, Marc André Selosse, Claire M. M. Gachon, Jean-Christophe Auguet, Mónica Medina, Sarah M. Griffiths, Damien Eveillard, Ulisse Cardini, Arite Bigalke, Mahasweta Saha, Catherine Leblanc, Soizic Prado, Elena Kazamia, Simon M. Dittami, Shinichi Sunagawa, Aschwin H. Engelen, Enrique Arboleda, Teresa Maria Morganti, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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)-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), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Laboratoire Phycotoxines, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Uppsala University, Stazione Zoologica Anton Dohrn (SZN), Photosymbiose, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], 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 Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Scottish Marine Institute, School of Science and the Environment (Manchester Metropolitan University), University of Bremen, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-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), Pennsylvania State University (Penn State), Penn State System, Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Sydney, NSW 2052 Australia, Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Instituto de Investigaciones Marinas de Vigo, Instituto de Investigaciones Marinas, Helmholtz Center for Ocean Research, Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Gdańsk (UG), University of Pennsylvania, University of Ghent, Universiteit Gent = Ghent University [Belgium] (UGENT), Institute of Microbiology and Swiss Institute of Bioinformatics, 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), CEA / Institut de Biologie François Jacob / Génoscope, 2, Rue Gaston Crémieux, CP5706, 91057 Evry cedex, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Phycotoxines (PHYC), 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), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Combinatoire et Bioinformatique (LS2N - équipe COMBI), 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), Universiteit Gent = Ghent University (UGENT), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), 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), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Biodiversity, DIVERSITY, lcsh:Medicine, 01 natural sciences, Ecosystem services, CORAL-REEF FISH, Evolutionsbiologi, Evolution, Symbiosis, Host-microbiota interactions, Marine holobionts, Dysbiosis, SponGES, MICROORGANISMS, Sociology, 0303 health sciences, Ecology, General Neuroscience, Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation, Environmental resource management, General Medicine, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Holobiont, Engineering ethics, Current (fluid), General Agricultural and Biological Sciences, Ecology (disciplines), Complex system, Genetics and Molecular Biology, Marine Biology, BACTERIAL INTERACTIONS, Community perspective, ECOLOGY, 010603 evolutionary biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Marine ecosystem, 14. Life underwater, PLANT, 030304 developmental biology, 0105 earth and related environmental sciences, Evolutionary Biology, Horizon 2020, business.industry, Experimental model, 010604 marine biology & hydrobiology, lcsh:R, ANIMALS, Biology and Life Sciences, Grant Agreement No 679849, MICROBIOME, 13. Climate action, General Biochemistry, European Union (EU), [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 34 pages, 4 figures.-- Distributed under Creative Commons CC-BY 4.0, Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever, This paper is based on the results of a foresight workshop funded by the EuroMarine network, Sorbonne University, and the UMRs 8227 and 7144 of the Roscoff Biological Station. Ezequiel M. Marzinelli was funded by an Australian Research Council Discovery Project (DP180104041), and José Pintado Valverde was funded by the Galician Innovation Agency (IN607A 2017/4). The work of Simon M. Dittami ad Catherine Leblanc was funded by the ANR project IDEALG (ANR-10-TBR-04). Claire M.M. Gachon, Catherine Leblanc, and SimonMDittami received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement number 624575 (ALFF). The work of Fabrice Not was funded by the ANR project IMPEKAB (ANR-15-CE02-001). Ulisse Cardini was funded by the Research Council of Lithuania project INBALANCE (09.3.3-LMT-K-712-01-0069). Johan Decelle was supported by the CNRS and the ATIP-Avenir program, the LabEx GRAL (ANR-10-LABX-49-01) and Pôle Dittami et CBS from the University of Grenoble Alpes. Paco Cardenas received support from the European Union's Horizon 2020 research and innovation program through the SponGES project (grant agreement No. 679849). Elena Kazamia was funded by a Marie Curie Individual Fellowship (Horizon 2020, IRONCOMM). Aschwin H Engelen was supported by Portuguese national funds from FCT - Foundation for Science and Technology through projects UID/Multi/04326/2019 and UIDB/04326/2020
Published: 2021
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5. Cytoklepty in the plankton: a host strategy to optimize the bioenergetic machinery of endosymbiotic algae

Author: Johan Decelle, Yannick Schwab, Hryhoriy Stryhanyuk, Nicole L. Schieber, Margaret Mars Brisbin, Denis Falconet, Satoshi Mitarai, Charlotte LeKieffre, Clarisse Uwizeye, Lukas Schertel, Fabien Chevalier, Niculina Musat, Benoit Gallet, Giovanni Finazzi, Daniel Wangpraseurt, Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), LIPID, Marine Biophysics Unit, Okinawa Institute of Science and Technology, Institut de biologie structurale (IBS - UMR 5075), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), European Molecular Biology Laboratory (EMBL), Department of Nanoengineering, University of California San Diego, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K, Scripps Institution of Oceanography (SIO), University of California [San Diego] (UC San Diego), University of California-University of California, Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry (UFZ), Photosymbiose, Department of NanoEngineering [Univ California San Diego] (NE - UC San Diego), University of California (UC)-University of California (UC), Department of Biochemistry, University of Cambridge, Scripps Institution of Oceanography (SIO - UC San Diego), ATIP-Avenir program, Japan Society for the Promotion of Science, Gordon and Betty Moore Foundation, Isaac Newton Trust, European Regional Development Funds (EFRE—Europe funds Saxony), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), European Project: 833184, ChloroMito, European Project: 654248,H2020,H2020-INFRADEV-1-2014-1,CORBEL(2015), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), and University of Cambridge [UK] (CAM)
Subjects: 0106 biological sciences, Cell division, Photosynthesis, 01 natural sciences, Pyrenoid, Carbon Cycle, 03 medical and health sciences, Algae, oceanic plankton, Microalgae, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastids, 14. Life underwater, Plastid, Phagosome, 030304 developmental biology, Cell Nucleus, 0303 health sciences, Multidisciplinary, photosynthesis, biology, 010604 marine biology & hydrobiology, photosynthesis&nbsp, Carbon fixation, fungi, Haptophyta, food and beverages, Biological Sciences, Plankton, biology.organism_classification, 3D electron microscopy, symbiosis, Mitochondria, Cell biology, Symbiosome, Acantharia, Energy Metabolism, single-cell transcriptomics, Cell Division
Abstract: International audience; Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts ( Phaeocystis ) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.
Published: 2020
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6. In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

Author: Nicole L. Schieber, Gilles Curien, Rachel Templin, Johan Decelle, Jean-Baptiste Keck, Samuel C. Zeeman, Denis Falconet, Pierre-Henri Jouneau, Christine Moriscot, Guy Schoehn, Fabien Chevalier, Giovanni Finazzi, Clarisse Uwizeye, Benoit Gallet, Yannick Schwab, LIPID, Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Light Photosynthesis & Metabolism (Photosynthesis), Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Institut de biologie structurale (IBS - UMR 5075), Calcul des Variations, Géométrie, Image (CVGI), Laboratoire Jean Kuntzmann (LJK), Institut National de Recherche en Informatique et en Automatique (Inria)-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)-Institut National de Recherche en Informatique et en Automatique (Inria)-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), Integrated Structural Biology Grenoble (ISBG - UMS 3518 ), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-European Molecular Biology Laboratory [Grenoble] (EMBL)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), European Molecular Biology Laboratory (EMBL), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), This project received funding from the European Research Council: ERC Chloro-mito (grant no. 833184). Research was also supported by a Défi X-Life grant from CNRS, funds from the CEA DRF impulsion FIB-Bio program, the LabEx GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003) and the ANR ‘Momix’ (Projet-ANR-17-CE05-0029). This project also received funds from the European Union’s Horizon 2020 research and innovation programme CORBEL under the grant agreement No 654248. This work used the platforms of the Grenoble Instruct-ERIC centre (ISBG, UMS 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-05-02) and GRAL. The electron microscope facility is supported by the Auvergne-Rhône-Alpes Region, the Fondation Recherche Medicale (FRM), the funds FEDER and the GIS-Infrastructures en Biologie Santé et Agronomie (IBISA). J.D. was supported by ATIP-Avenir program. C.U. is supported by a joint UGA-ETH Zurich PhD grant in the framework of the 'Investissements d’avenir' programme (ANR-15-IDEX-02). The authors thank the Roscoff Culture Collection that provided phytoplankton strains and Noan Le Bescot (Ternog Design) for help in the conception and realisation of the figures of this article., ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-CE05-0029,MoMix,Modélisation de la Mixotrophie chez l'algue extrêmophile Galdieria sulphuraria(2017), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), and Integrated Structural Biology Grenoble (ISBG)
Subjects: 0106 biological sciences, Abiotic component, 0303 health sciences, Biomass (ecology), Biotic component, Chemistry, [SDV]Life Sciences [q-bio], fungi, Genomics, 01 natural sciences, Chromatin, 03 medical and health sciences, Phytoplankton, Organelle, Biophysics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, 010606 plant biology & botany, Biomineralization
Abstract: Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.
Published: 2020

