Author: "Bigelow Laboratory for Ocean Sciences" - Searchworks@Jio Institute Digital Library Search Results

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49 results on '"Bigelow Laboratory for Ocean Sciences"'

1. Environmental benchmark studies in Casco Bay, Portland Harbor, Maine, April 1980 / Peter F. Larsen, Anne C. Johnson, and Lee F. Doggett.

Author: Larsen, Peter F., Doggett, Lee F., Johnson, Anne C., Bigelow Laboratory for Ocean Sciences, Northeast Fisheries Center (U.S.), United States. National Marine Fisheries Service, MBLWHOI Library, Larsen, Peter F., Doggett, Lee F., Johnson, Anne C., Bigelow Laboratory for Ocean Sciences, Northeast Fisheries Center (U.S.), and United States. National Marine Fisheries Service
Subjects: Casco Bay, Environmental impact analysis, Environmental monitoring, Maine, Marine biology
Published: 1983

2. Growth on ATP elicits a P-stress response in the picoeukaryote Micromonas pusilla

Author: Lomas, Michael [Bigelow Laboratory for Ocean Sciences, East Boothbay, ME (United States)]
Published: 2016
Full Text: View/download PDF

3. Novel chlorophyll-related compounds in marine phytoplankton: Distributions and geochemical implications

Author: Guillard, R [Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME (USA)]
Published: 2020
Full Text: View/download PDF

4. MIxS-SA: a MIxS extension defining the minimum information standard for sequence data from symbiont-associated micro-organisms

Author: Fátima Jorge, Jaelle C. Brealey, Paul J. Brindley, Marie Buysse, Cinzia Cantacessi, Olivier Duron, Raina Fichorova, Connor R. Fitzpatrick, Megan Hahn, Christopher Hunter, Vincent Hervé, Laura J. Knoll, Kevin D. Kohl, Marco Lalle, Julius Lukeš, Joaquín Martínez Martínez, Susan L. Perkins, Robert Poulin, Karyna Rosario, Adam C. Schneider, Lynn M. Schriml, Luke R. Thompson, Ramona L. Walls, Nolwenn M. Dheilly, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM), Centre de Recherche en Ecologie et Evolution de la Santé (CREES), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Unité de virologie, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], University of Otago [Dunedin, Nouvelle-Zélande], NTNU University Museum [Trondheim], Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU)-Norwegian University of Science and Technology (NTNU), The George Washington University (GW), Department of Veterinary Medicine, University of Cambridge [UK] (CAM), Harvard Medical School [Boston] (HMS), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), NYC Department of Health and Mental Hygiene (NYC Health), University of Wisconsin-Madison, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Istituto Superiore di Sanità (ISS), 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), Bigelow Laboratory for Ocean Sciences, The City College of New York (CCNY), City University of New York [New York] (CUNY), University of South Florida [Tampa] (USF), Hendrix College, University of Maryland School of Medicine, University of Maryland System, Mississippi State University [Mississippi], National Oceanic and Atmospheric Administration (NOAA), Critical Path Institute [Tucson, AZ], Virologie UMR1161 (VIRO), École nationale vétérinaire - Alfort (ENVA)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Cantacessi, Cinzia [0000-0001-6863-2950], and Apollo - University of Cambridge Repository
Subjects: 3107 Microbiology, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, FOS: Biological sciences, Human Genome, Genetics, General Medicine, Infection, 31 Biological Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments.
Published: 2022

5. Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems

Author: Michael Hoffert, Rika E. Anderson, Julie Reveillaud, Leslie G. Murphy, Ramunas Stepanauskas, Julie A. Huber, Carleton College, Finch Therapeutics Group, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Marine Biological Laboratory (MBL), University of Chicago, Bigelow Laboratory for Ocean Sciences, Woods Hole Oceanographic Institution (WHOI), Deep Carbon Observatory’s Deep Life Initiative, NASA Exobiology Grant Number 80NSSC18K1076, NASA Astrobiology Science and Technology for Exploring Planets (ASTEP) Grant NNX-327 09AB75G, NSF Science and Technology Center for Dark Energy Biosphere Investigations (C-DEBI), and NSF Grants OCE-1136488 and OIA-1826734
Subjects: Microbiology (medical), Population, Microbiology, single-cell genome, 03 medical and health sciences, Abundance (ecology), [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], hydrothermal vents, 14. Life underwater, methanogen, education, 030304 developmental biology, Original Research, Ecological niche, 0303 health sciences, education.field_of_study, biology, Phylogenetic tree, 030306 microbiology, biology.organism_classification, nitrogenase, Methanogen, QR1-502, fitness, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Metagenomics, Evolutionary biology, Archaea, Hydrothermal vent
Abstract: Hydrogenotrophic methanogens are ubiquitous chemoautotrophic archaea inhabiting globally distributed deep-sea hydrothermal vent ecosystems and associated subseafloor niches within the rocky subseafloor, yet little is known about how they adapt and diversify in these habitats. To determine genomic variation and selection pressure within methanogenic populations at vents, we examined five Methanothermococcus single cell amplified genomes (SAGs) in conjunction with 15 metagenomes and 10 metatranscriptomes from venting fluids at two geochemically distinct hydrothermal vent fields on the Mid-Cayman Rise in the Caribbean Sea. We observed that some Methanothermococcus lineages and their transcripts were more abundant than others in individual vent sites, indicating differential fitness among lineages. The relative abundances of lineages represented by SAGs in each of the samples matched phylogenetic relationships based on single-copy universal genes, and genes related to nitrogen fixation and the CRISPR/Cas immune system were among those differentiating the clades. Lineages possessing these genes were less abundant than those missing that genomic region. Overall, patterns in nucleotide variation indicated that the population dynamics of Methanothermococcus were not governed by clonal expansions or selective sweeps, at least in the habitats and sampling times included in this study. Together, our results show that although specific lineages of Methanothermococcus co-exist in these habitats, some outcompete others, and possession of accessory metabolic functions does not necessarily provide a fitness advantage in these habitats in all conditions. This work highlights the power of combining single-cell, metagenomic, and metatranscriptomic datasets to determine how evolution shapes microbial abundance and diversity in hydrothermal vent ecosystems.
Published: 2021

6. Production primaire en mer Ligure

Author: Mayot, Nicolas, Nival, Paul, Lévy, Marina, Bigelow Laboratory for Ocean Sciences, 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), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Chistophe Migon, Antoine Sciandra, Paul Nival, Sciandra, Antoine, Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)
Subjects: [SDE] Environmental Sciences, [SDE]Environmental Sciences, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

7. No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic

Author: John A. Burns, Fabrice Not, Florence Le Gall, Daniel Vaulot, Valeria Jimenez, Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), ECOlogy of MArine Plankton (ECOMAP), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Bigelow Laboratory for Ocean Sciences, and Nanyang Technological University [Singapour]
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], MESH: Arctic Regions, Zoology, Plant Science, Aquatic Science, 010603 evolutionary biology, 01 natural sciences, MESH: Chlorophyta, Ochromonas, Arctic, Polaris, Chlorophyta, Phytoplankton, Micromonas, phago-mixotrophy, biology, Bacteria, Arctic Regions, 010604 marine biology & hydrobiology, biology.organism_classification, The arctic, Phago, MESH: Bacteria, phytoplankton, Seasons, MESH: Seasons, geographic locations
Abstract: International audience; In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.
Published: 2020

8. Under-ice phytoplankton blooms: Shedding light on the 'invisible' part of Arctic primary production

Author: Lisa C. Matthes, Philipp Assmy, Kevin R. Arrigo, Igor A. Melnikov, Eva Leu, C. J. Mundy, Christopher Horvat, Patricia A. Matrai, Laurent Oziel, Victoria Hill, Mathieu Ardyna, Matthew A. Gale, Nicolas Mayot, 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), Centre for Earth Observation Science [Winnipeg], University of Manitoba [Winnipeg], Bigelow Laboratory for Ocean Sciences, University of East Anglia [Norwich] (UEA), Takuvik International Research Laboratory, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), MOM: La meiose dans l'ovocyte des mammifères = MOM: mammalian oocyte meiosis (LBD-E13), Laboratoire de Biologie du Développement [Paris] (LBD), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Sorbonne Université (SU)-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), Brown University, Akvaplan-Niva [Tromsø], Norwegian Institute for Water Research (NIVA), Norwegian Polar Institute, Old Dominion University [Norfolk] (ODU), P.P. Shirshov Institute of Oceanology (SIO), Russian Academy of Sciences [Moscow] (RAS), Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Gestionnaire, HAL Sorbonne Université 5, Laboratoire de Biologie du Développement [IBPS] (LBD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-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)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-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)
Subjects: [SDE] Environmental Sciences, 0106 biological sciences, Biogeochemical cycle, lcsh:QH1-199.5, 010504 meteorology & atmospheric sciences, Ecology (disciplines), Climate change, Ocean Engineering, lcsh:General. Including nature conservation, geographical distribution, Aquatic Science, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Oceanography, 01 natural sciences, Latitude, Water column, Phytoplankton, Arctic Ocean, Sea ice, 14. Life underwater, lcsh:Science, under-ice phytoplankton blooms, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Water Science and Technology, Global and Planetary Change, geography, geography.geographical_feature_category, 010604 marine biology & hydrobiology, nutrient, biogeochemical cycles, sea ice, climate change, Arctic, 13. Climate action, [SDE]Environmental Sciences, Environmental science, lcsh:Q
Abstract: The growth of phytoplankton at high latitudes was generally thought to begin in open waters of the marginal ice zone once the highly reflective sea ice retreats in spring, solar elevation increases, and surface waters become stratified by the addition of sea-ice melt water. In fact, virtually all recent large-scale estimates of primary production in the Arctic Ocean (AO) assume that phytoplankton production in the water column under sea ice is negligible. However, over the past two decades, an emerging literature showing significant under-ice phytoplankton production on a pan-Arctic scale has challenged our paradigms of Arctic phytoplankton ecology and phenology. This evidence, which builds on previous, but scarce reports, requires the Arctic scientific community to change its perception of traditional AO phenology and urgently revise it. In particular, it is essential to better comprehend, on small and large scales, the changing and variable icescapes, the under-ice light field and biogeochemical cycles during the transition from sea-ice covered to ice-free Arctic waters. Here, we provide a baseline of our current knowledge of under-ice blooms (UIBs), by defining their ecology and their environmental setting, but also their regional peculiarities (in terms of occurrence, magnitude, and assemblages), which is shaped by a complex AO. To this end, a multidisciplinary approach, i.e., combining expeditions and modern autonomous technologies, satellite, and modeling analyses, has been used to provide an overview of this pan-Arctic phenological feature, which will become increasingly important in future marine Arctic biogeochemical cycles.
Published: 2020

9. Roadmap for naming uncultivated Archaea and Bacteria

Author: William P. Inskeep, Iain C. Sutcliffe, Roland Hatzenpichler, Takuro Nunoura, William B. Whitman, Paul Carini, Alison E. Murray, Kristen M. DeAngelis, Carlos Pedrós-Alió, Daniel R. Colman, Stephanus N. Venter, Rudolf Amann, Karen G. Lloyd, David R. Emerson, Donovan H. Parks, Simonetta Gribaldo, Roman A. Barco, Jonathan A. Eisen, Duane P. Moser, Andrew D. Steen, Elena P. Ivanova, Damien Eveillard, Laura A. Hug, Konstantinos T. Konstantinidis, Hans-Peter Klenk, J. Cameron Thrash, Alexander J. Probst, Brett J. Baker, Anja Spang, Fengping Wang, Paulina Estrada-de los Santos, Peter R. Girguis, Ramon Rosselló-Móra, Anna-Louise Reysenbach, Maria Asuncion de los Rios, Jean Armengaud, R. Thane Papke, Emma Theodora Steenkamp, Theo H. M. Smits, Ute Hentschel, John V. Freudenstein, Frank E. Löffler, Victor Parro, Peter Kämpfer, Wen-Jun Li, Frank J. Stewart, Christopher A. Dunlap, Karthik Anantharaman, Thulani P. Makhalanyane, Christopher E. Lane, Helge B. Bode, Philip Hugenholtz, Eric S. Boyd, Carrie Brady, Marike Palmer, Matthew B. Stott, Michael Wagner, Thisjs J. G. Ettema, James M. Tiedje, Brian P. Hedlund, Patrick S. G. Chain, Pablo Yarza, James T. Hollibaugh, Silvia G. Acinas, Peter Vandamme, Desert Research Institute (DRI), Ecology and Organismal Biology, Ohio State University [Columbus] (OSU), Biologie Evolutive de la Cellule Microbienne - Evolutionary Biology of the Microbial Cell, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Montana State University (MSU), University of Queensland [Brisbane], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), Botanical and Environmental Consultant, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Laboratoire Environnement Profond (LEP), Etudes des Ecosystèmes Profonds (EEP), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin [Austin], Buchmann Institute for Molecular Life Sciences [Frankfurt am Main] (BMLS), Goethe-Universität Frankfurt am Main, Istituto delle Scienze dell' Atmosfera e dell'Oceano [Bologna] (ISAO), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM), Bigelow Laboratory for Ocean Sciences, Uppsala University, Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Department of Theoretical Mechanics, St. Petersburg State Polytechnical University, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), Sun Yat-Sen University [Guangzhou] (SYSU), Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Universiteit Gent = Ghent University (UGENT), SANOFI (Research and Development), Research and Development, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658), We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent discussions and provided comments to mature the concept communicated here., Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Justus-Liebig-Universität Gießen (JLU), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Consiglio Nazionale delle Ricerche (CNR), Universidad Nacional Autónoma de México (UNAM), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), University of California [Berkeley], University of California-University of California, Universiteit Gent = Ghent University [Belgium] (UGENT), Unidad de Excelencia Científica María de Maeztu Centro de Astrobiología del Instituto Nacional de Técnica Aeroespacial y CSIC, MDM-2017-0737, Murray, A. E. [0000-0001-5790-7584], Gribaldo, S. [0000-0002-7662-021X], Hatzenpichler, R. [0000-0002-5489-3444], Hugenholtz, P. [0000-0001-5386-7925], Lane, C. [0000-0003-2558-2767], Parks, D. H. [0000-0001-6662-9010], Stott, M. B. [0000-0002-2082-9460], Thrash, J. C. [0000-0003-0896-9986], Anantharaman, K. [0000-0002-9584-2491], Armegaud, J. [0000-0003-1589-445X], Bode, H. B. [0000-0001-6048-5909], De Angelis, K. M. [0000-0002-5585-4551], De los Santos, P. E. [0000-0003-2407-0284], Eisen, J. A. [0000-0002-0159-2197], Ettema, T. J. G. [0000-0002-6898-6377], Eveillard, D. [0000-0002-8162-7360], Hentschel, U. [0000-0003-0596-790X], Inskeep, W. P. [0000-0002-5203-817X], Klenk, H. P. [0000-0001-6758-8150], Palmer, M. [0000-0001-8395-8465], Probst, A. [0000-0002-9392-6544], Smits, T. H. M. [0000-0002-1237-235X], Steen, A. D. [0000-0003-4297-4332], Spang, A. [0000-0002-6518-8556], Wang, F. [0000-0002-3429-8410], Hedlund, B. [0000-0001-8530-0448], Reysenbach, A. L. [0000-0001-9130-7750], Amann, R. [0000-0002-0846-7372], National Science Foundation (NSF), National Science Foundation, DEB-1841658, National Science Foundation (US), and Agencia Estatal de Investigación (España)
Subjects: [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Applied Microbiology and Biotechnology, Genome, Microbiologie, Nomenclature, Phylogeny, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Environmental microbiology, Bacterial, C500, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Microbes, Medical Microbiology, Taxonomy (biology), Biologie, Sequence Analysis, Microbiology (medical), DNA, Bacterial, Immunology, Chemie, Computational biology, Biology, Microbiology, DNA sequencing, 03 medical and health sciences, Type (biology), Microbial ecology, Terminology as Topic, Genetics, Life Science, Author Correction, 030304 developmental biology, Taxonomy, WIMEK, Bacteria, 030306 microbiology, Consensus Statement, Biology and Life Sciences, NEED, Cell Biology, DNA, Sequence Analysis, DNA, 570: Biologie, Archaea, Mikrobiologi, Taxon, Prokaryotic Cells, Metagenomics, AD-HOC COMMITTEE, Metagenome, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 8 pages, 2 figures, 1 table, 2 boxes, supplementary information https://doi.org/10.1038/s41564-020-0733-x.-- Author Correction: Roadmap for naming uncultivated Archaea and Bacteria: n the version of this Consensus Statement originally published, Pablo Yarza was mistakenly not included in the author list. Also, in Supplementary Table 1, Alexander Jaffe was missing from the list of endorsees. These errors have now been corrected and the updated Supplementary Table 1 is available online, The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as ‘type material’, thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity, Support for this effort was provided by the National Science Foundation (grant no. DEB-1841658). We extend deep appreciation to all who attended the Microbial Taxonomy 2018 seminars, the Microbial Systematics for the Next Decade workshop held in Hood River, Oregon, USA, in October 2018, and those that participated in subsequent, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2020

10. Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Author: Freudenstein, John, Gribaldo, Simonetta, Hatzenpichler, Roland, Hugenholtz, Philip, Kämpfer, Peter, Konstantinidis, Konstantinos, Lane, Christopher, Papke, R. Thane, Parks, Donovan, Rossello-Mora, Ramon, Stott, Matthew, Sutcliffe, Iain, Thrash, J. Cameron, Venter, Stephanus, Whitman, William, Acinas, Silvia, Amann, Rudolf, Anantharaman, Karthik, Armengaud, Jean, Baker, Brett, Barco, Roman, Bode, Helge, Boyd, Eric, Brady, Carrie, Carini, Paul, Chain, Patrick, Colman, Daniel, DeAngelis, Kristen, de los Rios, Maria Asuncion, Estrada-De Los Santos, Paulina, Dunlap, Christopher, Eisen, Jonathan, Emerson, David, Ettema, Thijs, Girguis, Peter, Hentschel, Ute, Hollibaugh, James, Hug, Laura, Inskeep, William, Ivanova, Elena, Klenk, Hans-Peter, Li, Wen-Jun, Lloyd, Karen, Löffler, Frank, Makhalanyane, Thulani, Moser, Duane, Nunoura, Takuro, Palmer, Marike, Parro, Victor, Pedrós-Alió, Carlos, Probst, Alexander, Smits, Theo, Steen, Andrew, Steenkamp, Emma, Spang, Anja, Stewart, Frank, Tiedje, James, Vandamme, Peter, Wagner, Michael, Wang, Feng-Ping, Hedlund, Brian, Reysenbach, Anna-Louise, Murray, Alison, Avalon, Nicole, Bishop, Lucas, Davenport, Karen, Delage, Erwan, Dichosa, Armand E.K., Eveillard, Damien, Higham, Mary, Kokkaliari, Sofia, Lo, Chien-Chi, Riesenfeld, Christian, Young, Ryan, Chain, Patrick S.G., Baker, Bill, Metacohorts Consortium, Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), 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), Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], University of Queensland [Brisbane], Justus-Liebig-Universität Gießen (JLU), Louisiana State University (LSU), Botanical and Environmental Consultant, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Laboratoire de Biochimie des Systèmes Perturbés (LBSP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), University of Texas at Austin [Austin], Buchmann Institute for Molecular Life Sciences [Frankfurt am Main] (BMLS), Goethe-Universität Frankfurt am Main, ISAO [Bologna, Italy], Universidad Nacional Autónoma de México (UNAM), Bigelow Laboratory for Ocean Sciences, Uppsala University, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Montana State University (MSU), Laboratoire de l'intégration, du matériau au système (IMS), Université Sciences et Technologies - Bordeaux 1-Institut Polytechnique de Bordeaux-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH / Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China. Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China, Physikalisch-Technische Bundesanstalt [Braunschweig] (PTB), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Department of Earth and Planetary Science [UC Berkeley] (EPS), University of California [Berkeley], University of California-University of California, Royal Netherlands Institute for Sea Research (NIOZ), The Center for Microbial Ecology, Department of Microbiology and Molecular Genetics, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Universiteit Gent [Ghent], Hochschule Aalen, Institut für Angewandte Forschung, Hochschule Aalen, Martin-Luther-University Halle-Wittenberg, Université de Nantes - Faculté des Sciences et des Techniques, and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
Subjects: Range (biology), ascidian, [INFO.INFO-OH]Computer Science [cs]/Other [cs.OH], Antarctic Regions, microbiome, Pharmaceutical Science, Biology, Genome, Article, Polyketide, 03 medical and health sciences, RNA, Ribosomal, 16S, co-occurrence, Drug Discovery, Animals, Marine ecosystem, Urochordata, 14. Life underwater, Microbiome, palmerolide A, Gene, lcsh:QH301-705.5, Pharmacology, Toxicology and Pharmaceutics (miscellaneous), ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Islands, Whole genome sequencing, 0303 health sciences, geography, geography.geographical_feature_category, Phylum, 030306 microbiology, Microbiota, Bacterioplankton, 15. Life on land, 16S ribosomal RNA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Holobiont, Taxon, lcsh:Biology (General), Evolutionary biology, microbial diversity, Archipelago, Antarctica, Macrolides, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64&deg, 46'S, 64&deg, 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3&ndash, V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)&mdash, 20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.
Published: 2020

11. The impacts of ocean acidification on marine trace gases and the implications for atmospheric chemistry and climate

Author: Philip Williamson, Erik T. Buitenhuis, Stephen D. Archer, Jörg Schwinger, Laurent Bopp, Kitack Lee, Martin Johnson, Marion Gehlen, Frances E. Hopkins, Robert A. Duce, Martine Lizotte, Hema Naik, Cliff S. Law, Oliver Andrews, Fiona Seh-Lin Keng, Andrew P. Rees, Gillian Malin, Tim Jickells, J. Colin Murrell, Nadine Goris, Parvadha Suntharalingam, Isabelle Dadou, Peter S. Liss, Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), School of Geographical Sciences [Bristol], University of Bristol [Bristol], Bigelow Laboratory for Ocean Sciences, Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Department of Atmospheric Sciences [College Station], Texas A&M University [College Station], Bjerknes Centre for Climate Research (BCCR), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB)-University of Bergen (UiB), University of Malaya [Kuala Lumpur, Malaisie], National Institute of Water and Atmospheric Research [Wellington] (NIWA), Pohang University of Science and Technology (POSTECH), Groupe de Recherche sur les Enjeux de la Communication (GRESEC), Université Grenoble Alpes (UGA), Université Laval [Québec] (ULaval), National Institute of Oceanography (NIO), Council of Scientific and Industrial Research [India] (CSIR), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), and University of Malaya = Universiti Malaya [Kuala Lumpur, Malaisie] (UM)
Subjects: 0106 biological sciences, Ocean observations, atmospheric chemistry, 010504 meteorology & atmospheric sciences, General Mathematics, Effects of global warming on oceans, General Physics and Astronomy, ocean acidification, Review Article, Atmospheric sciences, 01 natural sciences, chemistry.chemical_compound, biogeochemistry, 14. Life underwater, climate, 0105 earth and related environmental sciences, Subject Areas: atmospheric chemistry, 010604 marine biology & hydrobiology, General Engineering, Biogeochemistry, Ocean acidification, marine trace gases, oceanography Keywords: ocean acidification, Trace gas, chemistry, 13. Climate action, Atmospheric chemistry, [SDE]Environmental Sciences, Upwelling, Dimethyl sulfide
Abstract: Surface ocean biogeochemistry and photochemistry regulate ocean–atmosphere fluxes of trace gases critical for Earth's atmospheric chemistry and climate. The oceanic processes governing these fluxes are often sensitive to the changes in ocean pH (or p CO 2 ) accompanying ocean acidification (OA), with potential for future climate feedbacks. Here, we review current understanding (from observational, experimental and model studies) on the impact of OA on marine sources of key climate-active trace gases, including dimethyl sulfide (DMS), nitrous oxide (N 2 O), ammonia and halocarbons. We focus on DMS, for which available information is considerably greater than for other trace gases. We highlight OA-sensitive regions such as polar oceans and upwelling systems, and discuss the combined effect of multiple climate stressors (ocean warming and deoxygenation) on trace gas fluxes. To unravel the biological mechanisms responsible for trace gas production, and to detect adaptation, we propose combining process rate measurements of trace gases with longer term experiments using both model organisms in the laboratory and natural planktonic communities in the field. Future ocean observations of trace gases should be routinely accompanied by measurements of two components of the carbonate system to improve our understanding of how in situ carbonate chemistry influences trace gas production. Together, this will lead to improvements in current process model capabilities and more reliable predictions of future global marine trace gas fluxes.
Published: 2020
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12. The Mediterranean Sea in the era of global change. Vol. 1 : 30 years of multidisciplinary study of the Ligurian sea

Author: Paul Nival, Marina Levy, Nicolas Mayot, Migon, C. (ed.), Nival, P. (ed.), Sciendra, A. (ed.), Bigelow Laboratory for Ocean Sciences, 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), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Recherche pour le Développement (IRD), Christophe Migon, Paul Nival, Antoine Sciandra, Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)
Subjects: 0106 biological sciences, biogeochemical modeling studies, PHYTOPLANCTON, VARIATION SAISONNIERE, 010504 meteorology & atmospheric sciences, Mixed layer, PRODUCTION PRIMAIRE, spatiotemporal processes, Mesoscale meteorology, primary production cycles, STRUCTURE DE POPULATION, 01 natural sciences, Ligurian Sea, CYCLE BIOGEOCHIMIQUE, OCEANOGRAPHIE BIOLOGIQUE, Phytoplankton, phytoplankton biomass, Photic zone, 14. Life underwater, Transect, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, BIOMASSE, 010604 marine biology & hydrobiology, Lead (sea ice), Biogeochemistry, Annual cycle, MODELISATION, Oceanography, 13. Climate action, VARIATION SPATIALE, DYNAMIQUE DE POPULATION
Abstract: International audience; The oceanographic and ecological characteristics of phytoplankton dynamics in the Ligurian Sea had been described in the 1960s from transects across the area and related to some physical–biogeochemical processes. This chapter provides an overview of the micro‐, nano‐ and picophytoplankton species. Recurrent estimations of annual primary production cycles in the euphotic layer of the central Ligurian Sea were obtained at the DYFAMED sampling station. Associated with general annual cycle of phytoplankton dynamics, small spatiotemporal processes occur and may play a lead role at local scales. The biogeochemistry of the Ligurian Sea shares important characteristics with other temperate regions of the ocean, such as the North Atlantic. Modeling studies of this complex system has paved the way for the understanding of the coupling between the physics of the ocean and the response of the biogeochemistry in environments that are prone to strong seasonal variations of the surface mixed layer and to strong mesoscale dynamics.
Published: 2020

13. The planktonic stages of the salmon louse ( Lepeophtheirus salmonis) are tolerant of end-of-century p CO2 concentrations

Author: Jeffrey A. Runge, Andrew S. Mount, Cameron Thompson, Steven Shema, Caroline M. F. Durif, Anne Berit Skiftesvik, David M. Fields, Vera B. S. Chan, Reidun M. Bjelland, Howard I. Browman, Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Bigelow Laboratory for Ocean Sciences, Austevoll Research Station (IMR), University of Bergen (UiB)-University of Bergen (UiB), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Department of Biological Sciences [Clemson], Clemson University, University of Maine, Gulf of Maine Research Institute (GMRI), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Zoology, lcsh:Medicine, Growth, Aquaculture, Biology, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, calanus-finmarchicus, Salmon louse, Lepeophtheirus salmonis, Energetics, 14. Life underwater, threat, impacts, business.industry, behavior, 010604 marine biology & hydrobiology, General Neuroscience, Marine larval ecology, ACL, Salmon lice, Ocean acidification, fungi, lcsh:R, General Medicine, Plankton, Lipid, biology.organism_classification, Copepod, infection, sea lice, Parasite, Metabolism, 13. Climate action, Lepeophtheirus, responses, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, business, respiration
Abstract: The copepod Lepeophtheirus salmonis is an obligate ectoparasite of salmonids. Salmon lice are major pests in salmon aquaculture and due to its economic impact Lepeophtheirus salmonis is one of the most well studied species of marine parasite. However, there is limited understanding of how increased concentration of pCO2 associated with ocean acidification will impact host-parasite relationships. We investigated the effects of increased pCO2 on growth and metabolic rates in the planktonic stages, rearing L. salmonis from eggs to 12 days post hatch copepodids under three treatment levels: Control (416 µatm), Mid (747 µatm), and High (942 µatm). The pCO2 treatment had a significant effect on oxygen consumption rate with the High treatment animals exhibiting the greatest respiration. The treatments did not have a significant effect on the other biological endpoints measured (carbon, nitrogen, lipid volume, and fatty acid content). The results indicate that L. salmonis have mechanisms to compensate for increased concentration of pCO2and that populations will be tolerant of projected future ocean acidification scenarios. The work reported here also describes catabolism during the lecithotrophic development of L. salmonis, information that is not currently available to parameterize models of dispersal and viability of the planktonic free-living stages.
Published: 2019

14. Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Author: Ann C. Gregory, Ahmed A. Zayed, Nádia Conceição-Neto, Ben Temperton, Ben Bolduc, Adriana Alberti, Mathieu Ardyna, Ksenia Arkhipova, Margaux Carmichael, Corinne Cruaud, Céline Dimier, Guillermo Domínguez-Huerta, Joannie Ferland, Stefanie Kandels, Yunxiao Liu, Claudie Marec, Stéphane Pesant, Marc Picheral, Sergey Pisarev, Julie Poulain, Jean-Éric Tremblay, Dean Vik, Marcel Babin, Chris Bowler, Alexander I. Culley, Colomban de Vargas, Bas E. Dutilh, Daniele Iudicone, Lee Karp-Boss, Simon Roux, Shinichi Sunagawa, Patrick Wincker, Matthew B. Sullivan, Silvia G. Acinas, Peer Bork, Emmanuel Boss, Guy Cochrane, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Lionel Guidi, Pascal Hingamp, Olivier Jaillon, Stefanie Kandels-Lewis, Eric Karsenti, Fabrice Not, Hiroyuki Ogata, Nicole Poulton, Jeroen Raes, Christian Sardet, Sabrina Speich, Lars Stemmann, University of Exeter, Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, 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), Utrecht University [Utrecht], 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), 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), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Université Laval [Québec] (ULaval), 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), European Molecular Biology Laboratory [Grenoble] (EMBL), Ohio State University [Columbus] (OSU), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), University of Maine, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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), Wellcome Trust Genome Campus, 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 Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Stazione Zoologica Anton Dohrn (SZN), 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), European Molecular Biology Laboratory [Heidelberg] (EMBL), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Pangea, Bigelow Laboratory for Ocean Sciences, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), Laboratoire de 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), 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), University of Arizona, Région Bretagne, Veolia Foundation, Fondation Prince Albert II de Monaco, Centre National de la Recherche Scientifique (France), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-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)-École normale supérieure - Paris (ENS-PSL), 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), Adaptation et diversité en milieu marin (ADMM), and Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR)
Subjects: Aquatic Organisms, [SDV]Life Sciences [q-bio], Coronacrisis-Taverne, species, [SDU.STU]Sciences of the Universe [physics]/Earth Sciences, marine biology, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, General Biochemistry, Genetics and Molecular Biology, diversity gradients, Article, 03 medical and health sciences, 0302 clinical medicine, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Humans, Human virome, Ecosystem, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Marine biology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, 0303 health sciences, metagenomics, Drowning, Community, Ecology, Microbiota, DNA Viruses, Biodiversity, DNA, Population ecology, Biodiversity hotspot, Arctic, 13. Climate action, Metagenomics, [SDU]Sciences of the Universe [physics], population ecology, DNA, Viral, Viruses, Metagenome, Water Microbiology, 030217 neurology & neurosurgery, community ecology, geographic locations
Abstract: 15 pages, 15 figures, 1 tables, supporting information https://doi.org/10.1016/j.cell.2019.03.040, Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models, Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, The French Ministry of Research, and the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL∗ Research University (ANR-11-IDEX-0001-02). We also thank the support and commitment of Agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST
Published: 2019

15. Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Author: Guillem Salazar, Lucas Paoli, Adriana Alberti, Jaime Huerta-Cepas, Hans-Joachim Ruscheweyh, Miguelangel Cuenca, Christopher M. Field, Luis Pedro Coelho, Corinne Cruaud, Stefan Engelen, Ann C. Gregory, Karine Labadie, Claudie Marec, Eric Pelletier, Marta Royo-Llonch, Simon Roux, Pablo Sánchez, Hideya Uehara, Ahmed A. Zayed, Georg Zeller, Margaux Carmichael, Céline Dimier, Joannie Ferland, Stefanie Kandels, Marc Picheral, Sergey Pisarev, Julie Poulain, Silvia G. Acinas, Marcel Babin, Peer Bork, Chris Bowler, Colomban de Vargas, Lionel Guidi, Pascal Hingamp, Daniele Iudicone, Lee Karp-Boss, Eric Karsenti, Hiroyuki Ogata, Stephane Pesant, Sabrina Speich, Matthew B. Sullivan, Patrick Wincker, Shinichi Sunagawa, Emmanuel Boss, Guy Cochrane, Michael Follows, Gabriel Gorsky, Nigel Grimsley, Olivier Jaillon, Stefanie Kandels-Lewis, Fabrice Not, Nicole Poulton, Jeroen Raes, Christian Sardet, Lars Stemmann, European Commission, Ministerio de Economía y Competitividad (España), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), 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), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Instituto de Fisica [Mexico] (UASLP), Universidad Autonoma de San Luis Potosi [México] (UASLP), Institute of Microbiology and Swiss Institute of Bioinformatics, CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Center for Genomic Regulation (CRG-UPF), CIBER de Epidemiología y Salud Pública (CIBERESP), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), European Molecular Biology Laboratory [Heidelberg] (EMBL), Bayer Cropscience, Immunobiologie Cellulaire et Moléculaire des Infections Parasitaires, Université Pierre et Marie Curie - Paris 6 (UPMC)-IFR113-Institut National de la Santé et de la Recherche Médicale (INSERM), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Institut de Chimie de Clermont-Ferrand - Clermont Auvergne (ICCF), Sigma CLERMONT (Sigma CLERMONT)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Grenoble] (EMBL), 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), Takuvik Joint ULaval/CNRS Laboratory, Centre National de la Recherche Scientifique (CNRS)-Laval University [Québec], 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), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), University of Maine, European Molecular Biology Laboratory European Bioinformatics Institute, Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), 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), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Sezione Ecologia Marina Integrata, Stazione Zoologica Anton Dohrn (SZN), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Bigelow Laboratory for Ocean Sciences, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), 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)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Laboratoire de physique des océans (LPO), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Université Paris-Saclay, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Kyoto University, Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Kyoto University [Kyoto], Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), and Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval)
Subjects: ASSEMBLY PROCESSES, Effects of global warming on oceans, DIVERSITY, microbial ecology, global ocean microbiome, CARBON, 0302 clinical medicine, biogeochemistry, Gene expression, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, CLIMATE-CHANGE, Geography, Microbiota, Temperature, CYANOBACTERIA, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], GENOME, BACTERIA, community turnover, Life Sciences & Biomedicine, Biochemistry & Molecular Biology, SURFACE, Oceans and Seas, Tara Oceans, Biology, Article, metagenome, General Biochemistry, Genetics and Molecular Biology, ocean warming, 03 medical and health sciences, eco-systems biology, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], metatranscriptome, Seawater, RNA, Messenger, 14. Life underwater, Gene, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 030304 developmental biology, Science & Technology, Biogeochemistry, Molecular Sequence Annotation, Cell Biology, Environmental variation, Gene Expression Regulation, Cardiovascular and Metabolic Diseases, 13. Climate action, Metagenomics, Evolutionary biology, BIODIVERSITY, sense organs, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcriptome, 030217 neurology & neurosurgery, gene expression change, BIOGEOGRAPHY
Abstract: This article is contribution number 94 of Tara Oceans.-- 37 pages, 20 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.014.-- All raw reads are available through ENA at https://www.ebi.ac.uk/ena using the identifiers listed in https://doi.org/10.5281/zenodo.3473199. Processed data are accessible at https://www.ebi.ac.uk/biostudies/studies/S-BSST297, and additional information is provided in https://doi.org/10.5281/zenodo.3473199 and at the companion website: https://www.ocean-microbiome.org. Scripts used in this manuscript are available through a Github repository at https://github.com/SushiLab/omrgc_v2_scripts, Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms, Tara Oceans (that includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Expeditions Foundation and the continuous support of 23 institutes (https://oceans.taraexpeditions.org). We further thank the commitment of the following sponsors: CNRS (in particular Groupement de Recherche GDR3280 and the Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans-GOSEE); European Molecular Biology Laboratory (EMBL); Genoscope/CEA; the French Ministry of Research; the French Government “Investissements d’Avenir” programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), and PSL∗ Research University (ANR-11-IDEX-0001-02); Gordon and Betty Moore Foundation (award 3790); the US National Science Foundation (OCE#1536989 and OCE#1829831 to M.B.S.); the European Union’s Horizon 2020 research and innovation programme (grant agreement 686070); and the Ohio Supercomputer and the EMBL and ETH Zürich HPC facilities for computational support. Funding for the collection and processing of the TARA data set was provided by NASA Ocean Biology and Biogeochemistry program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G to the University of Maine and Canada Excellence Research Chair on Remote sensing of Canada’s new Arctic frontier Canada Foundation for Innovation. C.B. acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement 835067). S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R). S. Sunagawa. is supported by the ETH and the Helmut Horten Foundation and by funding from the Swiss National Foundation (205321_184955)
Published: 2019
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16. Global biogeography of coral recruitment: tropical decline and subtropical increase

Author: Ruth D. Gates, Satoshi Mitarai, Kazuhiko Sakai, Put O. Ang, Robert S. Steneck, Robert C. Carpenter, Louis Legendre, Rebecca Albright, Haruko Kurihara, Tung-Yung Fan, Apy Chui, H. Kitano, Soyoka Muko, Jacqueline L. Padilla-Gamiño, Saki Harii, Peter J. Edmunds, Go Suzuki, Nichole N. Price, Mjh van Oppen, Bigelow Laboratory for Ocean Sciences, Nagasaki University, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Australian Institute of Marine Science (AIMS), University of Melbourne, Carnegie Institution for Science [Washington], The Chinese University of Hong Kong [Hong Kong], California State University [Northridge] (CSUN), National Museum of Marine Biology and Aquarium, University of Hawaii, University of the Ryukyus [Okinawa], Okinawa Institute of Science and Technology Graduate University (OIST), and University of Washington [Seattle]
Subjects: 0106 biological sciences, Retrospective analyses, Range (biology), Coral, Poleward range shift, Subtropics, Aquatic Science, 01 natural sciences, Latitude, 14. Life underwater, Reef, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Coral settlement, geography, geography.geographical_feature_category, Ecology, 010604 marine biology & hydrobiology, Global warming, Tropics, Ocean acidification, Equatorial retraction, Oceanography, 13. Climate action, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Range extension
Abstract: Despite widespread climate-driven reductions of coral cover on tropical reefs, little attention has been paid to the possibility that changes in the geographic distribution of coral recruitment could facilitate beneficial responses to the changing climate through latitudinal range shifts. To address this possibility, we compiled a global database of normalized densities of coral recruits on settlement tiles (corals m^) deployed from 1974 to 2012, and used the data therein to test for latitudinal range shifts in the distribution of coral recruits. In total, 92 studies provided 1253 records of coral recruitment, with 77% originating from settlement tiles immersed for 3-24 mo, herein defined as long-immersion tiles (LITs); the limited temporal and geographic coverage of data from short-immersion tiles (SITs; deployed for 20° latitude). These trends indicate that a global decline in coral recruitment has occurred since 1974, and the persistent reduction in the densities of recruits in equatorial latitudes, coupled with increased densities in sub-tropical latitudes, suggests that coral recruitment may be shifting poleward., 論文
Published: 2019

17. Single-cell genomics of multiple uncultured stramenopiles reveals underestimated functional diversity across oceans

Author: Seeleuthner, Yoann, Mondy, Samuel, Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-François, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Pesant, Stéphane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew, Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Acinas, Silvia G., Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Weissenbach, Jean, Velayoudon, Didier, 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), Architecture et fonction des macromolécules biologiques (AFMB), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Heidelberg] (EMBL), 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), 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), Sorbonne Université (SU), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Bigelow Laboratory for Ocean Sciences, Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Ohio State University [Columbus] (OSU), Stazione Zoologica Anton Dohrn (SZN), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia, National Science Foundation [Arlington] (NSF), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), 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), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Université de Brest (UBO), DVIP Consulting, CNRS [GDR3280], European Molecular Biology Laboratory (EMBL), Genoscope/CEA, French Governement 'Investissement d'Avenir' programs Oceanomics [ANR-11-BTBR-0008], FRANCE GENOMIQUE [ANR-10-INBS-09], MEMO LIFE [ANR-10-LABX-54], PSL* Research University [ANR-11-IDEX-0001-02], Fund for Scientific Research-Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR [PHYTBACK/ANR-2010-1709-01, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, ARA-GIRUS/ANR-09-PCS-GENM-218], EU FP7 [IHMS/HEALTH-F4-2010-261376], ERC Advanced Grant Award [294823], US NSF grant [DEB-1031049], FWO, BIO5, Biosphere 2, agnes b., Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, EDF Foundation EDF Diversiterre, FRB, Prince Albert II de Monaco Foundation, 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-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), ANR-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Institut de Génomique d'Evry (IG), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, 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), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), 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), Sorbonne Universités, Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN)-Aix Marseille Université (AMU)-Institut de Recherche pour le Développement (IRD), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Rega Institute for Medical Research, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris), ANR-11-BTBR-0008/11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-09-01/10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-IDEX-0001-02/10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-09-BLAN-0348,POSEIDON,PrOtiSts EcologIcal bioDiversity in Tara-OceaNs(2009), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Hingamp, Pascal, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, BLANC - Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton - - PHYTBACK2010 - ANR-10-BLAN-1709 - BLANC - VALID, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Génomique et biotechnologies végétales - Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans. - - PROMETHEUS2009 - ANR-09-GENM-0031 - GENOM-BTV - VALID, 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, Marine Microbial Biodiversity, Bioinformatics and Biotechnology - MICRO B3 - - EC:FP7:KBBE2012-01-01 - 2015-12-31 - 287589 - VALID, International Human Microbiome Standards - IHMS - - EC:FP7:HEALTH2011-02-01 - 2015-01-31 - 261376 - VALID, Genome-enabled dissection of marine diatom ecophysiology - DIATOMITE - - EC:FP7:ERC2012-06-01 - 2017-05-31 - 294823 - VALID, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Toulon (UTLN), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Unité de Biologie du développement et biotechnologies (JOUY BIOLOG DEVELOP BIOTECHNOL), Institut National de la Recherche Agronomique (INRA), European Molecular Biology Laboratory, 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), University of Hawai'i [Honolulu] (UH), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), and 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)
Subjects: [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDE]Environmental Sciences, fungi, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS, Article, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides hypotheses for specialization in terms of cell motility, food spectra, and trophic stages, including the potential impact on their lifestyles of horizontal gene transfer from prokaryotes. Our results support the idea that prominent heterotrophic marine protists perform diverse functions in ocean ecology., The biology of many marine protists, such as stramenopiles, remains obscure. Here, the authors exploit single-cell genomics and metagenomics to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles.
Published: 2018