7. Subcellular Chemical Imaging: New Avenues in Cell Biology

Author: Pietro Benettoni, Benoit Gallet, Giulia Veronesi, Sylvain Bohic, Rémi Tucoulou, Johan Decelle, Matthias Schmidt, Peta L. Clode, Niculina Musat, Hryhoriy Stryhanyuk, Melissa K. Passarelli, Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Groupe modélisation et chimie théorique (MCT ), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), European Synchrotron Radiation Facility (ESRF), Groupe Microscopie Electronique et Méthodes (IBS-MEM), Institut de biologie structurale (IBS - UMR 5075), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry (UFZ), Laboratory for Biological Geochemistry, École Polytechnique Fédérale de Lausanne (EPFL), Synchrotron Radiation for Biomedicine = Rayonnement SynchroTROn pour la Recherche BiomédicalE (STROBE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Centre for Microscopy, Characterisation and Analysis (CMCA), The University of Western Australia (UWA), UWA School of Biological Sciences, Défi X-Life grant from CNRS, Landmark ESFRI project, ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Groupe modélisation et chimie théorique (MCT), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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 Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Synchrotron Radiation for Biomedicine [Grenoble] (STROBE), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), GON, Nathalie, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID, Infrastructures - CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES - - EMBRC-France2010 - ANR-10-INBS-0002 - INBS - VALID, and Ecole Polytechnique Fédérale de Lausanne (EPFL)
Subjects: Chemical imaging, Elemental imaging, [SDV.IB.IMA]Life Sciences [q-bio]/Bioengineering/Imaging, Cells, elemental imaging, x-ray-fluorescence, Correlative microscopy, X-ray fluorescence, neurons, Computational biology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Biology, ion mass-spectrometry, Multimodal Imaging, localization, nanosims, 03 medical and health sciences, 0302 clinical medicine, Imaging, Three-Dimensional, Animals, Humans, correlative microscopy, chemical imaging, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, 030304 developmental biology, lateral resolution, 0303 health sciences, electron microscopy, Cell Biology, elements, [SDV.IB.IMA] Life Sciences [q-bio]/Bioengineering/Imaging, speciation, reveals, SIMS, electron-microscopy, 030217 neurology & neurosurgery, Subcellular Fractions
Abstract: International audience; To better understand the physiology and acclimation capability of the cell, one of the great challenges of the future is to access the interior of a cell and unveil its chemical landscape (composition and distribution of elements and molecules). Chemical imaging has greatly improved in sensitivity and spatial resolution to visualize and quantify nutrients, metabolites, toxic elements, and drugs in single cells at the subcellular level. This review aims to present the current potential of these emerging imaging technologies and to guide biologists towards a strategy for interrogating biological processes at the nanoscale. We also describe various solutions to combine multiple imaging techniques in a correlative way and provide perspectives and future directions for integrative subcellular imaging across different disciplines
Published: 2020
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8. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Author: Mónica Medina, Arite Bigalke, Ezequiel M. Marzinelli, Eve Toulza, Elena Kazamia, Tilmann Harder, Ulisse Cardini, Soizic Prado, Johan Decelle, François H. Lallier, Fabrice Not, Claire M. M. Gachon, Sarah Griffiths, Enora Briand, Paco Cárdenas, Ehsan Kayal, Marc-André Selosse, José Pintado Valverde, Willem Stock, Derek J. Skillings, Damien Eveillard, Mahasweta Saha, Simon M. Dittami, Enrique Arboleda, Teresa Maria Morganti, Catherine Leblanc, Shinichi Sunagawa, Laura Núñez Pons, Ashwin Engelen, Alexey Vorobev, Jean-Christophe Auguet, Laboratoire de Biologie Intégrative des Modèles Marins (LBI2M), 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)-Centre National de la Recherche Scientifique (CNRS), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institute for Inorganic and Analytical Chemistry, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Medicinal Chemistry, Uppsala University, Sweden, Uppsala University, Stazione Zoologica Anton Dohrn (SZN), Laboratoire de physiologie cellulaire végétale, Institut National de la Recherche Agronomique (INRA), Centre of Marine Sciences [Faro] (CCMAR), University of Algarve [Portugal], 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), Scottish Association for Marine Science, Scottish Marine Institute, School of Science and the Environment, Manchester Metropolitan University (MMU), University of Bremen, 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)-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 Biologie des Invertébrés en Conditions Extrêmes (ABICE), 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), Pennsylvania State University (Penn State), Penn State System, Faculty of Science, School of Life and Environmental Sciences, University of Sydney, Singapore Centre for Environmental Life Sciences Engineering [Singapore] (SCELSE), Nanyang Technological University [Singapour], University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Molécules de Communication et Adaptation des Micro-organismes (MCAM), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), IIM CSIC, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Department of Biological Sciences, University of Essex, Origine, structure et évolution de la biodiversité (OSEB), University of Gdansk, University of Pennsylvania, Laboratory of Protistology & Aquatic Ecology, Institute of Microbiology and Swiss Institute of Bioinformatics, Interactions Hôtes-Pathogènes-Environnements (IHPE), Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), Stazione Zoologica Anton Dohrn, Université de Nantes - Faculté des Sciences et des Techniques, 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), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques, ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science (FR2424), 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), 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), Singapore Centre for Environmental Life Sciences Engineering [Singapore, Singapore] (SCELSE), Nanyang Technological University [Singapour]-Interdisciplinary Graduate School [Singapore, Singapore], Helmholtz Center for Ocean Research, University of Pennsylvania [Philadelphia], Université de Perpignan Via Domitia (UPVD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Adaptation and Diversity in the Marine Environment, Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Station biologique de Roscoff [Roscoff] (SBR), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), 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), 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), 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, and 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)
Subjects: 0106 biological sciences, 0303 health sciences, 010604 marine biology & hydrobiology, media_common.quotation_subject, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Populations and Evolution (q-bio.PE), Complex system, Community perspective, 01 natural sciences, Data science, Holobiont, 03 medical and health sciences, State (polity), 13. Climate action, FOS: Biological sciences, Marine ecosystem, Evolutionary ecology, 14. Life underwater, Sociology, Quantitative Biology - Populations and Evolution, 030304 developmental biology, media_common
Abstract: Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences with comparisons to terrestrial science whenever appropriate. A deeper understanding of such complex systems, however, will require further technological and conceptual advances. The most significant challenge will be to bridge functional research on simple and tractable model systems and global approaches. This will require scientists to work together as an (inter)active community in order to address, for instance, ecological and evolutionary questions and the roles of holobionts in biogeochemical cycles., PeerJ Preprints, Computer Science Preprints., 2019
Published: 2019
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9. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

Author: Margot Tragin, Mary-Hélène Noël, Johan Decelle, Sarah Romac, Adriana Lopes dos Santos, Priscillia Gourvil, and Daniel Vaulot
Subjects: 0301 basic medicine, Oceans and Seas, Chlorophyta, DNA, Ribosomal, Microbiology, 18S ribosomal RNA, 03 medical and health sciences, Mediterranean sea, Phylogenetics, Phytoplankton, Botany, Mediterranean Sea, Seawater, 14. Life underwater, Photosynthesis, Clade, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, Ecology, fungi, Eukaryota, Genetic Variation, Ribosomal RNA, biology.organism_classification, 030104 developmental biology, Original Article, Green algae
Abstract: Prasinophytes clade VII is a group of pico/nano-planktonic green algae (division Chlorophyta) for which numerous ribosomal RNA (rRNA) sequences have been retrieved from the marine environment in the last 15 years. A large number of strains have also been isolated but have not yet received a formal taxonomic description. A phylogenetic analysis of available strains using both the nuclear 18S and plastidial 16S rRNA genes demonstrates that this group composes at least 10 different clades: A1–A7 and B1–B3. Analysis of sequences from the variable V9 region of the 18S rRNA gene collected during the Tara Oceans expedition and in the frame of the Ocean Sampling Day consortium reveal that clade VII is the dominant Chlorophyta group in oceanic waters, replacing Mamiellophyceae, which have this role in coastal waters. At some location, prasinophytes clade VII can even be the dominant photosynthetic eukaryote representing up to 80% of photosynthetic metabarcodes overall. B1 and A4 are the overall dominant clades and different clades seem to occupy distinct niches, for example, A6 is dominant in surface Mediterranean Sea waters, whereas A4 extend to high temperate latitudes. Our work demonstrates that prasinophytes clade VII constitute a highly diversified group, which is a key component of phytoplankton in open oceanic waters but has been neglected in the conceptualization of marine microbial diversity and carbon cycle.
Published: 2016
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10. Algal remodeling in a ubiquitous planktonic photosymbiosis

Author: Josselin Lupette, Rémi Tucoulou, Pierre-Henri Jouneau, Juliette Jouhet, Johan Decelle, Sophie Marro, Yannick Schwab, Sergio Balzano, Hans H. Richnow, Giovanni Finazzi, Benoit Gallet, Giulia Veronesi, Niculina Musat, Eric Maréchal, Matthias Schmidt, Nicole L. Schieber, Clarisse Uwizeye, Hryhoriy Stryhanyuk, Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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 Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry (UFZ), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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), European Synchrotron Radiation Facility (ESRF), Groupe modélisation et chimie théorique (MCT), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Royal Netherlands Institute for Sea Research (NIOZ), 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), LIPID, Laboratoire d'Etude des Matériaux par Microscopie Avancée (LEMMA ), Modélisation et Exploration des Matériaux (MEM), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de génétique et biologie moléculaire et cellulaire (IGBMC), Université Louis Pasteur - Strasbourg I-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Cell Biology and Biophysics Unit, European Molecular Biology Laboratory [Grenoble] (EMBL), Helmholtz Association, The electron microscope facility is supported by the Rhoˆ ne-Alpes Region, the Fondation Recherche Medicale (FRM), the fonds FEDER, the Centre National de la Recherche Scientifique (CNRS), the CEA, the University of Grenoble Alpes (UGA), EMBL, and the GIS-Infrastrutures en Biologie Sante et Agronomie (IBISA), RGP0052 HFSP grant, CEA_DRF_impulsion (Fib-Bio) grant, ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), European Project: 658442,H2020,H2020-MSCA-IF-2014,MINOTAUR(2016), European Project: EFRE, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de biologie structurale (IBS - UMR 5075), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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 Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire d'Etude des Matériaux par Microscopie Avancée (LEMMA), Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, ANR-10-INBS-02-01/10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-11-BTBR-0008/11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-15-IDEX-02,DATA@UGA,Grenoble Alpes Data Institute(2016), Martin-Laffon, Jacqueline, Grenoble Alliance for Integrated Structural Cell Biology - - GRAL2010 - ANR-10-LABX-0049 - LABX - VALID, Infrastructures - CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES - - EMBRC-France2010 - ANR-10-INBS-0002 - INBS - VALID, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, IDEX UGA - - UGA2015 - ANR-15-IDEX-0002 - IDEX - VALID, Metabolic interactions in oceanic photosymbioses - MINOTAUR - - H20202016-01-01 - 2017-12-31 - 658442 - VALID, and European Regional Development Funds - Europe fonds Saxony - EFRE - INCOMING
Subjects: 0301 basic medicine, mass spectrometry imaging, Photosynthesis, General Biochemistry, Genetics and Molecular Biology, Haptophyte, 03 medical and health sciences, 0302 clinical medicine, eukaryotes, Algae, Symbiosis, Botany, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastid, plastid, Cell Size, Trophic level, Phaeocystis, photosynthesis, biology, plankton, fungi, Haptophyta, food and beverages, [SDV.EE.IEO] Life Sciences [q-bio]/Ecology, environment/Symbiosis, Plankton, Metal homeostasis, biology.organism_classification, microalga, 3D electron microscopy, symbiosis, Rhizaria, 030104 developmental biology, Thylakoid, General Agricultural and Biological Sciences, single-cell imaging, Cell Division, 030217 neurology & neurosurgery, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: International audience; Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.
Published: 2019
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11. Diatom diversity through HTS-metabarcoding in coastal European seas

Author: Bente Edvardsen, Dominik Forster, Sarah Romac, Jean-Michel Claverie, Adriana Zingone, Marina Montresor, Fabrice Not, Jan Pawlowski, Hiroyuki Ogata, Micah Dunthorn, Wiebe H. C. F. Kooistra, Diana Sarno, Ramiro Logares, Ramon Massana, Johan Decelle, Roberta Piredda, Colomban de Vargas, Thorsten Stoeck, Wenche Eikrem, Stazione Zoologica Anton Dohrn (SZN), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Light Photosynthesis & Metabolism (Photosynthesis), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), University of Oslo (UiO), Marine Botany, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Dept of Ecology, University of Kaiserslautern, EU [2008-6530], Stazione Zoologica Anton Dohrn, Italian Ministry of Education, University and Research (MIUR) [RBAP10A2T4], Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), University of Geneva [Switzerland], Ministero dell'Istruzione, dell'Università e della Ricerca, European Commission, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Stazione Zoologica A. Dohrn, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Stazione Zoologica Napoli, Stazione Zoologica di Napoli (SZN), Stazione Zoologica di Napoli, and Zingone, Adriana
Subjects: 0301 basic medicine, taxonomie, Oceans and Seas, [SDV]Life Sciences [q-bio], lcsh:Medicine, Biotechnologies, diatomée, medicine.disease_cause, Article, 03 medical and health sciences, Water column, medicine, DNA Barcoding, Taxonomic, plancton, 14. Life underwater, milieu marin, lcsh:Science, Phylogeny, Diatoms, Multidisciplinary, biology, Ecology, Aquatic ecosystem, lcsh:R, fungi, Protist, Biodiversity, Plankton, DNA, Protozoan, biology.organism_classification, protiste, 030104 developmental biology, Diatom, Habitat, Benthic zone, RNA, Ribosomal, metabarcoding, Metagenome, Taxonomy (biology), lcsh:Q
Abstract: Piredda, Roberta ... et al.-- 12 pages, 5 figures, 1 table, supporting information https://doi.org/10.1038/s41598-018-36345-9, Diatoms constitute a diverse lineage of unicellular organisms abundant and ecologically important in aquatic ecosystems. Compared to other protists, their biology and taxonomy are well-studied, offering the opportunity to combine traditional approaches and new technologies. We examined a dataset of diatom 18S rRNA- and rDNA- (V4 region) reads from different plankton size-fractions and sediments from six European coastal marine sites, with the aim of identifying peculiarities and commonalities with respect to the whole protistan community. Almost all metabarcodes (99.6%) were assigned to known genera (121) and species (236), the most abundant of which were those already known from classic studies and coincided with those seen in light microscopy. rDNA and rRNA showed comparable patterns for the dominant taxa, but rRNA revealed a much higher diversity particularly in the sediment communities. Peculiar to diatoms is a tight bentho-pelagic coupling, with many benthic or planktonic species colonizing both water column and sediments and the dominance of planktonic species in both habitats. Overall metabarcoding results reflected the marked specificity of diatoms compared to other protistan groups in terms of morphological and ecological characteristics, at the same time confirming their great potential in the description of protist communities, Financial support to the project BioMarKs was provided by the EU (2008-6530, ERA-net BIODIVERSA, EU) and, for the Italian participation, by Stazione Zoologica Anton Dohrn and the projects FIRB Biodiversitalia-Approccio multitaxa allo studio delle risposte della biodiversità italiana al cambiamento climatico (RBAP10A2T4), funded by the Italian Ministry of Education, University and Research (MIUR), which also supported Roberta Piredda’s fellowship
Published: 2018
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12. A de novo approach to disentangle partner identity and function in holobiont systems