18. The GEOTRACES Intermediate Data Product 2017

Author: Thomas J. Browning, Hans-Jürgen Brumsack, Katharina Pahnke, Saeed Roshan, Stephanie Owens, Rosie Chance, Peter Croot, Steven van Heuven, Alison E. Hartman, Mercedes López-Lora, Pu Zhang, Heather A. Bouman, Géraldine Sarthou, François Lacan, Robyn E. Tuerena, José Marcus Godoy, Ester Garcia-Solsona, Steven L. Goldstein, Hans A. Slagter, Celia Venchiarutti, A. Russell Flegal, Emily Townsend, Ralph Till, Christopher T. Hayes, Melanie Gault-Ringold, Ros Watson, Peter N. Sedwick, Chandranath Basak, Bronwyn Wake, Loes J. A. Gerringa, Noriko Nakayama, Lars-Eric Heimbürger, Paul J. Morris, François Fripiat, Paul B. Henderson, Chris J. Daniels, Catherine Jeandel, Helen M. Snaith, Patrizia Ziveri, Toshitaka Gamo, Yanbin Lu, Oliver J. Lechtenfeld, Yingzhe Wu, Andreas Wisotzki, Hajime Obata, Cynthia Dumousseaud, Ashley T. Townsend, Sebastian Mieruch, Donna Cockwell, Laurent Bopp, Elena Masferrer Dodas, Bernhard Schnetger, J. K. Klar, Sunil K. Singh, Joaquin E. Chaves, Kuo-Fang Huang, Louise A. Zimmer, Laura F. Robinson, Michiel M Rutgers van der Loeff, Corey Archer, Feifei Deng, Karen Grissom, Robert Rember, Nicholas J. Hawco, Jingfeng Wu, Robert M. Sherrell, Rachel U. Shelley, Jan-Lukas Menzel Barraqueta, E. Malcolm S. Woodward, Fanny Chever, Yuichiro Kumamoto, Hélène Planquette, Dorothea Bauch, Frank Dehairs, Daniel C. Ohnemus, Akira Nishiuchi, Paul D. Quay, Sanjin Mehic, Zichen Xue, Maxi Castrillejo, Brian Peters, Michael J. Ellwood, Stephen R. Rintoul, Tobias Roeske, Jing Zhang, Gretchen J. Swarr, Peng Ho, Ken O. Buesseler, Gwenaelle Moncoiffe, Martin Frank, Maureen E. Auro, Abby Bull, David Kadko, Montserrat Roca-Martí, Maeve C. Lohan, Roulin Khondoker, Patricia Cámara Mor, Melissa Gilbert, Sebastian M. Vivancos, Erin E. Black, Santiago R. Gonzalez, Gideon M. Henderson, David J. Janssen, Sylvain Rigaud, Amandine Radic, Maxence Paul, Cyril Abadie, Ana Aguliar-Islas, Seth G. John, Marie Boye, Evgenia Ryabenko, Abigail E. Noble, Luke Bridgestock, Brian Duggan, Hisayuki Yoshikawa, Jun Nishioka, Kathrin Wuttig, Pieter van Beek, Jana Friedrich, Thomas M. Church, Maija Heller, Stephen J.G. Galer, Pier van der Merwe, Claire P. Till, Xin Yuan Zheng, Henning Fröllje, John Niedermiller, Howie D. Scher, Johnny Stutsman, Patricia Zunino, Christel S. Hassler, Ye Zhao, Tim M. Conway, William M. Landing, Yang Xiang, Katrin Bluhm, Maria T. Maldonado, Elena Chamizo, Sabrina Speich, Claudine H. Stirling, Guillaume Brissebrat, Matthew A. Charette, Jeremy E. Jacquot, Yu-Te Hsieh, Pinghe Cai, Ivia Closset, Yoshiki Sohrin, Ejin George, Jong-Mi Lee, Leopoldo D. Pena, Edward Mawji, Damien Cardinal, Catherine Pradoux, Martin Q. Fleisher, Virginie Sanial, Derek Vance, Craig A. Carlson, Pere Masqué, Katlin L. Bowman, Evaline M. van Weerlee, Oliver Baars, Ruifang C. Xie, María Villa-Alfageme, Hein J W de Baar, M. Alexandra Weigand, Tina van de Flierdt, J. Bown, Timothy C. Kenna, Kenneth W. Bruland, Jeroen E. Sonke, Hai Cheng, Mark J. Warner, Sven Ober, Rob Middag, Jessica N. Fitzsimmons, Emilie Le Roy, Yishai Weinstein, Nicholas R. Bates, Joerg Rickli, Daniel M. Sigman, Hendrik M. van Aken, Angela Milne, Cheryl M. Zurbrick, Gregory A. Cutter, Igor Semiletov, Marie Labatut, Torben Stichel, Pascale Lherminier, Gabriel Dulaquais, Jay T. Cullen, Christopher I. Measures, Mark Rosenberg, Tomoharu Minami, Mariko Hatta, Alexander L. Thomas, Gonzalo Carrasco, Karel Bakker, Clifton S. Buck, Maarten B Klunder, Willard S. Moore, Reiner Schlitzer, Tomas A. Remenyi, Susan H. Little, Eberhard Fahrbach, Charles R. McClain, Edward A. Boyle, Ursula Schauer, Linjie Zheng, Alex R. Baker, Emma Slater, Kay Thorne, Patrick Laan, Christina Schallenberg, Reiner Steinfeldt, Benjamin S. Twining, Yolanda Echegoyen-Sanz, Neil J. Wyatt, Alison M. Agather, Viena Puigcorbé, Peter Scott, Gillian Stewart, Matthew P. Humphreys, Frédéric A. C. Le Moigne, Phoebe J. Lam, Núria Casacuberta, Josh Helgoe, Edward C.V. Butler, Mark Rehkämper, Elizabeth M. Jones, Karen L. Casciotti, James W. Moffett, Tristan J. Horner, Sue Velazquez, Yuzuru Nakaguchi, Micha J.A. Rijkenberg, Antje H L Voelker, Joseph A. Resing, Lesley Salt, Eric P. Achterberg, Sven Kretschmer, Jan van Ooijen, Dominik J. Weiss, Moritz Zieringer, Carl H. Lamborg, Rick Kayser, Pierre Branellec, John M. Rolison, Sara Rauschenberg, Walter Geibert, Raja S. Ganeshram, Myriam Lambelet, Janice L. Jones, Chad R. Hammerschmidt, William J. Jenkins, Jordi Garcia-Orellana, Alessandro Tagliabue, Philip W. Boyd, Alan M. Shiller, Marcus Christl, Mark Baskaran, Mak A. Saito, Huong Thi Dieu, Morten B. Andersen, Kenji Isshiki, Taejin Kim, Christian Schlosser, Melanie K. Behrens, Albert S. Colman, Frédéric Planchon, Bettina Sohst, Andrew R. Bowie, Mark A. Brzezinski, R. Lawrence Edwards, Kristen N. Buck, Jeanette O'Sullivan, William M. Smethie, Wafa Abouchami, Valentí Rodellas, Ed C Hathorne, Robert F. Anderson, James H. Swift, Frank J. Pavia, Daniel Cossa, Lauren Kipp, Peter L. Morton, Fabien Quéroué, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Centre for Automotive Safety Research, University of Adelaide, University of California, National Oceanography Centre (NOC), Scottish Association for Marine Science (SAMS), Department of Oceanography [Cape Town], University of Cape Town, Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Chemistry (MPIC), Max-Planck-Gesellschaft, University of Toyama, Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Royal Netherlands Institute for Sea Research (NIOZ), Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Department of Geology, Wayne State University [Detroit], The Bartlett, University College of London [London] (UCL), Institute for Environmental Research, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris), Department of Earth Sciences [Oxford], University of Oxford [Oxford], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Cycles biogéochimiques marins : processus et perturbations (CYBIOM), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institute for Research on Learning, Services communs OMP - UMS 831 (UMS 831), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Marine Science Institute [Santa Barbara] (MSI), University of California [Santa Barbara] (UCSB), University of California-University of California, National Oceanography Centre [Southampton] (NOC), University of Southampton, Institut Français de Recherche pour l'Exploitation de la Mer - Nantes (IFREMER Nantes), Université de Nantes (UN), University of Victoria [Canada] (UVIC), Massachusetts Institute of Technology (MIT), Universidad de Dakota del Sur, Analytical, Environmental and Geo- Chemistry, Vrije Universiteit [Brussels] (VUB), Wright State University, School of Geography, Earth and Environmental Sciences [Plymouth] (SoGEES), Plymouth University, Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Alfred Wegener Institute [Potsdam], Institute of Global Environmental Change [China] (IGEC), Xi'an Jiaotong University (Xjtu), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Department of Mathematics and Science, National Taiwan Normal University (NTNU), School of Information Technology [Kharagpur], Indian Institute of Technology Kharagpur (IIT Kharagpur), GEOMAR - Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), University of California [Davis] (UC Davis), Institut de Ciencia i Tecnologia Ambientals (ICTA), Universitat Autònoma de Barcelona [Barcelona] (UAB), Institute of Low Temperature Science, Hokkaido University, The University of Tokyo, Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania (UTAS), Joint Institute for the Study of the Atmosphere and Ocean (JISAO), University of Washington [Seattle], Institute of Geochemistry and Petrology, Détection, évaluation, gestion des risques CHROniques et éMErgents (CHROME) / Université de Nîmes (CHROME), Université de Nîmes (UNIMES), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Collège de France (CdF)-Institut national des sciences de l'Univers (INSU - CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), School of Earth and Ocean Sciences, University of Victoria, Knowledge Media Institute (KMI), The Open University [Milton Keynes] (OU), Bermuda Biological Station for Research (BBSR), Bermuda Biological Station for Research, Department of Geosciences [Princeton], Princeton University, Kyoto University [Kyoto], Géochimie des Isotopes Stables (GIS), Géosciences Environnement Toulouse (GET), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National d'Études Spatiales [Toulouse] (CNES), School of Earth and Environmental Sciences [Queens New York], Queens College [New York], City University of New York [New York] (CUNY)-City University of New York [New York] (CUNY), SOEST, University of Hawai‘i [Mānoa] (UHM), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Bigelow Laboratory for Ocean Sciences, Department of Earth Science and Technology [Imperial College London], Imperial College London, Plymouth Marine Laboratory, Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], Tsinghua National Laboratory for Information Science and Technology (TNList), RITE, Research Institute of Innovative Technology for the Earth, Agricultural Information Institute (AII), Chinese Academy of Agricultural Sciences (CAAS), Department of Mathematics [Shanghai], Shanghai Jiao Tong University [Shanghai], University of California [Irvine] (UCI), Institute of Environmental Science and Technology [Barcelona] (ICTA), University of California (UC), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University of Oxford, Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Southern California (USC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Services communs OMP (UMS 831), Université Toulouse III - Paul Sabatier (UT3), Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France, University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), Institut des Sciences de la Terre (ISTerre), Institut Français des Sciences et Technologies des Transports, de l'Aménagement et des Réseaux (IFSTTAR)-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de recherche pour le développement [IRD] : UR219-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Vrije Universiteit Brussel (VUB), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Florida International University [Miami] (FIU), Department of Earth Science and Engineering [Imperial College London], Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Universitat Autònoma de Barcelona (UAB), British Oceanographic Data Centre (BODC), Institute of Low Temperature Science [Sapporo], Hokkaido University [Sapporo, Japan], The University of Tokyo (UTokyo), Institute of Geochemistry and Petrology [ETH Zürich], Department of Earth Sciences [Swiss Federal Institute of Technology - ETH Zürich] (D-ERDW), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)- Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), College of Earth, Ocean, and Environment [Newark] (CEOE), University of Delaware [Newark], Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Knowledge Media Institute (KMi), Kyoto University, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Academia Sinica, University of California [Irvine] (UC Irvine), Danish Technological Institute (DTI), Scientific Committee on Oceanic Research (SCOR) from the U.S. National Science Foundation [OCE-0608600, OCE-0938349, OCE-1243377, OCE-1546580], UK Natural Environment Research Council (NERC), Ministry of Earth Science of India, Centre National de Recherche Scientifique, l'Universite Paul Sabatier de Toulouse, Observatoire Midi-Pyrenees Toulouse, Universitat Autonoma de Barcelona, Kiel Excellence Cluster The Future Ocean, Swedish Museum of Natural History, University of Tokyo, University of British Columbia, Royal Netherlands Institute for Sea Research, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Alfred Wegener Institute, Scientific Committee on Oceanic Research, National Science Foundation (US), Natural Environment Research Council (UK), Ministry of Earth Sciences (India), Centre National de la Recherche Scientifique (France), Université Toulouse III Paul Sabatier, Observatoire Midi-Pyrénées (France), Universidad Autónoma de Barcelona, Helmholtz Centre for Ocean Research Kiel, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (Germany), Schlitzer, Reiner [0000-0002-3740-6499], Masferrer Dodas, Elena [0000-0003-0879-1954], Chamizo, Elena [0000-0001-8266-6129], Christl, M. [0000-0002-3131-6652], Masqué, Pere [0000-0002-1789-320X], Villa-Alfageme, María [0000-0001-7157-8588], Universitat de Barcelona, Natural Environment Research Council (NERC), Leverhulme Trust, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Carrasco Rebaza, Gonzalo, Echegoyen Sanz, Yolanda, Kayser, Richard A, Isotope Research, Ocean Ecosystems, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de 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), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER Centre de Bretagne), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Collège de France (CdF (institution))-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Hassler, Christel, Schlitzer, Reiner, Masferrer Dodas, Elena, Chamizo, Elena, Christl, M., Masqué, Pere, and Villa-Alfageme, María
Subjects: Geochemistry & Geophysics, 010504 meteorology & atmospheric sciences, Isòtops, sub-01, Geotraces, MODELS, Digital data, Context (language use), 010502 geochemistry & geophysics, 01 natural sciences, IDP2017, Isotopes, Geochemistry and Petrology, Oceans, Electronic atlas, ddc:550, 0402 Geochemistry, 14. Life underwater, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, NetCDF, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Trace elements, Science & Technology, Information retrieval, ACL, Geology, computer.file_format, Ocean Data View, Metadata, Data processing, GEOTRACES, 0403 Geology, Data extraction, 13. Climate action, Data quality, Physical Sciences, [SDE]Environmental Sciences, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 0406 Physical Geography and Environmental Geoscience, computer, Processament de dades, Trace elements Isotopes
Abstract: The GEOTRACES Intermediate Data Product 2017 (IDP2017) is the second publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2016. The IDP2017 includes data from the Atlantic, Pacific, Arctic, Southern and Indian oceans, with about twice the data volume of the previous IDP2014. For the first time, the IDP2017 contains data for a large suite of biogeochemical parameters as well as aerosol and rain data characterising atmospheric trace element and isotope (TEI) sources. The TEI data in the IDP2017 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at crossover stations. The IDP2017 consists of two parts: (1) a compilation of digital data for more than 450 TEIs as well as standard hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing an on-line atlas that includes more than 590 section plots and 130 animated 3D scenes. The digital data are provided in several formats, including ASCII, Excel spreadsheet, netCDF, and Ocean Data View collection. Users can download the full data packages or make their own custom selections with a new on-line data extraction service. In addition to the actual data values, the IDP2017 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering and for statistical analysis. Metadata about data originators, analytical methods and original publications related to the data are linked in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2017 as section plots and rotating 3D scenes. The basin-wide 3D scenes combine data from many cruises and provide quick overviews of large-scale tracer distributions. These 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of tracer plumes near ocean margins or along ridges. The IDP2017 is the result of a truly international effort involving 326 researchers from 25 countries. This publication provides the critical reference for unpublished data, as well as for studies that make use of a large cross-section of data from the IDP2017. This article is part of a special issue entitled: Conway GEOTRACES - edited by Tim M. Conway, Tristan Horner, Yves Plancherel, and Aridane G. González., National Science Foundation (U.S.) (Grant OCE-0608600), National Science Foundation (U.S.) (Grant OCE0938349), National Science Foundation (U.S.) (Grant OCE-1243377), National Science Foundation (U.S.) (Grant OCE-1546580)
Published: 2018

19. Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

Author: Eric D. Becraft, Jeremy A. Dodsworth, Senthil K. Murugapiran, Scott C. Thomas, J. Ingemar Ohlsson, Ramunas Stepanauskas, Brian P. Hedlund, Wesley D. Swingley, Department of Biological Sciences, The Open University [Milton Keynes] (OU), Bigelow Laboratory for Ocean Sciences, California State University, Partenaires INRAE, School of Life Sciences, University of Nevada [Reno], Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), NASA [EXO-NNX11AR78G], U.S. National Science Foundation [OISE 0968421, DEB-1441717], U.S. Department of Energy [DE-EE-0000716], Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231], Northern Illinois University, and Swingley, Wesley D.
Subjects: 0301 basic medicine, Microbiology (medical), [SDV]Life Sciences [q-bio], Lineage (evolution), Population, lcsh:QR1-502, extreme microbiology, Genomics, microbial ecology, Microbiology, Genome, lcsh:Microbiology, 03 medical and health sciences, uncultivated archaea, NAG1 lineage, Great Boiling Spring, Microbial ecology, Extreme environment, education, Original Research, education.field_of_study, biology, Ecology, biology.organism_classification, 030104 developmental biology, Metagenomics, Evolutionary biology, Archaea
Abstract: International audience; Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated "Novel Archaeal Group 1" (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.
Published: 2017

20. Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

Author: Alberti, Adriana, Poulain, Julie, Engelen, Stefan, Labadie, Karine, Romac, Sarah, Ferrera, Isabel, Albini, Guillaume, Aury, Jean-Marc, Belser, Caroline, Bertrand, Alexis, Cruaud, Corinne, Da Silva, Corinne, Dossat, Carole, Gavory, Frédérick, Gas, Shahinaz, Guy, Guy, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Bazire, Pascal, Beluche, Odette, Bertrand, Laurie, Besnard-Gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Espérance, Aiach, Nathalie, Guerin, Thomas, Hamon, Chadia, Brun, Élodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Céline, Payen, Emilie, Perroud, Peggy, Petit, Emmanuel, Robert, Dominique, Ronsin, Murielle, Vacherie, Benoit, Acinas, Silvia, Royo-Llonch, Marta, Cornejo-Castillo, Francisco, Logares, Ramiro, Fernández-Gómez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Hoopen, Petra Ten, de Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-Lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael, Stepanauskas, Ramunas, Sullivan, Matthew, Brum, Jennifer, Duhaime, Melissa, Poulos, Bonnie, Hurwitz, Bonnie, Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Pesant, Stéphane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Wincker, Patrick, CNS, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Recherches sur les lois Fondamentales de l'Univers (IRFU), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Unité Mathématique Informatique et Génome (MIG), Institut National de la Recherche Agronomique (INRA), Centre National de Génotypage (CNG), Universidad Politécnica de Madrid (UPM), Structure et évolution des génomes (SEG), CNS-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université de Toulon - Faculté de Droit de Toulon (UTLN UFR Droit), Université de Toulon (UTLN), Actilia Multimedia, Pharmacochimie et Biologie pour le Développement (PHARMA-DEV), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT), Biologie des Plantes et Innovation - UR UPJV 3900 (BIOPI), Université de Picardie Jules Verne (UPJV)-Transfrontalière BioEcoAgro - UMR 1158 (BioEcoAgro), Université d'Artois (UA)-Université de Liège-Université de Picardie Jules Verne (UPJV)-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL)-Université d'Artois (UA)-Université de Liège-Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-JUNIA (JUNIA), Université catholique de Lille (UCL)-Université catholique de Lille (UCL), Grande Rue, Auteur indépendant, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Informatics Department, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), European Molecular Biology Laboratory [Heidelberg] (EMBL), Bigelow Laboratory for Ocean Sciences, University of Arizona, Ecology and Evolutionary Biology [Tucson] (EEB), European Molecular Biology Laboratory, School of Marine Sciences, University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Diversité et Interactions au sein du Plancton Océanique (DIPO), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Department of Bioscience Engineering, Vrije Universiteit Brussel (VUB), Groupe de Biologie Marine du CEA, Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Informatique, Biologie Intégrative et Systèmes Complexes (IBISC), Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Adaptation et diversité en milieu marin (ADMM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) - Grenoble, LIttoral ENvironnement et Sociétés - UMR 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut de Chimie de Toulouse (ICT-FR 2599), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), EA 3900 BIOPI Laboratoire de Phytotechnologie, Université de Picardie Jules Verne (UPJV), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn, Vrije Universiteit [Brussels] (VUB), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2017

21. Exploring Microdiversity in Novel Kordia sp. (Bacteroidetes) with Proteorhodopsin from the Tropical Indian Ocean via Single Amplified Genomes

Author: Marta Royo-Llonch, Isabel Ferrera, Francisco M. Cornejo-Castillo, Pablo Sánchez, Guillem Salazar, Ramunas Stepanauskas, José M. González, Michael E. Sieracki, Sabrina Speich, Lars Stemmann, Carlos Pedrós-Alió, Silvia G. Acinas, Ministerio de Economía y Competitividad (España), National Science Foundation (US), Fundación BBVA, Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Institut de Chimie de Clermont-Ferrand (ICCF), SIGMA Clermont (SIGMA Clermont)-Institut de Chimie du CNRS (INC)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Bigelow Laboratory for Ocean Sciences, National Science Foundation [Arlington] (NSF), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Laboratoire 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), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), MLSA, proteorhodopsin, Rare biosphere, 030106 microbiology, lcsh:QR1-502, Biology, Microbiology, lcsh:Microbiology, 03 medical and health sciences, 23S ribosomal RNA, 14. Life underwater, Internal transcribed spacer, SAGs, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Original Research, Proteorhodopsin, Phylogenetic tree, Ecology, Bacteroidetes, fungi, Bacterioplankton, 16S ribosomal RNA, biology.organism_classification, 3. Good health, 030104 developmental biology, Kordia, Evolutionary biology, biology.protein
Abstract: Royo-Llonch, Marta ... et al.-- 14 pages, 6 figures, supplementary material http://journal.frontiersin.org/article/10.3389/fmicb.2017.01317/full#supplementary-material, Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in most cases do not represent the actual abundant or ecologically relevant microorganisms in the natural environment. In this study, we explored the microdiversity of 98 Single Amplified Genomes (SAGs) retrieved from the surface waters of the underexplored North Indian Ocean, whose most closely related isolate is Kordia algicida OT-1. Using Multi Locus Sequencing Analysis (MLSA) we found no microdiversity in the tested conserved phylogenetic markers (16S rRNA and 23S rRNA genes), the fast-evolving Internal Transcribed Spacer and the functional markers proteorhodopsin and the beta-subunit of RNA polymerase. Furthermore, we carried out a Fragment Recruitment Analysis (FRA) with marine metagenomes to learn about the distribution and dynamics of this microorganism in different locations, depths and size fractions. This analysis indicated that this taxon belongs to the rare biosphere, showing its highest abundance after upwelling-induced phytoplankton blooms and sinking to the deep ocean with large organic matter particles. This uncultured Kordia lineage likely represents a novel Kordia species (Kordia sp. CFSAG39SUR) that contains the proteorhodopsin gene and has a widespread spatial and vertical distribution. The combination of SAGs and MLSA makes a valuable approach to infer putative ecological roles of uncultured abundant microorganisms, Funding was provided by the Spanish Ministry of Economy and Competitivity grants CTM2013-48292-C3 “EcoBGM” to CP-A and JG, United States NSF grants OCE-1232982 and OCE-1335810 to RS and CGL2011-26848/BOS MicroOcean PANGENOMICS to SGA, as well as grant BIOSENSOMICS through “Ayudas Fundación BBVA a investigadores y creadores culturales” to SGA. MR-L held a Ph.D. Fellowship FPI (BES-2014-068285) funded by the Spanish Ministry of Economy and Competitivity.
Published: 2017
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22. Accessing the genomic information of unculturable oceanic picoeukaryotes by combining multiple single cells