Author: Stéphane Le Crom, Eric Pelletier, Patrick Wincker, Ian Probert, Fabrice Not, Camille Marchet, Erwan Corre, Pierre Peterlongo, Johan Decelle, Adriana Alberti, Arnaud Meng, Corinne Da Silva, Lucie Bittner, Sorbonne Université (SU), Université Pierre et Marie Curie - Paris 6 - UFR de Médecine Pierre et Marie Curie (UPMC), Université Pierre et Marie Curie - Paris 6 (UPMC), Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-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), 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), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), 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 (... - 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 de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), 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), 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), 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), Université Nice Sophia Antipolis (... - 2019) (UNS), and 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)
Subjects: 0301 basic medicine, Microbiology (medical), Sequence assembly, Genomics, Computational biology, Biology, Holobiont, Microbiology, lcsh:Microbial ecology, k-mer based similarity, Transcriptome, Cnidaria, 03 medical and health sciences, Functional diversity, De novo assembly, Microalgae, Animals, Symbiosis, 030304 developmental biology, Genetics, 0303 health sciences, Marine, Coral Reefs, 030306 microbiology, Research, Meta-transcriptomic, Computational Biology, Plankton, Short read, Porifera, Rhizaria, 030104 developmental biology, Identity (object-oriented programming), lcsh:QR100-130, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Function (biology), [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: BackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.ResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partner’s transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. ConclusionsIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.
Published: 2018
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13. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

Author: Stéphane Audic, Daniel J. Richter, Colomban de Vargas, Xavier Pochon, Cédric Berney, Johan Decelle, Solenn Mordret, Sébastien Colin, Nicolas Henry, Sarah Romac, Margaux Carmichael, 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), 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), 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: 0301 basic medicine, Genotype, Oceans and Seas, [SDV]Life Sciences [q-bio], DNA, Ribosomal, Microbiology, 03 medical and health sciences, Symbiodinium, Microbial ecology, Animals, DNA Barcoding, Taxonomic, 14. Life underwater, Ciliophora, Symbiosis, Ecosystem, Phylogeny, Ecology, Evolution, Behavior and Systematics, Ecology, Geography, biology, fungi, Dinoflagellate, Marine habitats, Pelagic zone, Biodiversity, Plankton, biology.organism_classification, Biological Evolution, 030104 developmental biology, Haplotypes, Benthic zone, [SDE]Environmental Sciences, Dinoflagellida, Original Article, Evolutionary ecology, Metagenomics
Abstract: International audience; Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.
Published: 2015
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14. NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis

Author: Matt R. Kilburn, Johan Decelle, Haibo Jiang, and Niculina Musat
Subjects: 0301 basic medicine, Chemical imaging, Correlative, In situ, Biological studies, Atomic force microscopy, Biomedical Engineering, Stable-isotope probing, Correlative microscopy, Spectrometry, Mass, Secondary Ion, Bioengineering, Nanotechnology, Biology, Microscopy, Atomic Force, Lipids, Peptide Fragments, Secondary ion mass spectrometry, 03 medical and health sciences, 030104 developmental biology, Isotopes, Isotope Labeling, Image Processing, Computer-Assisted, Humans, In Situ Hybridization, Fluorescence, Biotechnology
Abstract: Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS) is one of the most powerful in situ elemental and isotopic analysis techniques available to biologists. The combination of stable isotope probing with NanoSIMS (nanoSIP) has opened up new avenues for biological studies over the past decade. However, due to limitations inherent with any analytical methodology, additional information from correlative techniques is usually required to address real biological questions. Here we review recent developments in correlative analysis applied to complex biological systems: first, high-resolution tracking of molecules (e.g. peptides, lipids) by correlation with electron microscopy and atomic force microscopy; second, identification of a specific microbial taxon with fluorescence in situ hybridization and quantification of its metabolic capacities; and, third, molecular specific imaging with new probes.
Published: 2016

15. Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

Author: Quentin Carradec, Patrick Wincker, Xavier Pochon, Colomban de Vargas, Artem Kourlaiev, Frédéric Mahé, Christian R. Voolstra, Micah Dunthorn, Nicolas Henry, Sarah Romac, Johan Decelle, Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche pour le Développement (IRD [France-Nord])-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), 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), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Cawthron Institute, Institute of Marine Science, University of Auckland, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Kaiserslautern [Kaiserslautern], King Abdullah University of Science and Technology (KAUST), project OCEANOMICS from the French government ANR-11-BTBR-0008 ANR-10-INBS-09, France Genomique from the French government ANR-11-BTBR-0008 ANR-10-INBS-09, LabEx GRAL ANR-10-LABX-49-01, University of Grenoble Alpes, ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), European Project: MSCA- IF-2014, Tara Oceans-GOSEE (FR2022), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-11-BTBR-0008/11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10- INBS0009,INBS,France-Génomique, ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay
Subjects: 0106 biological sciences, 0301 basic medicine, ADN ribosomal, Coral, ADN, Symbiodinium, phytoplankton, marine plankton, symbiosis, metabarcoding, open ocean, metatranscriptomics, coral reefs, Tara Oceans, 01 natural sciences, Symbiodinium, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, metatranscriptomics, geography.geographical_feature_category, biology, Ecology, 000 - Autres thèmes, Biodiversity, Coral reef, Plankton, Biological Evolution, symbiosis, Dinoflagellida, coral reefs, General Agricultural and Biological Sciences, geographic locations, Genetic Markers, Population, Tara Oceans, 010603 evolutionary biology, General Biochemistry, Genetics and Molecular Biology, Plancton, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, ddc:570, Phytoplankton, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Corail, 14. Life underwater, education, Reef, open ocean, geography, Gene Expression Profiling, fungi, Dinoflagellate, Genetic Variation, L60 - Taxonomie et géographie animales, DNA, Protozoan, biology.organism_classification, 030104 developmental biology, marine plankton, metabarcoding, phytoplankton
Abstract: International audience; The dinoflagellate microalga Symbiodinium sustains coral reefs, one of the most diverse ecosystems of the biosphere, through mutualistic endosymbioses with a wide diversity of benthic hosts [1]. Despite its ecological and economic importance, the presence of Symbiodinium in open oceanic waters remains unknown, which represents a significant knowledge gap to fully understand the eco-evolutionary trajectory and resilience of endangered Symbiodinium-based symbioses. Here, we document the existence of Symbiodinium (i.e., now the family Symbiodiniaceae [2]) in tropical- and temperate-surface oceans using DNA and RNA metabarcoding of size-fractionated plankton samples collected at 109 stations across the globe. Symbiodinium from clades A and C were, by far, the most prevalent and widely distributed lineages (representing 0.1% of phytoplankton reads), while other lineages (clades B, D, E, F, and G) were present but rare. Concurrent metatranscriptomics analyses using the Tara Oceans gene catalog [3] revealed that Symbiodinium clades A and C were transcriptionally active in the open ocean and expressed core metabolic pathways (e.g., photosynthesis, carbon fixation, glycolysis, and ammonium uptake). Metabarcodes and expressed genes of clades A and C were detected in small and large plankton size fractions, suggesting the existence of a free-living population and a symbiotic lifestyle within planktonic hosts, respectively. However, high-resolution genetic markers and microscopy are required to confirm the life history of oceanic Symbiodinium. Overall, the previously unknown, metabolically active presence of Symbiodinium in oceanic waters opens up new avenues for investigating the potential of this oceanic reservoir to repopulate coral reefs following stress-induced bleaching.
Published: 2018
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16. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