Author: Colomban de Vargas, Ramon Massana, Yoann Seeleuthner, Patrick Wincker, Pablo Sánchez, Jean-François Mangot, Fran Latorre, Samuel Mondy, Olivier Jaillon, Ramiro Logares, Michael E. Sieracki, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (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)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Bigelow Laboratory for Ocean Sciences, National Science Foundation [Arlington] (NSF), 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 de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Ministerio de Economía y Competitividad (España), Agence Nationale de la Recherche (France), National Science Foundation (US), European Commission, France Génomique, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Aquatic Organisms, Lineage (evolution), Oceans and Seas, 030106 microbiology, Genomics, Computational biology, Biology, Genome, Article, 03 medical and health sciences, Single-cell analysis, Phylogenetics, 14. Life underwater, Phylogeny, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Whole Genome Amplification, Genetics, Multidisciplinary, Base Sequence, Eukaryota, Sequence Analysis, DNA, Ecological genetics, 3. Good health, 030104 developmental biology, Evolutionary ecology, Single-Cell Analysis, Ribosomes
Abstract: Mangot, Jean-François et al.-- 12 pages, 7 figures, 2 tables, supplementary information https://dx.doi.org/10.1038/srep41498, Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promising tools to retrieve genomic information from these uncultured organisms. However, SCG are based on whole genome amplification, which normally introduces amplification biases that limit the amount of genomic data retrieved from a single cell. Here, we increase the recovery of genomic information from two MAST-4 lineages by co-assembling short reads from multiple Single Amplified Genomes (SAGs) belonging to evolutionary closely related cells. We found that complementary genomic information is retrieved from different SAGs, generating co-assembly that features >74% of genome recovery, against about 20% when assembled individually. Even though this approach is not aimed at generating high-quality draft genomes, it allows accessing to the genomic information of microbes that would otherwise remain unreachable. Since most of the picoeukaryotes still remain uncultured, our work serves as a proof-of-concept that can be applied to other taxa in order to extract genomic data and address new ecological and evolutionary questions, This work was supported by the US NSF grants DEB-1031049 and OCE-821374 (to M.E.S.), by the ANR French projects Oceanomics (ANR-11-BTBR-0008, to C.V.), France Génomique (ANR-10-INBS-09, to P.W.), and Prometheus (ANR-09-PCS-GENM_217, to O.J.), by the EU project SINGEK (H2020-MSCA-ITN-2015-675752, to R.M.), and by the Spanish project MEFISTO (CTM2013-43767-P, MINECO). J.-F.M. was supported by a Marie Curie Intra-European Fellowship (PIEF-GA-2012-331190, EU). R.L. was supported by Juan de la Cierva (JCI-2010-06594, MINECO) and Ramón y Cajal fellowships (RYC-2013-12554, MINECO)
Published: 2017

23. How well can we quantify dust deposition to the ocean?

Author: Laura F. Robinson, R. Shelley, Yumin Lu, Phoebe J. Lam, William M. Landing, Richard Lawrence Edwards, Daniel C. Ohnemus, Christopher T. Hayes, Martin Q. Fleisher, David Kadko, S.B. Moran, Peter L. Morton, Y. Lao, Kuo-Fang Huang, Christopher I. Measures, Hai Cheng, Robert F. Anderson, Earth Observatory of Singapore, Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Institute of Global Environmental Change [China] (IGEC), Xi'an Jiaotong University (Xjtu), Department of Earth Sciences [Minneapolis], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, University of Southern Mississippi (USM), Academia Sinica, Florida International University [Miami] (FIU), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Department of Earth, Ocean and Atmospheric Science [Tallahassee] (FSU | EOAS), Florida State University [Tallahassee] (FSU), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), University of Alaska [Fairbanks] (UAF), Bigelow Laboratory for Ocean Sciences, University of Bristol [Bristol], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of California [Santa Cruz] (UCSC), University of California, and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Biogeochemical cycle, equatorial pacific, 010504 meteorology & atmospheric sciences, General Science & Technology, General Mathematics, Geotraces, chibido, General Physics and Astronomy, Geology [Science], 010502 geochemistry & geophysics, Atmospheric sciences, 01 natural sciences, Deep sea, Water column, boundary current systems, 14. Life underwater, Life Below Water, 0105 earth and related environmental sciences, Aerosols, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography, geography.geographical_feature_category, north-atlantic transect, northeast tropical Atlantic, ACL, be-7 measurements, General Engineering, Trace element, Dust, Articles, biogeochemical cycles, global distribution, thorium isotopes, particle fluxes, Deposition (aerosol physics), Oceanography, GEOTRACES, 13. Climate action, Ridge, deep-ocean, Seawater, dust, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, aerosols, pacific-ocean
Abstract: WOS:000391139900001; International audience; Deposition of continental mineral aerosols (dust) in the Eastern Tropical North Atlantic Ocean, between the coast of Africa and the Mid-Atlantic Ridge, was estimated using several strategies based on the measurement of aerosols, trace metals dissolved in seawater, particulate material filtered from the water column, particles collected by sediment traps and sediments. Most of the data used in this synthesis involve samples collected during US GEOTRACES expeditions in 2010 and 2011, although some results from the literature are also used. Dust deposition generated by a global model serves as a reference against which the results from each observational strategy are compared. Observation-based dust fluxes disagree with one another by as much as two orders of magnitude, although most of the methods produce results that are consistent with the reference model to within a factor of 5. The large range of estimates indicates that further work is needed to reduce uncertainties associated with each method before it can be applied routinely to map dust deposition to the ocean. Calculated dust deposition using observational strategies thought to have the smallest uncertainties is lower than the reference model by a factor of 2-5, suggesting that the model may overestimate dust deposition in our study area. This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.
Published: 2016

24. Elevated Colonization of Microborers at a Volcanically Acidified Coral Reef

Author: Aline Tribollet, Renée Carlton, Graham Kolodziej, Ian C. Enochs, Mark D. Fitchett, Lauren Valentino, Nichole N. Price, Emily M. Donham, Derek P. Manzello, Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables], NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), National Oceanic and Atmospheric Administration (NOAA), Biogéochimie-Traceurs-Paléoclimat (BTP), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Moss Landing Marine Laboratories, Bigelow Laboratory for Ocean Sciences, Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636))
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Carbonates, lcsh:Medicine, Marine and Aquatic Sciences, 01 natural sciences, chemistry.chemical_compound, lcsh:Science, Calcite, Minerals, Multidisciplinary, geography.geographical_feature_category, Animal Behavior, Ecology, Coral Reefs, Marine Ecology, Ocean acidification, Coral reef, Hydrogen-Ion Concentration, Mineralogy, Chemistry, Grazing, Physical Sciences, Corals, Carbonate, Research Article, Micronesia, Marine Biology, Volcanic Eruptions, Sea Water, Ecosystem, 14. Life underwater, Reef, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Behavior, geography, 010604 marine biology & hydrobiology, lcsh:R, Ecology and Environmental Sciences, Bioerosion, Chemical Compounds, Biology and Life Sciences, Carbon Dioxide, Calcium carbonate, chemistry, Earth Sciences, Reefs, Environmental science, lcsh:Q, Hydrology, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Zoology, Acids
Abstract: International audience; Experiments have demonstrated that ocean acidification (OA) conditions projected to occur by the end of the century will slow the calcification of numerous coral species and accelerate the biological erosion of reef habitats (bioerosion). Microborers, which bore holes less than 100 μm diameter, are one of the most pervasive agents of bioerosion and are present throughout all calcium carbonate substrates within the reef environment. The response of diverse reef functional groups to OA is known from real-world ecosystems, but to date our understanding of the relationship between ocean pH and carbonate dissolution by microborers is limited to controlled laboratory experiments. Here we examine the settlement of microborers to pure mineral calcium carbonate substrates (calcite) along a natural pH gradient at a volcanically acidified reef at Maug, Commonwealth of the Northern Mariana Islands (CNMI). Colonization of pioneer microborers was higher in the lower pH waters near the vent field. Depth of microborer penetration was highly variable both among and within sites (4.2–195.5 μm) over the short duration of the study (3 mo.) and no clear relationship to increasing CO2 was observed. Calculated rates of biogenic dissolution, however, were highest at the two sites closer to the vent and were not significantly different from each other. These data represent the first evidence of OA-enhancement of microboring flora colonization in newly available substrates and provide further evidence that microborers, especially bioeroding chlorophytes, respond positively to low pH. The accelerated breakdown and dissolution of reef framework structures with OA will likely lead to declines in structural complexity and integrity, as well as possible loss of essential habitat.
Published: 2016

25. Structural Iron (II) of Basaltic Glass as an Energy Source for Zetaproteobacteria in an Abyssal Plain Environment, Off the Mid Atlantic Ridge

Author: Adam C. Mumford, Céline Rommevaux-Jestin, David R. Emerson, Anne Godfroy, Pauline Henri, Françoise Lesongeur, Bénédicte Ménez, Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de microbiologie des environnements extrêmophiles (LM2E), Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Bigelow Laboratory for Ocean Sciences, and Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Université Paris Diderot - Paris 7 (UPD7)-IPG PARIS-Institut national des sciences de l'Univers (INSU - CNRS)
Subjects: 0301 basic medicine, Microbiology (medical), iron-oxidation, 030106 microbiology, lcsh:QR1-502, Artificial seawater, Mineralogy, Mid-Atlantic Ridge, Microbiology, lcsh:Microbiology, 03 medical and health sciences, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Original Research, Basalt, Chemosynthesis, abyssal plain, geography, geography.geographical_feature_category, biology, Zetaproteobacteria, Chemistry, Abyssal plain, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 030104 developmental biology, Mariprofundus ferrooxydans, basaltic glass, Energy source, bio-mediated alteration
Abstract: International audience; To explore the capability of basaltic glass to support the growth of chemosynthetic microorganisms, complementary in situ and in vitro colonization experiments were performed. Microbial colonizers containing synthetic tholeitic basaltic glasses, either enriched in reduced or oxidized iron, were deployed off-axis from the Mid Atlantic Ridge on surface sediments of the abyssal plain (35 • N; 29 • W). In situ microbial colonization was assessed by sequencing of the 16S rRNA gene and basaltic glass alteration was characterized using Scanning Electron Microscopy, micro-X-ray Absorption Near Edge Structure at the Fe-K-edge and Raman microspectroscopy. The colonized surface of the reduced basaltic glass was covered by a rind of alteration made of iron-oxides trapped in a palagonite-like structure with thicknesses up to 150 μm. The relative abundance of the associated microbial community was dominated (39% of all reads) by a single operational taxonomic unit (OTU) that shared 92% identity with the iron-oxidizer Mariprofundus ferrooxydans PV-1. Conversely, the oxidized basaltic glass showed the absence of iron-oxides enriched surface deposits and correspondingly there was a lack of known iron-oxidizing bacteria in the inventoried diversity. In vitro, a similar reduced basaltic glass was incubated in artificial seawater with a pure culture of the iron-oxidizing M. ferrooxydans DIS-1 for 2 weeks, without any additional nutrients or minerals. Confocal Laser Scanning Microscopy revealed that the glass surface was covered by twisted stalks characteristic of this iron-oxidizing Zetaproteobacteria. This result supported findings of the in situ experiments indicating that the Fe(II) present in the basalt was the energy source for the growth of representatives of Zetaproteobacteria in both the abyssal plain and the in vitro experiment. In accordance, the surface alteration rind observed on the reduced basaltic glass incubated in situ could at least partly result from their activity.
Published: 2016

26. Net primary productivity estimates and environmental variables in the Arctic Ocean: An assessment of coupled physical-biogeochemical models

Author: Lee, Younjoo J., Matrai, Patricia A., Friedrichs, Marjorie A.M., Saba, Vincent S., Aumount, Olivier, Babin, Marcel, Buitenhuis, Erik T., Chevallier, Matthieu, de Mora, Lee, Dessert, Morgane, Dunne, John P., Ellingsen, Ingrid H., Feldman, Doron, Frouin, Robert, Gehlen, Marion, Gorguess, Thomas, Ilyina, Tatiana, Jin, Meibing, John, Jasmin G., Lawrence, Jon, Manizza, Manfredi, Menkes, Christophe E., Perruche, Coralie, Le Fouest, Vincent, Popova, Ekaterina E., Romanou, Anastasia, Samuelsen, Annette, Schwinger, Jörg, Séférian, Roland, Stock, Charles A., Tjiputra, Jerry, Tremblay, L. Bruno, Ueyoshi, Kyozo, Vichi, Marcello, Yool, Andrew, Zhang, Jinlun, Bigelow Laboratory for Ocean Sciences, Virginia Institute of Marine Science (VIMS), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), NOAA Geophysical Fluid Dynamics Laboratory (GFDL), Nucleus for European Modeling of the Ocean (NEMO R&D ), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Centre national de recherches météorologiques (CNRM), Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory (PML), Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), SINTEF Fisheries and Aquaculture, NASA Goddard Institute for Space Studies (GISS), NASA Goddard Space Flight Center (GSFC), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Modelling the Earth Response to Multiple Anthropogenic Interactions and Dynamics (MERMAID), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Max Planck Institute for Meteorology (MPI-M), Max-Planck-Gesellschaft, International Arctic Research Center (IARC), University of Alaska [Fairbanks] (UAF), National Oceanography Centre [Southampton] (NOC), University of Southampton, PaleoEnvironnements et PaleobioSphere (PEPS), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Mercator Océan, Société Civile CNRS Ifremer IRD Météo-France SHOM, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), LIttoral ENvironnement et Sociétés (LIENSs), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Nansen Environmental and Remote Sensing Center [Bergen] (NERSC), Bjerknes Centre for Climate Research (BCCR), Department of Biological Sciences [Bergen] (BIO / UiB), University of Bergen (UiB)-University of Bergen (UiB), Department of Atmospheric and Oceanic Sciences [Montréal], McGill University = Université McGill [Montréal, Canada], Department of Oceanography [Cape Town], University of Cape Town, Applied Physics Laboratory [Seattle] (APL-UW), University of Washington [Seattle], Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Centre National de la Recherche Scientifique (CNRS)-Université Laval [Québec] (ULaval), Météo France-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Plymouth Marine Laboratory, 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), Scripps Institution of Oceanography (SIO), University of California-University of California, Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Naval Postgraduate School (U.S.), and Oceanography
Subjects: Arctic models underestimated net primary productivity (NPP) but overestimated nitrate, mixed layer depth, and euphotic depth, [SDU.STU.GC]Sciences of the Universe [physics]/Earth Sciences/Geochemistry, Arctic NPP model skill was greatest in low production regions, Arctic NPP model skill was constrained by different environmental factors in different Arctic Ocean regions, Article, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: The article of record as published may be found at http://dx.doi.org/10.1002/2016JC011993 Upon publication, the in situ data will be available for academic purposes through the NASA SeaWiFS Bio-optical Archive and Storage System (http:// seabass.gsfc.nasa.gov/), including NPP, NO3, and Zeu. The relative skill of 21 regional and global biogeochemical models was assessed in terms of how well the models reproduced observed net primary productivity (NPP) and environmental variables such as nitrate concentration (NO3), mixed layer depth (MLD), euphotic layer depth (Zeu), and sea ice concentration, by comparing results against a newly updated, quality-controlled in situ NPP database for the Arctic Ocean (1959–2011). The models broadly captured the spatial features of integrated NPP (iNPP) on a pan-Arctic scale. Most models underestimated iNPP by varying degrees in spite of overestimating surface NO3, MLD, and Zeu throughout the regions. Among the models, iNPP exhibited little difference over sea ice condition (ice-free versus ice-influenced) and bottom depth (shelf versus deep ocean). The models performed relatively well for the most recent decade and toward the end of Arctic summer. In the Barents and Greenland Seas, regional model skill of surface NO3 was best associated with how well MLD was reproduced. Regionally, iNPP was relatively well simulated in the Beaufort Sea and the central Arctic Basin, where in situ NPP is low and nutrients are mostly depleted. Models performed less well at simulating iNPP in the Greenland and Chukchi Seas, despite the higher model skill in MLD and sea ice concentration, respectively. iNPP model skill was constrained by different factors in different Arctic Ocean regions. Our study suggests that better parameterization of biological and ecological microbial rates (phytoplankton growth and zooplankton grazing) are needed for improved Arctic Ocean biogeochemical modeling. National Aeronautics and Space Agency (NASA) Ocean Biology and Biogeochemistry (OBB) The project ‘‘Green Mercator’’ National Program CNRS/LEFE/INSU. NSF Office of Polar Programs FP7 MyOcean2 PAVE (Polish-Norwegian Research Program) Norwegian Supercomputing Project (NOTUR2) Research Council of Norway funded project ORGANIC NASA Cryosphere program CNRM-CM climate model Météo-France/DSI supercomputing Ocean Biology and Biogeochemistry (OBB) NNX13AE81G NSF Office of Polar Programs PLR- 1417925 NSF Office of Polar Programs PLR-1416920 FP7 MyOcean2 (project number 283367) Research Council of Norway funded project ORGANIC (239965/RU) NASA Cryosphere program (NNX15AG68G).
Published: 2016

27. The geotraces intermediate data product 2014

Author: Edward Mawji, Andrew R. Bowie, François Lacan, Kenneth W. Bruland, Oliver J. Lechtenfeld, Laura F. Robinson, Martin Frank, Kuo-Fang Huang, Louise A. Zimmer, Loes J. A. Gerringa, Tobias Roeske, Jingfeng Wu, Célia Venchiarutti, Yanbin Lu, Géraldine Sarthou, Reiner Schlitzer, Tomas A. Remenyi, Yuichiro Kumamoto, Hein J W de Baar, Santiago R. Gonzalez, Mark J. Warner, Mak A. Saito, Peter N. Sedwick, Daniel C. Ohnemus, Evgenia Ryabenko, Emilie Grossteffan, Moritz Zieringer, William J. Jenkins, Gregory F. de Souza, Pinghe Cai, Martin Q. Fleisher, Johnny Stutsman, Yolanda Echegoyen-Sanz, Alessandro Tagliabue, Delphine Lannuzel, Mark Rehkämper, Abigail E. Noble, A. Radic, Lijuan Sha, Micha J. A. Rijkenberg, Mark A. Brzezinski, François Fripiat, Nicholas R. Bates, Toshitaka Gamo, Hisayuki Yoshikawa, Maija Heller, Alan M. Shiller, William M. Smethie, Joaquin E. Chaves, Elena Masferrer Dodas, Torben Stichel, Mark Rosenberg, Hai Cheng, Alicia Navidad, Patrick Laan, Peter Scott, Mark Baskaran, Stephen J.G. Galer, Frédéric Planchon, Jan van Ooijen, Huong Thi Dieu, Steven van Heuven, Feifei Deng, José Marcus Godoy, Catherine Jeandel, Xin Yuan Zheng, Frank Dehairs, Stephen R. Rintoul, Wafa Abouchami, R. Lawrence Edwards, Gideon M. Henderson, Eberhard Fahrbach, Yoshiki Sohrin, Tim M. Conway, Bronwyn Wake, Urumu Tsunogai, Evaline van Weerlee, Maeve C. Lohan, Katrin Bluhm, Robert F. Anderson, Eva Bucciarelli, Ken O. Buesseler, Marie Labatut, Peter Croot, Jana Friedrich, Christopher T. Hayes, Hendrik M. van Aken, James H. Swift, Seth G. John, Sven Kretschmer, Zichen Xue, Karel Bakker, Albert S. Colman, Pierre Branellec, Timothy C. Kenna, Benjamin S. Twining, Marie Boye, Alexander L. Thomas, Karen L. Casciotti, Jessica N. Fitzsimmons, Sabrina Speich, Jun Nishioka, Thomas M. Church, Mariko Hatta, Pere Masqué, Damien Cardinal, Charles R. McClain, Oliver Baars, Frederique le Moigne, Geoffrey J. Smith, Daniel M. Sigman, Edward A. Boyle, Ursula Schauer, Stephanie Owens, E. Malcolm S. Woodward, Maarten B Klunder, Lesley Salt, Gregory A. Cutter, Christopher I. Measures, Hajime Obata, Catherine Pradoux, Ester Garcia Solsona, James W. Moffett, Antje H L Voelker, Gabriel Dulaquais, Paul D. Quay, Saeed Roshan, Rob Middag, Johann Bown, Neil J. Wyatt, Phoebe J. Lam, Edward C.V. Butler, Michiel M Rutgers van der Loeff, Fanny Chever, Cyril Abadie, Viena Puigcorbé, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut für Meereswissenschaften (IFM-GEOMAR), Department of Geosciences [Princeton], Princeton University, Institute for Environmental Research, Rheinisch-Westfälische Technische Hochschule Aachen (RWTH), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania [Hobart, Australia] (UTAS), 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), University of California, Marine Science Institute [Santa Barbara] (MSI), University of California [Santa Barbara] (UCSB), University of California-University of California, Woods Hole Oceanographic Institution (WHOI), Australian Institute of Marine Science (AIMS), State Key Laboratory of Marine Environmental Science (MEL), Xiamen University, Biogéochimie-Traceurs-Paléoclimat (BTP), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), NASA Goddard Space Flight Center (GSFC), Institute of Global Environmental Change [China] (IGEC), Xi'an Jiaotong University (Xjtu), Department of Earth Sciences [Minneapolis], University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Bonn University Hospital, College of Earth, Ocean, and Environment [Newark] (CEOE), University of Delaware [Newark], University College of London [London] (UCL), Department of Earth and Ocean Sciences [Columbia], University of South Carolina [Columbia], Old Dominion University [Norfolk] (ODU), Royal Netherlands Institute for Sea Research (NIOZ), Instituto de Química, Universidade de São Paulo, British Oceanographic Data Centre (BODC), National Oceanography Centre (NOC), Lamont-Doherty Earth Observatory (LDEO), Columbia University [New York], Massachusetts Institute of Technology (MIT), Universidad de Dakota del Sur, Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Bermuda Institute of Ocean Sciences (BIOS), Vrije Universiteit Brussel (VUB), Department of Mathematics and Science, National Taiwan Normal University (NTNU), GEOMAR LEGOS, Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Department of Chemistry, School of Life Sciences, University of Sussex, National Oceanography Centre [Southampton] (NOC), University of Southampton, Institut de Ciencia i Tecnologia Ambientals (ICTA), Universitat Autònoma de Barcelona (UAB), Oceans Institute and School of Physics, The University of Western Australia (UWA), School of Natural Sciences and Centre for Marine Ecosystems Research, Edith Cowan University, EDITH COWAN UNIVERSITY-EDITH COWAN UNIVERSITY, Department of Chemistry [Dunedin], University of Otago [Dunedin, Nouvelle-Zélande], Atmosphere and Ocean Research Institute [Kashiwa-shi] (AORI), The University of Tokyo (UTokyo), Bermuda Biological Station for Research (BBSR), Bermuda Biological Station for Research, Kyoto University [Kyoto], Laboratoire d'Océanographie Physique et Spatiale (LOPS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), SOEST, University of Hawai‘i [Mānoa] (UHM), FM-GEOMAR, Leibniz Institute of Marine Sciences at the University of Kiel, Department of Earth Ocean and Ecological Sciences [Liverpool], University of Liverpool, Bigelow Laboratory for Ocean Sciences, Department of Biology, Tufts University [Medford], RITE, Research Institute of Innovative Technology for the Earth, Royal Museum for Central Africa [Tervuren] (RMCA), IMT Lille Douai, Ecole nationale supérieure Mines-Télécom Lille Douai (IMT Lille Douai), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Analytical, Environmental and Geo- Chemistry, Chemistry, Analytical and Environmental Chemistry, Earth System Sciences, Analytical, Environmental & Geo-Chemistry, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National d'Études Spatiales [Toulouse] (CNES)-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), University of Tasmania (UTAS), Institut Français de Recherche pour l'Exploitation de la Mer - Brest (IFREMER), Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Muséum national d'Histoire naturelle (MNHN), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), University of Minnesota [Twin Cities], Laboratoire de Mécanique des Contacts et des Structures [Villeurbanne] (LaMCoS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Universitat Autònoma de Barcelona [Barcelona] (UAB), The University of Tokyo, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Rheinisch-Westfälische Technische Hochschule Aachen University (RWTH), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institute for Marine and Antarctic Studies [Hobart] (IMAS), University of California (UC), University of California [Santa Barbara] (UC Santa Barbara), University of California (UC)-University of California (UC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-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)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris Diderot - Paris 7 (UPD7)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), University Hospital Bonn, Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), University of Sussex, Kyoto University, Laboratoire de physique des océans (LPO), Natural Environment Research Council (NERC), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Boyle, Edward A, Fitzsimmons, Jessica Nicole, Echegoyen Sanz, Yolanda, Ocean Ecosystems, and Isotope Research
Subjects: Chemistry, Multidisciplinary, Geotraces, Digital data, trace elements, [PHYS.PHYS.PHYS-GEO-PH]Physics [physics]/Physics [physics]/Geophysics [physics.geo-ph], Biology, Oceanography, ASCII, Isotopes, 0399 Other Chemical Sciences, Electronic atlas, GEOTRACES, Trace elements, 0402 Geochemistry, Environmental Chemistry, Bathymetry, 0405 Oceanography, 14. Life underwater, isotopes, Water Science and Technology, Stable isotopes, NetCDF, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Science & Technology, Information retrieval, ACL, General Chemistry, computer.file_format, Seawater samples, Ocean Data View, Metadata, Marine Sciences, Chemistry, electronic atlas, 13. Climate action, Data quality, Physical Sciences, geotraces, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, computer
Abstract: The GEOTRACES Intermediate Data Product 2014 (IDP2014) is the first publicly available data product of the international GEOTRACES programme, and contains data measured and quality controlled before the end of 2013. It consists of two parts: (1) a compilation of digital data for more than 200 trace elements and isotopes (TEIs) as well as classical hydrographic parameters, and (2) the eGEOTRACES Electronic Atlas providing a strongly inter-linked on-line atlas including more than 300 section plots and 90 animated 3D scenes. The IDP2014 covers the Atlantic, Arctic, and Indian oceans, exhibiting highest data density in the Atlantic. The TEI data in the IDP2014 are quality controlled by careful assessment of intercalibration results and multi-laboratory data comparisons at cross-over stations. The digital data are provided in several formats, including ASCII spreadsheet, Excel spreadsheet, netCDF, and Ocean Data View collection. In addition to the actual data values the IDP2014 also contains data quality flags and 1-σ data error values where available. Quality flags and error values are useful for data filtering. Metadata about data originators, analytical methods and original publications related to the data are linked to the data in an easily accessible way. The eGEOTRACES Electronic Atlas is the visual representation of the IDP2014 data providing section plots and a new kind of animated 3D scenes. The basin-wide 3D scenes allow for viewing of data from many cruises at the same time, thereby providing quick overviews of large-scale tracer distributions. In addition, the 3D scenes provide geographical and bathymetric context that is crucial for the interpretation and assessment of observed tracer plumes, as well as for making inferences about controlling processes., National Science Foundation (U.S.) (OCE-0608600), National Science Foundation (U.S.) (OCE-0938349), National Science Foundation (U.S.) (OCE-1243377)
Published: 2015

28. Solid-State Au/Hg Microelectrode for the Investigation of Fe and Mn Cycling in a Freshwater Wetland: Implications for Methane Production

Author: Jason K. Keller, Andrew S. Madison, George W. Luther, David Emerson, Shufen Ma, J. Patrick Megonigal, Edouard Metzger, Bio-Indicateurs Actuels et Fossiles (BIAF), Université d'Angers (UA), and Bigelow Laboratory for Ocean Sciences
Subjects: chemistry.chemical_classification, Rhizosphere, 010504 meteorology & atmospheric sciences, Sulfide, Methanogenesis, Inorganic chemistry, Sediment, 010501 environmental sciences, 01 natural sciences, Redox, 6. Clean water, Methane, Analytical Chemistry, Diagenesis, chemistry.chemical_compound, chemistry, [SDU]Sciences of the Universe [physics], Environmental chemistry, Electrochemistry, Dissolution, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences
Abstract: The solid-state voltammetric gold-amalgam microelectrode was used to measure multiple redox species (O, S, Fe and Mn) in situ at (sub)millimeter vertical resolution to elucidate rhizosphere processes in Jug Bay wetlands. In vegetated soil, a classic diagenetic redox sequence without any dissolved sulfide was observed in summer. However, the rhizosphere can be quite variable which is due to the introduction of O2 to the anoxic sediments by plants. In nonvegetated soil, the vertical concentration–depth profiles were relatively constant. The presence of Fe(II), Mn(II) and soluble Fe(III) in deeper sediments indicates the oxidation of Fe(II) as well as the nonreductive dissolution of Fe(III) and the reductive dissolution of Fe(III) and Mn(III, IV) solids. Mn(III, IV) and Fe(III) redox chemistry is important in organic matter mineralization mediated by bacteria and in suppressing methane formation. In addition, Mn(III, IV) also can oxidize Fe(II) to supply Fe(III) for bacterial Fe(III) reduction. Studying Fe and Mn cycling via voltammetric methods can give insights to methane production and loss as there is no methane sensor for sediment work at present.
Published: 2008

29. Open science resources for the discovery and analysis of Tara Oceans data

Author: Pesant, Stéphane, Not, Fabrice, Picheral, Marc, Kandels-Lewis, Stefanie, Le Bescot, Noan, Gorsky, Gabriel, Iudicone, Daniele, Karsenti, Eric, Speich, Sabrina, Troublé, Romain, Dimier, Céline, Searson, Sarah, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Grimsley, Nigel, Hingamp, Pascal, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, Follows, Michael J, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, PANGAEA Consulting Engineers, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie 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), European Molecular Biology Laboratory [Heidelberg] (EMBL), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Stazione Zoologica Anton Dohrn (SZN), 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), 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), Tara Expéditions, Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Grenoble] (EMBL), University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), 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), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), School of Biology & Environmental Science, University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Bigelow Laboratory for Ocean Sciences, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, European Molecular Biology Laboratory, DVIPC, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National 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), Department of Marine Biology and Oceanography, 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), Kyoto University [Kyoto], Department of Ecology and Evolutionary Biology, Research Foundation - Flanders, Stazione Zoologica Anton Dohrn, Università degli Studi di Milano-Bicocca, Agence Nationale de la Recherche (France), European Research Council, Ministerio de Ciencia e Innovación (España), Japan Society for the Promotion of Science, Veolia Foundation, Région Bretagne, World Courier, Illumina, Lorient Agglomération, Fondation EDF, Fondation Prince Albert II de Monaco, Centre National de Séquençage (France), Centre National de la Recherche Scientifique (France), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Raes, Jeroen, and Lorient Agglomération (France)
Subjects: [SDE] Environmental Sciences, Statistics and Probability, Open science, Data Descriptor, 010504 meteorology & atmospheric sciences, Oceans and Seas, [SDV]Life Sciences [q-bio], Context (language use), Library and Information Sciences, 01 natural sciences, Education, Environmental data, 03 medical and health sciences, Seawater, 14. Life underwater, Ecosystem, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, business.industry, Information Dissemination, Environmental resource management, Ecological genetics, Biodiversity, Plankton, Biooceanography, Computer Science Applications, [SDV] Life Sciences [q-bio], Oceanography, Geography, Ocean sciences, 13. Climate action, Viruses, [SDE]Environmental Sciences, Expeditions, Statistics, Probability and Uncertainty, business, Information Systems
Abstract: Pesant, Stéphane ... et. al.-- 16 pages, 5 figures, 2 tables.-- This article is contribution number 26 of the Tara Oceans Consortium, The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular the Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA- 003, PROMETHEUS/ANR-09-GENM-031, PROMETHEUS/ANR-09-PCS-GENM-217, TARAGIRUS/ANR-09-PCS-GENM-218, OCEANOMICS/ANR-11-BTBR-0008, FRANCE GENOMIQUE/ANR-10-INBS-09-08), EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, MetaCardis/HEALTH-F4-2012-305312), ERC Advanced Grant Awards to CB (Diatomite: 294823) and PB (CancerBiome: 268985), Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to SGA, JSPS KAKENHI Grant Number 26430184 to HO, FWO, BIO5, Biosphere 2, agne`s 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 continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015