Author: Meinhard Simon, Helge-Ansgar Giebel, Johan Decelle, Mathias Milici, Melissa L. Wos-Oxley, Dietmar H. Pieper, Haiyan Wang, Irene Wagner-Döbler, Ruy Jauregui, Iris Plumeier, Mascha Wurst, Jürgen Tomasch, Zhi-Luo Deng, Thomas H. Badewien, Helmholtz Centre for Infection Research (HZI), 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), and University of Oldenburg
Subjects: 0301 basic medicine, Microbiology (medical), phytoplankton-bacteria interactions, lcsh:QR1-502, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, lcsh:Microbiology, 03 medical and health sciences, Water column, co-occurrence, Photic zone, 14. Life underwater, Atlantic Ocean, Original Research, next generation sequencing, biology, Bacteria-bacteria interactions, Ecology, bacterioplankton, Verrucomicrobia, Bacteroidetes, 16S rRNA analysis, Pelagic zone, Bacterioplankton, Plankton, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Network analysis, Prochlorococcus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; We determined the taxonomic composition of the bacterioplankton of the epipelagic zone of the Atlantic Ocean along a latitudinal transect (51°S–47°N) using Illumina sequencing of the V5-V6 region of the 16S rRNA gene and inferred co-occurrence networks. Bacterioplankon community composition was distinct for Longhurstian provinces and water depth. Free-living microbial communities (between 0.22 and 3 μm) were dominated by highly abundant and ubiquitous taxa with streamlined genomes (e.g., SAR11, SAR86, OM1, Prochlorococcus) and could clearly be separated from particle-associated communities which were dominated by Bacteroidetes, Planktomycetes, Verrucomicrobia, and Roseobacters. From a total of 369 different communities we then inferred co-occurrence networks for each size fraction and depth layer of the plankton between bacteria and between bacteria and phototrophic micro-eukaryotes. The inferred networks showed a reduction of edges in the deepest layer of the photic zone. Networks comprised of free-living bacteria had a larger amount of connections per OTU when compared to the particle associated communities throughout the water column. Negative correlations accounted for roughly one third of the total edges in the free-living communities at all depths, while they decreased with depth in the particle associated communities where they amounted for roughly 10% of the total in the last part of the epipelagic zone. Co-occurrence networks of bacteria with phototrophic micro-eukaryotes were not taxon-specific, and dominated by mutual exclusion (~60%). The data show a high degree of specialization to micro-environments in the water column and highlight the importance of interdependencies particularly between free-living bacteria in the upper layers of the epipelagic zone.
Published: 2016
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17. Benthic protists: the under-charted majority

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

Author: Patrick Wincker, Erwan Corre, Sergio Balzano, Johan Decelle, Julie Poulain, Corinne Da Silva, Fabrice Not, Jan Pawlowski, Roberto Sierra, 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), Université Pierre et Marie Curie - Paris 6 (UPMC)-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)-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), Department of genetics and evolution, University of Geneva [Switzerland], Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), and Université de Genève = University of Geneva (UNIGE)
Subjects: 0106 biological sciences, Microbiology (medical), lcsh:QR1-502, radiolarian, Biology, 010603 evolutionary biology, 01 natural sciences, Microbiology, photosymbiosis, lcsh:Microbiology, 03 medical and health sciences, Symbiosis, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Original Research Article, 14. Life underwater, Gene, 030304 developmental biology, Genetics, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, Expressed sequence tag, Phylogenetic tree, Host (biology), ESTs, plankton, Rhizaria, Ribosomal RNA, biology.organism_classification, Holobiont, c-type lectins
Abstract: International audience; Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.
Published: 2015
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19. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

Author: Stéphane Audic, Colomban de Vargas, Désiré Tessier, Florence Le Gall, Ian Probert, El Mahdi Bendif, Sarah Romac, Adriana Lopes dos Santos, Michel D Guiry, Rowena Stern, Richard Christen, Daniel Vaulot, Adriana Zingone, Laure Guillou, Priscillia Gourvil, Johan Decelle, 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), Sir Alister Hardy Foundation for Ocean Science (SAHFOS), Marine Biological Association, Stazione Zoologica Anton Dohrn (SZN), The AlgaeBase Foundation, National University of Ireland [Galway] (NUI Galway), Diversité et Interactions au sein du Plancton Océanique (DIPO), 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 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), and Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, plastidial 16S rRNA gene, diversity patterns, Molecular Sequence Data, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Genome, DNA, Ribosomal, DNA sequencing, Molecular ecology, 03 medical and health sciences, Phylogenetics, life-cycle, RNA, Ribosomal, 16S, Genetics, picoeukaryote community structure, Cluster Analysis, phylogenetic analyses, Plastids, Gene, Ecology, Evolution, Behavior and Systematics, Phylogeny, atlantic-ocean, 030304 developmental biology, protists, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, cryptomonas cryptophyceae, photosynthesis, Ecology, 010604 marine biology & hydrobiology, high-throughput sequencing, Eukaryota, online resource, Genes, rRNA, DNA, Sequence Analysis, DNA, 15. Life on land, Amplicon, Taxon, marine picophytoplankton, 13. Climate action, Evolutionary biology, metabarcoding, phytoplankton, Taxonomy (biology), Databases, Nucleic Acid, Biotechnology
Abstract: International audience; Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.
Published: 2014
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20. Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians

Author: Noritoshi Suzuki, Ian Probert, Akihiro Tuji, Raffaele Siano, Camille Poirier, Fabrice Not, Tristan Biard, Johan Decelle, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Dynamiques des Écosystèmes Côtiers (DYNECO), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), 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), Diversité et Interactions au sein du Plancton Océanique (DIPO), Department of Botany, National Museum of Nature and Science, Institute of Geology and Paleontology, Tohoku University [Sendai], and Dynamiques de l'Environnement Côtier (DYNECO)
Subjects: 0106 biological sciences, Polycystine, S crippsiella, royalty.order_of_chivalry, royalty, Zoology, Plant Science, Peridiniales, Aquatic Science, dinoflagellate, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, 03 medical and health sciences, taxonomy, Z ooxanthella, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 14. Life underwater, Radiolaria, 030304 developmental biology, 0303 health sciences, biology, Ecology, 010604 marine biology & hydrobiology, fungi, Dinoflagellate, biology.organism_classification, symbiosis, Nassellaria, Holobiont, Zooxanthella, Scrippsiella, Taxonomy (biology), Dinophyceae, polycystines
Abstract: International audience; Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.
Published: 2014
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21. Patterns of Rare and Abundant Marine Microbial Eukaryotes

Author: David Bass, Jan Pawlowski, Fabrice Not, Angélique Gobet, John R. Dolan, Sarah Romac, Christophe Boutte, Patrick Wincker, Wiebe H. C. F. Kooistra, Richard Christen, Raffaele Siano, Bente Edvardsen, Ramiro Logares, Colomban de Vargas, Thorsten Stoeck, Thomas A. Richards, Jean-Michel Claverie, Massimo C. Pernice, Nathalie Simon, Stéphane Audic, Frédéric Mahé, Kamran Shalchian-Tabrizi, Lucie Bittner, Adriana Zingone, Sébastien Santini, Micah Dunthorn, Hiroyuki Ogata, Ramon Massana, Johan Decelle, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), 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), Department of life sciences, The Natural History Museum [London] (NHM), Department of ecology, Universität Kaiserslautern, 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), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), 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 Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Laboratory of Ecology and Evolution of Plankton, Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Education academy of computational life sciences, Tokyo Institute of Technology [Tokyo] (TITECH), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 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), Biosciences, Geoffrey Pope Builing, University of Exeter, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-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), University of Geneva [Switzerland], 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 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), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and 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)
Subjects: Rare biosphere, Biogeography, Molecular Sequence Data, Rare species, Biodiversity, Marine Biology, microbial eukaryotes, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Species Specificity, abundance distribution, Abundance (ecology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Mediterranean Sea, RNA, Ribosomal, 18S, Cluster Analysis, Ecosystem, 14. Life underwater, Picoplankton, Atlantic Ocean, Phylogeny, 030304 developmental biology, Population Density, 0303 health sciences, Agricultural and Biological Sciences(all), Base Sequence, Community, Biochemistry, Genetics and Molecular Biology(all), 030306 microbiology, Ecology, Microbiota, Eukaryota, High-Throughput Nucleotide Sequencing, marine, 15. Life on land, Europe, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 13. Climate action, next-generation sequencing, North Sea, General Agricultural and Biological Sciences, community ecology
Abstract: Logares, Ramiro ... et. al.-- 9 pages, 5 figures, 1 table, Background. Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions. Results. Deep Illumina sequencing of the 18S rRNA indicated that the abundant regional community was mostly structured by organismal size fraction, whereas the rare regional community was mainly structured by geographic origin. However, some abundant and rare taxa presented similar biogeography, pointing to spatiotemporal structure in the rare microeukaryote biosphere. Abundant and rare subcommunities presented regular proportions across samples, indicating similar species-abundance distributions despite taxonomic compositional variation. Several taxa were abundant in one location and rare in other locations, suggesting large oscillations in abundance. The substantial amount of metabolically active lineages found in the rare biosphere suggests that this subcommunity constitutes a diversity reservoir that can respond rapidly to environmental change. Conclusions. We propose that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time, We thank the Biodiversity of Marine euKaryotes (BioMarKs, http://www. biomarks.eu) consortium, which was funded by the European Union ERANet program BiodivERsA (2008-6530). Extra financial support was provided by the Marie Curie Intra-European Fellowship (PIEF-GA-2009-235365) and Juan de la Cierva (JCI-2010-06594) programmes to R.L. and FLAME (CGL2010-16304, MICINN, Spain) to R.M. The Barcelona Supercomputing Center (BSC) provided access to the MareNostrum supercomputer (grants BCV-2011-2-0003/3-0005 and 2012-1-0006/2-0002 to R.L. and R.M.)
Published: 2014
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22. Ancient DNA complements microfossil record in deep-sea subsurface sediments