30. The Ocean Sampling Day Consortium

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

31. An assessment of phytoplankton primary productivity in the Arctic Ocean from satellite ocean color/in situ chlorophyll-a based models

Author: Patricia A. Matrai, Timothy J Smyth, Bernard Gentili, Frédéric Mélin, Takahiko Kameda, Younjoo Lee, David Antoine, Ichio Asanuma, Toru Hirawake, Michele Scardi, Zhongping Lee, Mathieu Ardyna, Christian Katlein, Toby K. Westberry, Marjorie A. M. Friedrichs, Marcel Babin, Simon Bélanger, Sang Heon Lee, Kevin R. Turpie, Shilin Tang, Emmanuel Devred, Vincent S. Saba, Mar Fernández-Méndez, Kirk Waters, Sung-Ho Kang, Maxime Benoît‐Gagné, Bigelow Laboratory for Ocean Sciences, Virginia Institute of Marine Science (VIMS), 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), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), Université du Québec à Rimouski (UQAR), Fisheries and Oceans Canada (DFO), Norwegian Polar Institute, Hokkaido University [Sapporo, Japan], KIOST, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), European Commission - Joint Research Centre [Ispra] (JRC), Università degli Studi di Roma Tor Vergata [Roma], Plymouth Marine Laboratory (PML), Plymouth Marine Laboratory, NASA, Department of Botany and Plant Pathology, Oregon State University (OSU), 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), and Université Laval [Québec] (ULaval)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, In situ, Chlorophyll a, 010504 meteorology & atmospheric sciences, Settore BIO/07, Arctic Ocean, model skill assessment, net primary productivity, ocean color model, remote sensing, subsurface chlorophyll‐a maximum, Oceanography, Atmospheric sciences, Biogeosciences, 01 natural sciences, Remote Sensing, chemistry.chemical_compound, Oceanography: Biological and Chemical, Forum for Arctic Modeling and Observational Synthesis (FAMOS): Results and Synthesis of Coordinated Experiments, Geochemistry and Petrology, Phytoplankton, Earth and Planetary Sciences (miscellaneous), 14. Life underwater, Arctic Region, Research Articles, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, 010604 marine biology & hydrobiology, Arctic and Antarctic oceanography, Primary production, Model Verification and Validation, The arctic, Sea surface temperature, Oceanography: General, Geophysics, chemistry, 13. Climate action, Space and Planetary Science, Ocean color, Chlorophyll, Environmental science, Antarctica, Geographic Location, Computational Geophysics, Research Article
Abstract: We investigated 32 net primary productivity (NPP) models by assessing skills to reproduce integrated NPP in the Arctic Ocean. The models were provided with two sources each of surface chlorophyll‐a concentration (chlorophyll), photosynthetically available radiation (PAR), sea surface temperature (SST), and mixed‐layer depth (MLD). The models were most sensitive to uncertainties in surface chlorophyll, generally performing better with in situ chlorophyll than with satellite‐derived values. They were much less sensitive to uncertainties in PAR, SST, and MLD, possibly due to relatively narrow ranges of input data and/or relatively little difference between input data sources. Regardless of type or complexity, most of the models were not able to fully reproduce the variability of in situ NPP, whereas some of them exhibited almost no bias (i.e., reproduced the mean of in situ NPP). The models performed relatively well in low‐productivity seasons as well as in sea ice‐covered/deep‐water regions. Depth‐resolved models correlated more with in situ NPP than other model types, but had a greater tendency to overestimate mean NPP whereas absorption‐based models exhibited the lowest bias associated with weaker correlation. The models performed better when a subsurface chlorophyll‐a maximum (SCM) was absent. As a group, the models overestimated mean NPP, however this was partly offset by some models underestimating NPP when a SCM was present. Our study suggests that NPP models need to be carefully tuned for the Arctic Ocean because most of the models performing relatively well were those that used Arctic‐relevant parameters., Key Points The models reproduced primary productivity better using in situ chlorophyll‐a than satellite valuesThe models performed well in low‐productivity seasons and in sea ice‐covered/deep‐water regionsNet primary productivity models need to be carefully tuned for the Arctic Ocean
Published: 2015

32. Geographic variation in long-term trajectories of change in coral recruitment: a global-to-local perspective

Author: Haruko Kurihara, Jacqueline L. Padilla-Gamiño, Robert S. Steneck, Ruth D. Gates, Yoko Nozawa, H. Kitano, Rebecca Albright, A. Yarid, Tung-Yung Fan, G. Suzuki, M. J. H. van Oppen, Satoshi Mitarai, L. Legendre, Soyoka Muko, Peter J. Edmunds, Saki Harii, Apple Pui Yi Chui, Nichole N. Price, Kazuhiko Sakai, Robert C. Carpenter, University of Hawaii, California State University [Northridge] (CSUN), University of Maine, Carnegie Institution for Science [Washington], Australian Institute of Marine Science (AIMS), The Chinese University of Hong Kong [Hong Kong], University of the Ryukyus [Okinawa], Okinawa Institute of Science and Technology Graduate University (OIST), 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), Nagasaki University, and Bigelow Laboratory for Ocean Sciences
Subjects: 0106 biological sciences, Coral, Scleractinia, Aquatic Science, Oceanography, 010603 evolutionary biology, 01 natural sciences, Juvenile, 14. Life underwater, Reef, Ecology, Evolution, Behavior and Systematics, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Invertebrate, geography, geography.geographical_feature_category, Ecology, biology, 010604 marine biology & hydrobiology, fungi, Community structure, technology, industry, and agriculture, Ocean acidification, social sciences, biology.organism_classification, Fishery, Phylogeography, population characteristics, geographic locations
Abstract: Compiled abundances of juvenile corals revealed no change over time in the Pacific, but a decline in the Caribbean. Using these analyses as a rationale, we explored recruitment and post-settlement success in determining coral cover using studies in the Caribbean (St John, Bonaire) and Pacific (Moorea, Okinawa). Juvenile corals, coral recruits, and coral cover have been censused in these locations for years, and the ratio of juvenile (J) to recruiting (R) corals was used to measure post-settlement success. In St John and Bonaire, coral cover was stable but different between studies, with the ratio of the density of juveniles to density of recruits (J:R) ~0.10; in Moorea, declines in coral cover were followed by recovery that was related to the density of juvenile corals 3 years before, with J:R ~0.40; and in Okinawa, a decline in coral cover in 1998 was followed by a slow recovery with J/R ~0.01. Coral cover was associated positively with juvenile corals in St John, and in Okinawa, the density of juvenile corals was associated positively with recruits the year before. J:R varied among studies, and standardised densities of juvenile corals declined in the Caribbean, but increased in the Pacific. These results suggest that differences in the post-settlement success may drive variation in coral community structure.
Published: 2015

33. The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing

Author: Mary Ann Moran, Ronald P. Kiene, Matthew D. Johnson, Jennifer L. Jacobi, Gwenael Piganeau, Kjetill S. Jakobsen, Simon K. Davy, Edward C. Theriot, Uwe John, Alexander Kudryavtsev, Sarah R. Smith, Bente Edvardsen, Cristina Miceli, Adrian Marchetti, Karin Rengefors, Tatiana A. Rynearson, John M. Archibald, Matthew C. Posewitz, Brian Palenik, Alexandra Z. Worden, Pooja E. Umale, Boris Wawrik, Laura A. Katz, Satoshi Nagai, Anja Kamp, Lisa Campbell, Kathryn J. Coyne, Thomas Mock, E. Virginia Armbrust, Fabien Burki, Adriana Zingone, Sonya T. Dyhrman, Mary E. Rumpho, Bank Beszteri, Giovanna Romano, Declan C. Schroeder, Callum J. Bell, Yan Xu, Bassem Allam, Kay D. Bidle, Bethany D. Jenkins, Kelly B. Schilling, Giulio Petroni, David Roy Smith, Aurora M. Nedelcu, Arvind K. Bharti, Connie Lovejoy, Stephanie Guida, Spencer J. Greenwood, Peter Stief, David A. Caron, Senjie Lin, Marina Montresor, Denis H. Lynn, Patrick J. Keeling, Glen L. Wheeler, Linda A. Amaral-Zettler, Daniel Vaulot, Jan Pawlowski, Ruth D. Gates, Brian S. Leander, Heather M. Wilcox, Andrew R. Juhl, Govind Nadathur, Erick R. James, Rose Ann Cattolico, Alastair G. B. Simpson, Susanne Menden-Deuer, G. Jason Smith, George B. McManus, Christopher J. Gobler, Heidi M. Sosik, Connor Cameron, Jackie L. Collier, Shauna A. Murray, Scott N. Twary, William H. Wilson, Claudio H. Slamovits, Peter B. Ngam, Phillipe Deschamps, Eric E. Allen, Roberts, Roland G, Canadian Institute for Advanced Research (CIFAR), Department of Botany, University of British Columbia [Vancouver], Monterey Bay Aquarium Research Institute (MBARI), Monterey Bay Aquarium Research Institute, School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Marine Biology Research Division, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), The Josephine Bay Paul Center for comparative molecular biology and evolution, Department of Geological Sciences [Providence], Brown University, School of Oceanography [Seattle], University of Washington [Seattle], Department of biochemistry & molecular biology, Dalhousie University [Halifax], National center for genome resources (NCGR), Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), Institute of Marine and Coastal Science, Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Department of Oceanography [College Station], Texas A&M University [College Station], Department of biology, University of Southern California (USC), University of Delaware [Newark], School of biological sciences, Victoria University of Wellington, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Department of earth and environmental sciences and the Lamont-Doherty earth observatory, Columbia University [New York], Department of Molecular Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Hawai'i Institute of Marine Biology, Hawai'i Institute of Marine Biology (HIMB), Department of biomedical sciences, University of Prince Edward Island, Graduate School of Oceanography [Narragansett], University of Rhode Island (URI), Department of cell and molecular biology, University of Rhode Island, University of Rhode Island (URI)-University of Rhode Island (URI), Woods Hole Oceanographic Institution (WHOI), Jacobs University [Bremen], Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Department of biological sciences, Smith College [Northampton], University of South Alabama, Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Department of Marine sciences, University of Connecticut (UCONN), département de biologie, Université Laval [Québec] (ULaval), Department of Integrative Biology, University of Guelph, Department of zoology, University of British Columbia (UBC), Department of Marine, Earth, and Atmospheric Sciences [NCSU] (MEAS), North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), University of New Brunswick (UNB), School of biosciences and biotechnology, Università degli Studi di Camerino = University of Camerino (UNICAM), School of Environmental Sciences [Norwich], University of East Anglia [Norwich] (UEA), Stazione Zoologica Anton Dohrn (SZN), Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney (UTS), Department of Marrine sciences, University of Puerto Rico (UPR), National Research Institute of Fisheries Science, University of Pisa - Università di Pisa, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Chemistry and Geochemistry, Colorado School of Mines, department of biology, Lund University [Lund], Department of molecular and cell biology, Marine Biological Association of the UK, University of Western Ontario (UWO), Moss Landing Marine Laboratories, Section of Integrative Biology, University of Texas at Austin [Austin], Los Alamos National Laboratory (LANL), 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), department of microbiology and plant biology, University of Oklahoma (OU), Plymouth Marine Laboratory (PML), Bigelow Laboratory for Ocean Sciences, Princeton University, University of Britsh Columbia [Vancouver], University of California-University of California, University of Geneva [Switzerland], Università degli Studi di Camerino (UNICAM), Plymouth Marine Laboratory, and Roberts, Roland G.
Subjects: Genetics and Molecular Biology (all), Databases, Factual, animal genomics, Immunology and Microbiology (all), Biochemistry, Medical and Health Sciences, Transcriptome, transcriptome analysis, Community Page, sequence databases, Environmental Microbiology, Biology (General), Molecular Sequence Data, Sequence Analysis, Biodiversity, Eukaryota, Oceans and Seas, Agricultural and Biological Sciences (all), Biochemistry, Genetics and Molecular Biology (all), Neuroscience (all), Medicine (all), Genetics, General Neuroscience, marine ecology, Biological Sciences, genome sequencing, General Agricultural and Biological Sciences, Biologie, QH301-705.5, Sequence analysis, Ecology (disciplines), Marine Biology, Genomics, Biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, DNA sequencing, Databases, Microbial ecology, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], 14. Life underwater, Life Below Water, Factual, Comparative genomics, Marine biology, Evolutionary Biology, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Ecology and Environmental Sciences, Human Genome, Biology and Life Sciences, 15. Life on land, Evolutionary biology, plant genomics, Generic health relevance, genomic library construction, Genomic databases, Developmental Biology
Abstract: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes [1]. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics [2]. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases [3],[4], raising the question as to whether this is fit for purpose.
Published: 2014

34. Role of diatoms in nickel biogeochemistry in the ocean

Author: Benjamin S. Twining, David M. Nelson, Stephen B. Baines, Stefan Vogt, Bigelow Laboratory for Ocean Sciences, Department of Ecology and Evolution, State University of New York (SUNY), X-ray Science Division (XSD), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)
Subjects: Atmospheric Science, 010504 meteorology & atmospheric sciences, Frustule, chemistry.chemical_element, Biology, 010502 geochemistry & geophysics, 01 natural sciences, chemistry.chemical_compound, Phytoplankton, Environmental Chemistry, Trace metal, 14. Life underwater, Silicic acid, Picoplankton, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 0105 earth and related environmental sciences, General Environmental Science, Global and Planetary Change, Metallurgy, fungi, Biogeochemistry, Phosphate, biology.organism_classification, Nickel, chemistry, Environmental chemistry, [SDE]Environmental Sciences
Abstract: International audience; Dissolved nickel (Ni) typically displays a 'nutrient-like' vertical profile in the ocean, with lower concentrations in surface waters and higher concentrations in deep waters, similar to other micronutrient metals such as iron and zinc. Vertical profiles of Ni show particular similarities to profiles of the macronutrients phosphate and silicic acid, suggesting that diatoms play an important role in mediating the vertical distribution of this metal. We performed synchrotron x-ray fluorescence (SXRF) analysis on individual phytoplankton cells collected from stations in the equatorial Pacific Ocean and from nutrient-addition incubation experiments conducted on the same cruise. Diatoms were enriched in Ni twofold to fivefold relative to picoplankton and flagellated cells. Changes in cellular quotas of Si, P and Ni observed in diatoms growing in response to Fe and Si additions were used to estimate the Ni:P (0.52 ± 0.10 mmol/mol) and Ni:Si (28 ± 13 μmol/mol) ratios of internal biomass and the frustule, respectively. Elevated internal Ni:P suggests a heightened role for urease or the Ni isoform of superoxide dismutase in diatoms (similar to cyanobacteria), while Ni associated with the frustule appears to contribute an additional 50% of cellular Ni found in the diatoms. The derived Ni:Si ratio for frustule material is comparable to Ni:Si ratios in published nutrient profiles, confirming the dominant role that diatoms play in ocean Ni biogeochemistry. While a molecular explanation for the association of Ni with frustules remains to be determined, this study demonstrates the unique biogeochemical insight that can be gained from microanalytical element analysis.
Published: 2012