Author: Philippe Esling, Jan Pawlowski, Franck Lejzerowicz, Cyril Obadia, Wojciech Majewski, Witold Szczuciński, Pedro Martínez Arbizu, Johan Decelle, Université de Genève = University of Geneva (UNIGE), Représentations musicales (Repmus), Sciences et Technologies de la Musique et du Son (STMS), Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche et Coordination Acoustique/Musique (IRCAM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of genetics and evolution, Swiss National Science Foundation [31003A-140766], and University of Geneva [Switzerland]
Subjects: Geologic Sediments, 010504 meteorology & atmospheric sciences, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Marine Biology, Foraminifera, 01 natural sciences, Deep sea, 03 medical and health sciences, Paleontology, Marine ecosystem, Environmental DNA, microfossils, 14. Life underwater, Atlantic Ocean, ancient DNA, deep-sea sediments, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, biology, Fossils, Sediment, Last Glacial Maximum, Sequence Analysis, DNA, DNA, Protozoan, 15. Life on land, biology.organism_classification, Agricultural and Biological Sciences (miscellaneous), Rhizaria, Ancient DNA, palaeogenomics, [SDE]Environmental Sciences, next-generation sequencing, General Agricultural and Biological Sciences, Radiolaria
Abstract: International audience; Deep-sea subsurface sediments are the most important archives of marine biodiversity. Until now, these archives were studied mainly using the microfossil record, disregarding large amounts of DNA accumulated on the deep-sea floor. Accessing ancient DNA (aDNA) molecules preserved down-core would offer unique insights into the history of marine biodiversity, including both fossilized and non-fossilized taxa. Here, we recover aDNA of eukaryotic origin across four cores collected at abyssal depths in the South Atlantic, in up to 32.5 thousand-year-old sediment layers. Our study focuses on Foraminifera and Radiolaria, two major groups of marine microfossils also comprising diverse non-fossilized taxa. We describe their assemblages in down-core sediment layers applying both micropalaeontological and environmental DNA sequencing approaches. Short fragments of the foraminiferal and radiolarian small subunit rRNA gene recovered from sedimentary DNA extracts provide evidence that eukaryotic aDNA is preserved in deep-sea sediments encompassing the last glacial maximum. Most aDNA were assigned to non-fossilized taxa that also dominate in molecular studies of modern environments. Our study reveals the potential of aDNA to better document the evolution of past marine ecosystems and opens new horizons for the development of deep-sea palaeogenomics.
Published: 2013
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23. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

Author: Christophe Boutte, Raphael Morard, Gaëtan Burgaud, Micah Dunthorn, Pascal Zimmermann, David Bass, Noan Le Bescot, Laure Guillou, Fabrice Not, Bente Edvardsen, Enrique Lara, Dipankar Bachar, Colomban de Vargas, Thorsten Stoeck, Anne Laure Sauvadet, Marina Montresor, Jan Pawlowski, Cédric Berney, Daniel Vaulot, Maria Holzmann, Lucie Bittner, Ramon Massana, Johan Decelle, Javier del Campo, Wiebe H. C. F. Kooistra, Ramiro Logares, Richard Christen, Stéphane Audic, Frédéric Mahé, John R. Dolan, Raffaele Siano, Ian Probert, 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), Systématique, adaptation, évolution (SAE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Department of life sciences, The Natural History Museum [London] (NHM), Groupe Plancton Océanique, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne (LUBEM), Université de Brest (UBO), Instituto de Ciencia de Materiales de Aragón [Saragoza, España] (ICMA-CSIC), University of Zaragoza - Universidad de Zaragoza [Zaragoza], Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), University of Kaiserslautern [Kaiserslautern], Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Evolutionary Genetics, Stazione Zoologica Anton Dohrn (SZN), Laboratory of Soil Biodiversity, Université de Neuchâtel (UNINE), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire de Géologie de Lyon - Terre, Planètes, Environnement [Lyon] (LGL-TPE), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École normale supérieure - Lyon (ENS Lyon), Department of genetics and evolution, University of Geneva [Switzerland], Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of ecology, Universität Kaiserslautern, Point Compétence Informatique, European Union [2008-6530, 287589], ANR (France), ANR Paralex (French), BIOMARKS, 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 de Géologie de Lyon - Terre, Planètes, Environnement (LGL-TPE), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Université Jean Monnet - Saint-Étienne (UJM)-Centre National de la Recherche Scientifique (CNRS), Université de Genève = University of Geneva (UNIGE), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], Computational biology, medicine.disease_cause, Ribosome, DNA, Ribosomal, DNA sequencing, 03 medical and health sciences, Genetics, medicine, DNA Barcoding, Taxonomic, Gene, 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, 0303 health sciences, Internet, biology, 030306 microbiology, fungi, Intron, Protist, Eukaryota, High-Throughput Nucleotide Sequencing, Genes, rRNA, Articles, Ribosomal RNA, biology.organism_classification, Molecular biology, RNA, Ribosomal, [SDE]Environmental Sciences, Eukaryote, Databases, Nucleic Acid, Cercozoa
Abstract: Laure Guillou ... et al. -- 8 pages, 1 figure, 1 table, The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssu-rrna.org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of high-troughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences consists of eight unique taxonomic fields. In total, 136 866 sequences are nuclear encoded, 45 708 (36 501 mitochondrial and 9657 chloroplastic) are from organelles, the remaining being putative chimeric sequences. The website allows the users to download sequences from the entire and partial databases (including representative sequences after clustering at a given level of similarity). Different web tools also allow searches by sequence similarity. The presence of both rRNA and rDNA sequences, taking into account introns (crucial for eukaryotic sequences), a normalized eight terms ranked-taxonomy and updates of new GenBank releases were made possible by a long-term collaboration between experts in taxonomy and computer scientists, The European Union’s Seventh Framework Programmes (FP7) BIOMARKS (2008-6530, ERA-net Biodiversa) and MicroB3 [287589] and the following ANR (France) projects: AQUAPARADOX, PARALEX and GIME. Funding for open access charge: ANR Paralex (French) and BIOMARKS (FP7)
Published: 2013
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24. Multiple microalgal partners in symbiosis with the acantharian Acanthochiasma sp. (Radiolaria)

Author: Johan Decelle, Fabrice Not, Raffaele Siano, Camille Poirier, Ian Probert, 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), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Diversité et Interactions au sein du Plancton Océanique (DIPO), network ``Bibliotheque du Vivant', CNRS, Museum National d'Histoire Naturelle, INRA, CEA (Centre National de Sequencage), Region Bretagne [DIPHOPE 044763], JST-CNRS program, EU, and KBBE project MACUMBA
Subjects: 0106 biological sciences, Acantharia, Chrysochromulina, [SDV]Life Sciences [q-bio], Zoology, 01 natural sciences, Haptophyte, 03 medical and health sciences, Symbiosis, Botany, Photosymbiosis, Microalgae, 14. Life underwater, Internal transcribed spacer, Ribosomal DNA, Radiolaria, 030304 developmental biology, 0303 health sciences, biology, 010604 marine biology & hydrobiology, fungi, Protists, biology.organism_classification, Plankton, Holobiont, [SDE]Environmental Sciences, General Agricultural and Biological Sciences
Abstract: International audience; Acantharia (Radiolaria) are widespread and abundant heterotrophic marine protists, some of which can host endosymbiotic eukaryotic microalgae. Although this photosymbiotic association was first described at the end of the 19th century, the diversity of the symbiotic microalgae remains poorly characterized. Here, we examined the identity of the microalgae associated with the acantharian species Acanthochiasma sp. by sequencing partial 18S and internal transcribed spacer (ITS) ribosomal DNA genes from cultured symbionts and directly from isolated holobiont specimens. Single Acanthochiasma cells contained multiple symbiotic partners, including distantly related dinoflagellates (Heterocapsa sp., Pelagodinium sp., Azadinium sp. and Scrippsiella sp.) as well as a haptophyte (Chrysochromulina sp.). This original association of multiple symbiotic microalgae within a single host cell raises questions about the specificity and functioning of the relationship. These microalgae exhibit the common ecological feature of being abundant and widely distributed in coastal and oceanic waters, some occasionally forming extensive blooms. Some of the microalgal genera found in association with Acanthochiasma (i.e. Pelagodinium and Chrysochromulina) are known to occur in symbiosis with other heterotrophic protists such as Foraminifera and other Radiolaria, whereas Heterocapsa, Scrippsiella and Azadinium have never previously been reported to be involved in putative symbiotic relationships. The unusual association unveiled in this study contributes to our understanding of the ecological and evolutionary significance of photosymbiosis in Acantharia and also provides new insights into the nature of such partnerships in the planktonic realm.
Published: 2012
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25. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms

Author: Jan Pawlowski, Stéphane Audic, Sina Adl, David Bass, Lassaâd Belbahri, Cédric Berney, Samuel S Bowser, Ivan Cepicka, Johan Decelle, Micah Dunthorn, Anna Maria Fiore-Donno, Gillian H Gile, Maria Holzmann, Regine Jahn, Miloslav Jirků, Patrick J Keeling, Martin Kostka, Alexander Kudryavtsev, Enrique Lara, Julius Lukeš, David G Mann, Edward A D Mitchell, Frank Nitsche, Maria Romeralo, Gary W Saunders, Alastair G B Simpson, Alexey V Smirnov, John L Spouge, Rowena F Stern, Thorsten Stoeck, Jonas Zimmermann, David Schindel, Colomban de Vargas, Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), 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), University of Saskatchewan [Saskatoon] (U of S), Department of life sciences, The Natural History Museum [London] (NHM), Laboratory of Soil Biology, Université de Neuchâtel (UNINE), Wadsworth Center, Department of Zoology, University of Kaiserslautern [Kaiserslautern], Institute of Botany and Landscape Ecology, Universität Greifswald - University of Greifswald, Department of Biochemistry and Molecular Biology, Department of Evolutionary Genetics, Botanischer Garten und Botanischer Museum Berlin-Dahlem, Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Canadian Institute for Advanced Research (CIFAR), Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Laboratory of Soil Biodiversity, Royal Botanic Garden [Edinburgh], Universität zu Köln = University of Cologne, Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, University of New Brunswick (UNB), Department of Biology - Life Sciences Centre, Department of Invertebrate Zoology, National Center for Biotechnology Information (NCBI), Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Dept of Ecology, University of Kaiserslautern, Smithsonian Institution National Museum of Natural History (NMNH), Consortium for the Barcoding of Life, European ERA-net program BiodivErsA under the BioMarKs project, French ANR project [09-BLAN-0348 POSEIDON], Swiss National Science Foundation [31003A-140766], University of Geneva [Switzerland], Royal Botanical Garden Edinburgh, Royal Botanical Garden, and Universität zu Köln
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Biodiversity, Protozoology, medicine.disease_cause, 01 natural sciences, DNA barcoding, ddc:590, Community Page, Naturvetenskap, Biology (General), Phylogeny, 0303 health sciences, Ecology, General Neuroscience, Protist, Eukaryota, Plants, Eukaryotic Cells, [SDE]Environmental Sciences, Taxonomy (biology), Natural Sciences, General Agricultural and Biological Sciences, Genetic Markers, QH301-705.5, Biology, 010603 evolutionary biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Microbial Ecology, 03 medical and health sciences, Species Specificity, Phylogenetics, medicine, RNA, Ribosomal, 18S, Genetics, Animals, DNA Barcoding, Taxonomic, Ecosystem, 030304 developmental biology, Internet, General Immunology and Microbiology, fungi, Genetic Variation, Genetic divergence, Multicellular organism, Species richness, Ribosomes, Zoology, Software
Abstract: Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.
Published: 2012
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26. An original mode of symbiosis in open ocean plankton

Author: Ian Probert, Martí Galí, Colomban de Vargas, Johan Decelle, Yves Desdevises, Sébastien Colin, Rafel Simó, Fabrice Not, Lucie Bittner, 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), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Circuits Multi-Projets (CMP), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Centre National de la Recherche Scientifique (CNRS), Marine Biology and Oceanography, Institut de Ciències del Mar, CSIC, Diversité et Interactions au sein du Plancton Océanique (DIPO), Laboratoire d'Oceanographie de Villefranche-sur-Mer, InterUniversity Institute for Marine Sciences in Eilat (Association of European Marine Biological Laboratories-EU) [227799], Stazione Zoologica Anton Dohrn in Naples, Akajima Marine Science Laboratory (Centre National de la Recherche Scientifique-Japan Science and Technology Agency program), Station Biologique de Roscoff, TaraOceans expedition, Region Bretagne (Diversite de la Photosymbiose Pelagique DIPHOPE) [044763], French Agence Nationale de la Recherche [09-BLAN-0348 POSEI-DON], French ``Investissements d'Avenir' projects OCEANOMICS, European Marine Biological Resource Centre-France, Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), and Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)
Subjects: 0106 biological sciences, Oceans and Seas, Biogeography, [SDV]Life Sciences [q-bio], Molecular Sequence Data, Biodiversity, Biology, 01 natural sciences, 03 medical and health sciences, eukaryote biodiversity, Ecosystem, 14. Life underwater, Symbiosis, DMSP, Radiolaria, 030304 developmental biology, protists, 0303 health sciences, geography, Multidisciplinary, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, fungi, Pelagic zone, Protists, Coral reef, Biological Sciences, 15. Life on land, Plankton, biology.organism_classification, Benthic zone, [SDE]Environmental Sciences, Acantharia, Eukaryote biodiversity
Abstract: 6 pages, 3 figures, 1 table, Symbiotic relationships are widespread in nature and are fundamental for ecosystem functioning and the evolution of biodiversity. In marine environments, photosymbiosis with microalgae is best known for sustaining benthic coral reef ecosystems. Despite the importance of oceanic microbiota in global ecology and biogeochemical cycles, symbioses are poorly characterized in open ocean plankton. Here, we describe a widespread symbiotic association between Acantharia biomineralizing microorganisms that are abundant grazers in plankton communities, and members of the haptophyte genus Phaeocystis that are cosmopolitan bloom-forming microalgae. Cophylogenetic analyses demonstrate that symbiont biogeography, rather than host taxonomy, is the main determinant of the association. Molecular dating places the origin of this photosymbiosis in the Jurassic (ca. 175 Mya), a period of accentuated marine oligotrophy. Measurements of intracellular dimethylated sulfur indicate that the host likely profits from antioxidant protection provided by the symbionts as an adaptation to life in transparent oligotrophic surface waters. In contrast to terrestrial and marine symbioses characterized to date, the symbiont reported in this association is extremely abundant and ecologically active in its free-living phase. In the vast and barren open ocean, partnership with photosymbionts that have extensive free-living populations is likely an advantageous strategy for hosts that rely on such interactions. Discovery of the Acantharia–Phaeocystis association contrasts with the widely held view that symbionts are specialized organisms that are rare and ecologically passive outside the host, We thank S. Romac, E. Boudoux, Y. Souab, and M. J. Garet-Delmas for technical assistance and N. Suzuki for morphological identification of Acantharia. We thank the institutes and funding agencies that supported the collection of samples: the Laboratoire d’Océanographie de Villefranche-sur-Mer, the InterUniversity Institute for Marine Sciences in Eilat (Association of European Marine Biological Laboratories-EU FP7 I3 project 227799), the Stazione Zoologica Anton Dohrn in Naples, the Akajima Marine Science Laboratory (Centre National de la Recherche Scientifique–Japan Science and Technology Agency program), the Station Biologique de Roscoff, and the TaraOceans expedition. This research was supported by the Region Bretagne (Diversité de la Photosymbiose Pélagique DIPHOPE044763), the French Agence Nationale de la Recherche 09-BLAN-0348 POSEIDON, and the French “Investissements d’Avenir” projects OCEANOMICS and European Marine Biological Resource Centre-France
Published: 2012
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27. Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria)