35. Evaluating the Ribosomal Internal Transcribed Spacer (ITS) as a Candidate Dinoflagellate Barcode Marker

Author: Benoît Véron, Frithjof C. Küpper, Florence Le Gall, Mary Alice Coffroth, Robert A. Andersen, Hayley Skelton, Jerry J. Brand, Ian Jameson, Emily L. Lilly, Rowena Stern, Daniel Vaulot, Patrick J. Keeling, Fumai Kasai, Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Bigelow Laboratory for Ocean Sciences, Australian National Algae Culture Collection, Industrial Research Organisation Marine and Atmospheric Research, Scottish Association for Marine Science (SAMS), University at Buffalo [SUNY] (SUNY Buffalo), State University of New York (SUNY), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Texas at Austin [Austin], Department of Marine Sciences, University of Connecticut (UCONN), National Institute for Environmental Studies (NIES), Biology Department - Virginia Military Institute, Department of Botany, University of Britsh Columbia [Vancouver], Genome Canada, United Kingdom Natural Environment Research Council [Oceans 2025 NF3, MGF 154], National Science Foundation [OCE 04-24994, OCE-09-26822], University of British Columbia [Vancouver], and Kolokotronis, Sergios-Orestis
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], lcsh:Medicine, 01 natural sciences, DNA barcoding, Biochemistry, Symbiodinium, DNA amplification, lcsh:Science, Phylogeny, 0303 health sciences, Multidisciplinary, Ecology, Cytochrome b, Microbial Mutation, Biodiversity, DNA Barcoding, Nucleic acids, [SDE]Environmental Sciences, Dinoflagellida, Phycology, Research Article, Genetic Markers, Species complex, Ecological Metrics, Life on Land, General Science & Technology, Biophysics, Marine Biology, Biology, Alveolate, Microbiology, Electron Transport Complex IV, 03 medical and health sciences, Marine Monitoring, Botany, Genetics, Animals, DNA Barcoding, Taxonomic, Internal transcribed spacer, 030304 developmental biology, 010604 marine biology & hydrobiology, lcsh:R, Species diversity, Taxonomic, Species Diversity, DNA, biology.organism_classification, Genetic marker, Evolutionary biology, Microbial Evolution, Genetic Polymorphism, lcsh:Q, Ribosomes, Population Genetics
Abstract: International audience; Background: DNA barcoding offers an efficient way to determine species identification and to measure biodiversity. For dinoflagellates, an ancient alveolate group of about 2000 described extant species, DNA barcoding studies have revealed large amounts of unrecognized species diversity, most of which is not represented in culture collections. To date, two mitochondrial gene markers, Cytochrome Oxidase I (COI) and Cytochrome b oxidase (COB), have been used to assess DNA barcoding in dinoflagellates, and both failed to amplify all taxa and suffered from low resolution. Nevertheless, both genes yielded many examples of morphospecies showing cryptic speciation and morphologically distinct named species being genetically similar, highlighting the need for a common marker. For example, a large number of cultured Symbiodinium strains have neither taxonomic identification, nor a common measure of diversity that can be used to compare this genus to other dinoflagellates. Methodology/Principal Findings: The purpose of this study was to evaluate the Internal Transcribed Spacer units 1 and 2 (ITS) of the rDNA operon, as a high resolution marker for distinguishing species dinoflagellates in culture. In our study, from 78 different species, the ITS barcode clearly differentiated species from genera and could identify 96% of strains to a known species or sub-genus grouping. 8.3% showed evidence of being cryptic species. A quarter of strains identified had no previous species identification. The greatest levels of hidden biodiversity came from Scrippsiella and the Pfiesteriaceae family, whilst Heterocapsa strains showed a high level of mismatch to their given species name. Conclusions/Significance: The ITS marker was successful in confirming species, revealing hidden diversity in culture collections. This marker, however, may have limited use for environmental barcoding due to paralogues, the potential for unidentifiable chimaeras and priming across taxa. In these cases ITS would serve well in combination with other markers or for specific taxon studies.
Published: 2012

36. 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

37. Anatomy of a red tide bloom off the southwest coast of Florida

Author: Yentsch, C. S., Lapointe, B. E., Poulton, N., Phinney, D. A., Bigelow Laboratory for Ocean Sciences, and LAHBIB, SOUMAYA
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 2008

38. RAPID Research on Automated Plankton Identification

Author: Phil F. Culverhouse, Allen Hansen, Qiao Hu, Gabriel Gorsky, Ángel López-Urrutia, Cynthia H. Pilskaln, Edward M. Riseman, Hans G. Dam, Philippe Grosjean, Michael E. Sieracki, Paul E. Utgoff, Mark C. Benfield, Xabier Irigoien, Cabell S. Davis, Howard Schultz, AZTI - Tecnalia, Bigelow Laboratory for Ocean Sciences, National Science Foundation [Arlington] (NSF), City University of Hong Kong [Hong Kong] (CUHK), 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), and Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Oceanography, 010504 meteorology & atmospheric sciences, Computer science, 010604 marine biology & hydrobiology, 14. Life underwater, Permission, 01 natural sciences, Data science, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences
Abstract: Author Posting. © Oceanography Society, 2007. This article is posted here by permission of Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 20, 2 (2007): 172-187.
Published: 2007

39. Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time

Author: Stepanauskas, R., Sieracki, M. E., University of New England (UNE), and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU]Sciences of the Universe [physics], ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; no abstract
Published: 2007

40. Biosphere-atmosphere interactions

Author: Scholes, Mary, Matrai, Patricia, Andreae, Meinrat, Smith, Keith, Manning, Martin, Artaxo, Paulo, Barrie, Leonard, Bates, Timothy, Butler, James, Ciccioli, Paolo, Cieslik, Stanislaw, Delmas, Robert, Dentener, Frank, Duce, Robert, III, David Erickson, Galbally, Ian, Guenther, Alex, Jaenicke, Ruprecht, Jähne, Bernd, Kettle, Anthony, Kiene, Ronald, Lacaux, Jean-Pierre, Liss, Peter, Malin, G., Matson, Pamela, Mosier, Arvin, Neue, Heinz-Ulrich, Paerl, Hans, Platt, Ulrich, Quinn, Patricia, Seiler, Wolfgang, Weiss, Ray, University of the Witwatersrand [Johannesburg] (WITS), Bigelow Laboratory for Ocean Sciences, Biogeochemistry Division, Max-Planck-Institut, Universidade de São Paulo = University of São Paulo (USP), Naval Research Laboratory (NRL), Istituto Di Biologia Cellulare [Monterotondo, Italie] (CNR-EMMA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Laboratoire de glaciologie et géophysique de l'environnement (LGGE), Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Commission - Joint Research Centre [Ispra] (JRC), Department of Atmospheric Sciences [College Station], Texas A&M University [College Station], CSIRO Climate Science Centre, Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), National Center for Atmospheric Research [Boulder] (NCAR), Institute of Atmospheric Physics, Institute of Environmental Physics [Heidelberg] (IUP), Universität Heidelberg [Heidelberg] = Heidelberg University, University of South Alabama, Laboratoire d'aérologie (LAERO), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), NOAA Pacific Marine Environmental Laboratory [Seattle] (PMEL), National Oceanic and Atmospheric Administration (NOAA), Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Universidade de São Paulo (USP), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Grenoble (OSUG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Joseph Fourier - Grenoble 1 (UJF)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), Universität Heidelberg [Heidelberg], Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Scripps Institution of Oceanography (SIO), and University of California-University of California
Subjects: [PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], 010504 meteorology & atmospheric sciences, 13. Climate action, 010501 environmental sciences, 15. Life on land, 01 natural sciences, 0105 earth and related environmental sciences
Abstract: The contemporary atmosphere was created as a result of biological activity some two billion years ago. To this day, its natural composition is supported and modified, mostly through biological processes of trace gas production and destruction, while also involving physical and chemical degradation processes. The biosphere has a major influence on present environmental conditions, both on a regional and global scale. One of the bestdocumented and most important indicators of global change is the progressive increase of a number of trace gases in the atmosphere, among them carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O), all of which are of biospheric origin. There is considerable uncertainty, however, regarding the processes that determine the concentration and distribution of trace gases and aerosols in the atmosphere and the causes and consequences of atmospheric change (Andreae and Schimel 1989). To improve our understanding IGAC created an environment for multi-disciplinary collaboration among biologists, chemists, and atmospheric scientists. This was essential to develop analytical methods, to characterise ecosystems, to investigate physiological controls, to develop and validate micrometeorological theory, and to design and develop diagnostic and predictive models (Matson and Ojima 1990).
Published: 2003

41. Flow cytometric analysis of 5-cyano-2,3-ditolyl tetrazolium chloride activity of marine bacterioplankton in dilution cultures

Author: Sieracki, M. E., Cucci, T. L., Nicinski, J., Beaussier, Catherine, University of New England (UNE), and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1999

42. An imaging-in-flow system for automated analysis of marine microplankton

Author: Sieracki, C. K., Sieracki, M. E., Yentsch, C. S., Beaussier, Catherine, Bigelow Laboratory for Ocean Sciences, and University of New England (UNE)
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; no abstract
Published: 1998

43. Cellular DNA content of marine phytoplankton using two new fluorochromes: Taxonomic and ecological implications

Author: Veldhuis, M. J. W., Cucci, T. L., Sieracki, M. E., Beaussier, Catherine, Royal Netherlands Institute for Sea Research (NIOZ), University of New England (UNE), and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1997

44. Overestimation of Heterotrophic Bacteria in the Sargasso-Sea - Direct Evidence by Flow and Imaging Cytometry

Author: Sieracki, M. E., Haugen, E. M., Cucci, T. L., Beaussier, Catherine, University of New England (UNE), and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1995

45. Strategies for flow cytometric analysis of marine microalgae and sponge cells

Author: Yentsch, C. M., Pomponi, S. A., LAHBIB, SOUMAYA, and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1994

46. Effects of Asphericity on Single-Particle Polarized-Light Scattering

Author: Spinrad, R. W., Brown, J., Bigelow Laboratory for Ocean Sciences, and Beaussier, Catherine
Subjects: [SDU] Sciences of the Universe [physics], [SDU]Sciences of the Universe [physics], [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract: International audience; no abstract
Published: 1993

47. Cytometry in the aquatic sciences

Author: Yentsch, C. M., Horan, P. K., LAHBIB, SOUMAYA, and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1989

48. Discrimination between Types of Pigments in Marine Synechococcus Spp by Scanning Spectroscopy, Epifluorescence Microscopy, and Flow-Cytometry

Author: Wood, A. M., Horan, P. K., Muirhead, K., Phinney, D. A., Yentsch, C. M., Waterbury, J. B., LAHBIB, SOUMAYA, University of Chicago, and Bigelow Laboratory for Ocean Sciences
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; no abstract
Published: 1985

49. Fostering multidisciplinary research on interactions between chemistry, biology, and physics within the coupled cryosphere-atmosphere system

Author: Jennie L. Thomas, Jochen Stutz, Markus M. Frey, Thorsten Bartels-Rausch, Katye Altieri, Foteini Baladima, Jo Browse, Manuel Dall’Osto, Louis Marelle, Jeremie Mouginot, Jennifer G. Murphy, Daiki Nomura, Kerri A. Pratt, Megan D. Willis, Paul Zieger, Jon Abbatt, Thomas A. Douglas, Maria Cristina Facchini, James France, Anna E. Jones, Kitae Kim, Patricia A. Matrai, V. Faye McNeill, Alfonso Saiz-Lopez, Paul Shepson, Nadja Steiner, Kathy S. Law, Steve R. Arnold, Bruno Delille, Julia Schmale, Jeroen E. Sonke, Aurélien Dommergue, Didier Voisin, Megan L. Melamed, Jessica Gier, Institut des Géosciences de l’Environnement (IGE), Institut de Recherche pour le Développement (IRD)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), TROPO - LATMOS, Laboratoire Atmosphères, Milieux, Observations Spatiales (LATMOS), Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS), Department of Atmospheric and Oceanic Sciences [Los Angeles] (AOS), University of California [Los Angeles] (UCLA), University of California-University of California, UCLA Joint Institute for Regional Earth System Science and Engineering (JIFRESSE), University of California-University of California-NASA, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Laboratory of Environmental Chemistry [Villigen] (LUC), Paul Scherrer Institute (PSI), Department of Oceanography [Cape Town], University of Cape Town, Geography and Environmental Science [Cornwall], University of Exeter, Biologia Marina i Oceanografia [Barcelona], Instituto de Ciencias del Mar de Barcelona (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Earth System Science [Irvine] (ESS), University of California [Irvine] (UCI), Department of Chemistry [University of Toronto], University of Toronto, Faculty of Fisheries Sciences [Hakodate], Hokkaido University [Sapporo, Japan], Arctic Research Center [Sapporo], Department of Earth and Environmental Sciences [Ann Arbor], University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, Department of Chemistry [Ann Arbor], Lawrence Berkeley National Laboratory [Berkeley] (LBNL), Department of Environmental Science and Analytical Chemistry [Stockholm] (ACES), Stockholm University, Bolin Centre for Climate Research, ERDC Cold Regions Research and Engineering Laboratory (CRREL), USACE Engineer Research and Development Center (ERDC), Istituto di Scienze dell'Atmosfera e del Clima [Bologna] (ISAC), Consiglio Nazionale delle Ricerche (CNR), Department of Earth Sciences [Egham], Royal Holloway [University of London] (RHUL), Korea Polar Research Institute (KOPRI), Bigelow Laboratory for Ocean Sciences, Department of Chemical Engineering [New York], Columbia University [New York], Instituto de Química Física Rocasolano (IQFR), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Department of Chemistry [West Lafayette], Purdue University [West Lafayette], Department of Earth, Atmospheric, and Planetary Sciences [West Lafayette] (EAPS), School of Marine and Atmospheric Sciences [Stony Brook] (SoMAS), Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), Institute of Ocean Sciences [Sidney] (IOS), Fisheries and Oceans Canada (DFO), Institute for Climate and Atmospheric Science [Leeds] (ICAS), School of Earth and Environment [Leeds] (SEE), University of Leeds-University of Leeds, Unité d'Océanographie Chimique, Interfacultary Center for Marine Research (MARE), Université de Liège-Université de Liège, Laboratory of Atmospheric Chemistry [Paul Scherrer Institute] (LAC), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Géosciences Environnement Toulouse (GET), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), Cooperative Institute for Research in Environmental Sciences (CIRES), University of Colorado [Boulder]-National Oceanic and Atmospheric Administration (NOAA), Helmholtz Centre for Ocean Research [Kiel] (GEOMAR), Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut de Recherche pour le Développement (IRD)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of California (UC)-University of California (UC), University of California (UC)-University of California (UC)-NASA, University of California [Irvine] (UC Irvine), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), International Global Atmospheric Chemistry, International Arctic Science Committee, and European Commission
Subjects: Atmospheric Science, Environmental Engineering, Atmospheric chemistry, modeling chemistry, 010504 meteorology & atmospheric sciences, Environmental change, snow photochemistry, aerosol, arctic sea-ice, Earth science, Stakeholder engagement, Cryosphere, Science coordiation, 010501 environmental sciences, Biology, ice-nucleating particles, black carbon, Oceanography, 7. Clean energy, 01 natural sciences, Atmospheric Sciences, Anthropocene, Multidisciplinary approach, 14. Life underwater, photochemical production, lcsh:Environmental sciences, 0105 earth and related environmental sciences, Physics, lcsh:GE1-350, [PHYS.PHYS.PHYS-AO-PH]Physics [physics]/Physics [physics]/Atmospheric and Oceanic Physics [physics.ao-ph], [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Ecology, dome c, Chemistry, Global warming, boundary-layer, Geology, Geotechnical Engineering and Engineering Geology, Snow, nitrogen-oxides, 13. Climate action
Abstract: 15 pages, 2 figures, The cryosphere, which comprises a large portion of Earth’s surface, is rapidly changing as a consequence of global climate change. Ice, snow, and frozen ground in the polar and alpine regions of the planet are known to directly impact atmospheric composition, which for example is observed in the large influence of ice and snow on polar boundary layer chemistry. Atmospheric inputs to the cryosphere, including aerosols, nutrients, and contaminants, are also changing in the anthropocene thus driving cryosphere-atmosphere feedbacks whose understanding is crucial for understanding future climate. Here, we present the Cryosphere and ATmospheric Chemistry initiative (CATCH) which is focused on developing new multidisciplinary research approaches studying interactions of chemistry, biology, and physics within the coupled cryosphere – atmosphere system and their sensitivity to environmental change. We identify four key science areas: (1) micro-scale processes in snow and ice, (2) the coupled cryosphere-atmosphere system, (3) cryospheric change and feedbacks, and (4) improved decisions and stakeholder engagement. To pursue these goals CATCH will foster an international, multidisciplinary research community, shed light on new research needs, support the acquisition of new knowledge, train the next generation of leading scientists, and establish interactions between the science community and society, CATCH is sponsored by the International Global Atmospheric Chemistry (IGAC) project igacproject.org, the International Surface Ocean – Lower Atmosphere Study (SOLAS) project solas-int.org, and the International Arctic Science Committee (IASC, iasc.info). Support for CATCH activities has been provided by the French Chantier Arctique Project Pollution in the Arctic System (PARCS). This work was supported by the H2020 ERA-PLANET (689443) iCUPE project

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