Author: Frédéric Mahé, Fabrice Not, Noritoshi Suzuki, Johan Decelle, Colomban de Vargas, 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 Geology and Paleontology, Tohoku University [Sendai], Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Diversité et Interactions au sein du Plancton Océanique (DIPO), Region Bretagne, Interuniversity Institute for Marine Sciences in Eilat, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)
Subjects: 0106 biological sciences, Acantharia, [SDV]Life Sciences [q-bio], Molecular Sequence Data, 01 natural sciences, Microbiology, single-cells, 03 medical and health sciences, Phylogenetics, strontium sulfate, Polyphyly, Seawater, 14. Life underwater, Clade, Phylogeny, molecular phylogeny, Radiolaria, 030304 developmental biology, 0303 health sciences, biology, Phylogenetic tree, Ecology, 010604 marine biology & hydrobiology, Rhizaria, 15. Life on land, biology.organism_classification, Biological Evolution, Molecular phylogenetics, [SDE]Environmental Sciences, Taxonomy (biology)
Abstract: International audience; Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W. T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia. (C) 2011 Elsevier GmbH. All rights reserved.
Published: 2012
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28. A Holistic Approach to Marine Eco-Systems Biology

Author: Poirot Olivier, Atsuko Tanaka, Johan Decelle, Sabrina Speich, Jeroen Raes, Aurelie Chambouvet, Peer Bork, Colomban De Vargas, Pascal Hingamp, Silvia De Monte, Chris Bowler, Silvia Acinas, Adriana Zingone, Jean-Michel Claverie, Eric Pelletier, LEILA TIRICHINE DELACOUR, Stéphane PESANT, Pascal Morin, Josep M Gasol, Corinne DA SILVA, Olivier Jaillon, Gwenael Piganeau, Nicole Poulton, Yves Desdevises, Emmanuel Boss, Raffaella Casotti, Carlos Pedrós-Alió, Eve Toulza, Gilles Reverdin, Alaguraj Veluchamy, Marina Montresor, Jean-Louis JAMET, Lucie Subirana, Hugo Sarmento, Ian Probert, Benjamin Noel, Jean-Marc AURY, Stéphane Audic, Julie Poulain, Gipsi Lima-Mendez, Daniele Iudicone, Francisco M. Cornejo-Castillo, Francesca Benzoni, Isabel Ferrera, Shinichi Sunagawa, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Karsenti, E, Acinas, S, Bork, P, Bowler, C, De Vargas, C, Raes, J, Sullivan, M, Arendt, D, Benzoni, F, Claverie, J, Follows, M, Gorsky, G, Hingamp, P, Iudicone, D, Jaillon, O, Kandels-Lewis, S, Krzic, U, Not, F, Ogata, H, Pesant, S, Reynaud, E, Sardet, C, Sieracki, M, Speich, S, Velayoudon, D, Weissenbach, J, Wincker, P, European Molecular Biology Laboratory [Heidelberg] (EMBL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Vrije Universiteit [Brussels] (VUB), University of Arizona, Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Institut de Microbiologie de la Méditerranée (IMM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Massachusetts Institute of Technology (MIT), 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), Information génomique et structurale (IGS), Stazione Zoologica di Napoli (SZN), Stazione Zoologica di Napoli, 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Universität Bremen, University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Bigelow Laboratory for Ocean Sciences, 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), DVIP Consulting, Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-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), ANR-09-BLAN-0348,POSEIDON,PrOtiSts EcologIcal bioDiversity in Tara-OceaNs(2009), ANR-08-BDVA-0003,BIOMARKS,Biodiversité des eucaryotes marins(2008), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), JAMET, Jean-Louis, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Eranet sur la Biodiversité - Biodiversité des eucaryotes marins - - BIOMARKS2008 - ANR-08-BDVA-0003 - BDIV - 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, Génomique et biotechnologies végétales - Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans - - TARA-GIRUS2009 - ANR-09-GENM-0032 - GENOM-BTV - VALID, Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de biologie de l'ENS Paris (IBENS), 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), Vrije Universiteit Brussel (VUB), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Stazione Zoologica Anton Dohrn (SZN), 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), ANR-09-BLAN-0348,POSEIDON(2009), Department of Bio-engineering Sciences, 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), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J., UCLouvain, 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), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano-Bicocca, Aix Marseille Université (AMU), Université de la Méditerranée - Aix-Marseille 2, Center for Marine Environmental Sciences [Bremen] (MARUM), Développement de l'enfant, Groupe de Biologie Marine du CEA, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), DVIPC, The Tara Oceans expedition is generously funded by CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR, FWO, BIO5, Biosphere 2, 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., and the Tara Oceans Consortium
Subjects: MESH: Oceans and Seas, Ecosystem modeling, Biodiversity, Marine and Aquatic Sciences, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Microbial ecology, Seas, Ecosystem model, Global Change Ecology, Community Page, Oceans, MESH: Plankton, [SDV.EE.ECO] Life Sciences [q-bio]/Ecology, environment/Ecosystems, MESH: Animals, MESH: Ecosystem, Genome Sequencing, Biology (General), MESH: Expeditions, 0303 health sciences, Biological data, Ecology, General Neuroscience, Systems Biology, Environmental resource management, MESH: Marine Biology, Genomics, Biogeochemistry, Plankton, Community Ecology, Expeditions, General Agricultural and Biological Sciences, Marine ecosystems, BIO/05 - ZOOLOGIA, QH301-705.5, Systems biology, Oceans and Seas, Tara Oceans, Marine Biology, Biological Data Management, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Carbon Cycle, Marine ecology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Systems Ecology, Animals, Marine ecosystem, 14. Life underwater, Biological oceanography, Ecosystem, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Marine biology, General Immunology and Microbiology, 030306 microbiology, business.industry, Computational Biology, xxx, 15. Life on land, Tara Oceans Consortium, Earth system science, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, 13. Climate action, Microbial Evolution, Earth Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Genome Expression Analysis, Environmental Sciences
Abstract: Eric Karsenti et al.-- 5 pages, 2 figures, With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system, We are keen to thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS, EMBL, Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON, BIOMARKS, PROMETHEUS, and TARA-GIRUS), FWO, BIO5, Biosphere 2, 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 Tara schooner and its captain and crew. Tara Oceans would not exist without the continuous support of the participating 23 institutes (see http://oceans.taraexpeditions.org). Special thanks also goes to Fabrice Not and Noan Le Bescot for creating the figures of this manuscript. This is contribution number 0001 of the Tara Oceans Expedition 2009–2012
Published: 2011
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28 results on '"Johan Decelle"'

1. Mixotrophic growth of the extremophile Galdieria sulphuraria reveals the flexibility of its carbon assimilation metabolism

2. Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae

3. Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging

4. A community perspective on the concept of marine holobionts: current status, challenges, and future directions

5. Cytoklepty in the plankton: a host strategy to optimize the bioenergetic machinery of endosymbiotic algae

6. In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy

7. Subcellular Chemical Imaging: New Avenues in Cell Biology

8. A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

9. Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters

10. Algal remodeling in a ubiquitous planktonic photosymbiosis

11. Diatom diversity through HTS-metabarcoding in coastal European seas

12. A de novo approach to disentangle partner identity and function in holobiont systems

13. The symbiotic life of Symbiodinium in the open ocean within a new species of calcifying ciliate (Tiarina sp.)

14. NanoSIMS chemical imaging combined with correlative microscopy for biological sample analysis

15. Worldwide Occurrence and Activity of the Reef-Building Coral Symbiont Symbiodinium in the Open Ocean

16. Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton

17. Benthic protists: the under-charted majority

18. Transcriptome analyses to investigate symbiotic relationships between marine protists

19. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy

20. Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians

21. Patterns of Rare and Abundant Marine Microbial Eukaryotes

22. Ancient DNA complements microfossil record in deep-sea subsurface sediments

23. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

24. Multiple microalgal partners in symbiosis with the acantharian Acanthochiasma sp. (Radiolaria)

25. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms

26. An original mode of symbiosis in open ocean plankton

27. Molecular Phylogeny and Morphological Evolution of the Acantharia (Radiolaria)

28. A Holistic Approach to Marine Eco-Systems Biology

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