Author: "Bowler, Chris" / Topic: fungi - Searchworks@Jio Institute Digital Library Search Results

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1. Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems

Author: Richter, Daniel J., Watteaux, Romain, Vannier, Thomas, Leconte, Jade, Frémont, Paul, Reygondeau, Gabriel, Maillet, Nicolas, Henry, Nicolas, Benoit, Gaëtan, da Silva, Ophélie, Delmont, Tom O., Fernández-Guerra, Antonio, Suweis, Samir, Narci, Romain, Berney, Cedric, Eveillard, Damien, Gavory, Frederick, Guidi, Lionel, Labadie, Karine, Mahieu, Eric, Poulain, Julie, Romac, Sarah, Roux, Simon, Dimier, Céline, Kandels‐Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Oceans, Tara, Pesant, Stéphane, Aury, Jean-Marc, Brum, Jennifer R., Lemaitre, Claire, Pelletier, Eric, Bork, Peer, Sunagawa, Shinichi, Lombard, Fabien, Karp-Boss, Lee, Bowler, Chris, Sullivan, Matthew B., Karsenti, Eric, Mariadassou, Mahendra, Probert, Ian, Peterlongo, Pierre, Wincker, Patrick, Vargas, Colomban de, Ribera d’Alcalà, Maurizio, Iudicone, Daniele, Jaillon, Olivier, Tara Oceans Coordinators, Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Centre National de Séquençage (France), National Fund for Scientific Research (Belgium), Stazione Zoologica Anton Dohrn, Università degli Studi di Milano, Université Paris Sciences & Lettres, Agence Nationale de la Recherche (France), National Science Foundation (US), Veolia Foundation, Région Bretagne, World Courier, Illumina, Cap L’Orient, Fondation EDF, Fondation pour la Recherche sur la Biodiversité, Fondation Prince Albert II de Monaco, Ministère de l'Europe et des Affaires étrangères (France), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut 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)), University of British Columbia (UBC), Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Max Planck Institute for Marine Microbiology, Max-Planck-Gesellschaft, Dipartimento di Fisica e Astronomia 'Galileo Galilei', Università degli Studi di Padova = University of Padua (Unipd), Consorzio Nazionale Interuniversitario per le Scienze FIsiche della Materia (CNISM), Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), 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), 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), Institut de Biologie François JACOB (JACOB), Ohio State University [Columbus] (OSU), 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), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Scalable, Optimized and Parallel Algorithms for Genomics (GenScale), Inria Rennes – Bretagne Atlantique, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-GESTION DES DONNÉES ET DE LA CONNAISSANCE (IRISA-D7), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes 1 (UR1), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut de Recherche en Informatique et Systèmes Aléatoires (IRISA), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), European Molecular Biology Laboratory [Heidelberg] (EMBL), University of Maine, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Fédération de recherche de Roscoff (FR2424), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), French National Research Agency (ANR)HYDROGEN/ANR-14CE23-0001, National Science Foundation (NSF)OCE-1536989, OCE-1829831, Commissariat a l'Energie Atomique et aux Energies Alternatives, Graphene Flagship, European Project: 634486,H2020,H2020-BG-2014-2,INMARE(2015), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Adaptation et diversité en milieu marin (AD2M), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-Institut National de Recherche en Informatique et en Automatique (Inria)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Universita degli Studi di Padova, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Bretagne Sud (UBS)-École normale supérieure - Rennes (ENS Rennes)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Centre de Mathématiques et de Leurs Applications (CMLA), École normale supérieure - Cachan (ENS Cachan)-Centre National de la Recherche Scientifique (CNRS), 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)-Institut Pasteur [Paris], Infectiologie Santé Publique (ISP-311), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Institut Pprime (PPRIME), Université de Poitiers-ENSMA-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National de Recherche en Informatique et en Automatique (Inria)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-CentraleSupélec-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Bretagne Sud (UBS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), and Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1)
Subjects: 010504 meteorology & atmospheric sciences, Biogeography, Oceans and Seas, Context (language use), 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, plankton biogeography, genomics, Ecosystem, genetics, 14. Life underwater, microbial oceanography, 030304 developmental biology, 0105 earth and related environmental sciences, Seascape, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, 0303 health sciences, metagenomics, General Immunology and Microbiology, Geography, General Neuroscience, Ocean current, fungi, Community structure, General Medicine, 15. Life on land, Plankton, Oceanography, 13. Climate action, Metagenomics, metabarcoding, ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the ‘seascape’) by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton., We thank the commitment of the following people and sponsors who made this expedition possible: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Paris Sciences et Lettres (PSL) Research University (ANR-11-IDEX-0001–02), the French Government ANR (projects FRANCE GENOMIQUE/ANR-10-INBS-09, MEMO LIFE/ANR-10-LABX-54, POSEIDON/ANR-09-BLAN-0348, PROMETHEUS/ANR-09-PCS-GENM-217, MAPPI/ANR-2010-COSI-004, TARA-GIRUS/ANR-09-PCS-GENM-218), US NSF grant DEB-1031049, FWO, BIO5, Biosphere 2, Agnès b., the Veolia Environment Foundation, Région 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. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. The bulk of genomic computations were performed using the Airain HPC machine provided through GENCI- [TGCC/CINES/IDRIS] (grants t2011076389, t2012076389, t2013036389, t2014036389, t2015036389 and t2016036389). We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who granted us sampling permissions.
Published: 2022

2. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela, Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea, Picheral, Marc, Henry, Nicolas, Acinas, Silvia, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Gorsky, Gabriel, Guidi, Lionel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sullivan, Matthew, Sunagawa, Shinichi, Wincker, Patrick, Stemmann, Lars, Lombard, Fabien, 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), 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), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), and Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC)
Subjects: [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, [SDU]Sciences of the Universe [physics], fungi
Abstract: International audience; Abstract Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO 2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
Published: 2021

3. Environmental vulnerability of the global ocean epipelagic plankton community interactome

Author: Chaffron, Samuel, Delage, Erwan, Budinich, Marko, Vintache, Damien, Henry, Nicolas, Nef, Charlotte, Ardyna, Mathieu, Zayed, Ahmed A., Junger, Pedro C., Galand, Pierre E., Lovejoy, Connie, Murray, Alison, Sarmento, Hugo, Tara Oceans Coordinators, Acinas, Silvia G., Babin, Marcel, Iudicone, Daniele, Jaillon, Olivier, Karsenti, Eric, Wincker, Patrick, Karp-Boss, Lee, Sullivan, Matthew B., Bowler, Chris, Vargas, Colomban de, Eveillard, Damien, Laboratoire des Sciences du Numérique de Nantes (LS2N), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-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), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut 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), 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), 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), Agencia Estatal de Investigación (España), Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Helmut Horten Foundation, Ministerio de Ciencia, Innovación y Universidades (España), European Research Council, European Commission, Fundação de Amparo à Pesquisa do Estado de São Paulo, Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), and Natural Sciences and Engineering Research Council of Canada
Subjects: fungi, [SDE]Environmental Sciences, sense organs
Abstract: This article is contribution number 120 of Tara Oceans.-- 15 pages, 4 figures, supplementary materials https://www.science.org/doi/suppl/10.1126/sciadv.abg1921/suppl_file/sciadv.abg1921_SM.pdf.-- Data and materials availability: Data described here are available at the EBI under the project identifiers PRJEB402 and PRJEB7988 and at PANGAEA (96). All data (raw abundance matrices and interactome graphML files) needed to evaluate the conclusions of the paper are available in the Supplementary Materials. A web server for exploring and searching the global ocean interactome is available at https://saas.ls2n.fr/Tara-Oceans-interactome/, Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network—the community interactome—and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change, 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), PSL* Research University (ANR-11-IDEX-0001-02), ETH and the Helmut Horten Foundation, MEXT/JSPS/KAKENHI (projects 16H06429, 16K21723, 16H06437, and 18H02279), the Spanish Ministry of Economy and Competitiveness (project MAGGY-CTM2017-87736-R), ERC Advanced Award Diatomic (grant agreement 835067 to CB), the CNRS MITI through the interdisciplinary program Modélisation du Vivant (GOBITMAP grant to SC), and the H2020 European Commission project AtlantECO (award number 862923). […]. E.D. is supported by the RFI ATLANSTIC2020 grant (PROBIOSTIC grant to DE). M.Bu. received financial support from the French Facility for Global Environment (FFEM) as part of the “Ocean Plankton, Climate and Development” project. P.C.J. was supported by Fundação de Amparo à Pesquisa do Estado de São Paulo, FAPESP (PhD grant 2017/26786-1). H.S. is supported by a Brazilian Research Council (CNPq) productivity grant (process 309514/2017-7) and FAPESP (grant 2014/14139-3). […] Additional funding from the Natural Sciences and Engineering Council (NSERC) Canada Discovery program is gratefully acknowledged., With the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)
Published: 2021

4. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Costa Brandao, Manoela, Benedetti, Fabio, Martini, Séverine, Dodji Soviadan, Yawouvi, Irisson, Jean-olivier, Romagnan, Jean-baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laetitia, Freire, Andrea S, Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-boss, Lee, Henry, Nicolas, De Vargas, Colomban, Sullivan, Matthew B, Tara Oceans Consortium Coordinators, Stemmann, Lars, Lombard, Fabien, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Cochrane, Guy, Grimsley, Nigel, Hingamp, Pascal, Ludicone, Daniele, Jaillon, Olivier, Kandels, Stefanie, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poultron, Nicole, Pesant, Stephane, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Sunagawa, Shinichi, Winckler, Patrick, 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), 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), Écologie et Modèles pour l'Halieutique (IFREMER EMH), Institut Français de Recherche pour l'Exploitation de la Mer - Atlantique (IFREMER Atlantique), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Universidade Federal de Santa Catarina = Federal University of Santa Catarina [Florianópolis] (UFSC), Centre National de la Recherche Scientifique (France), European Molecular Biology Laboratory, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fonds Français pour l'Environnement Mondial, European Commission, and Agencia Estatal de Investigación (España)
Subjects: Multidisciplinary, Ecology, Abundance (ecology), FOS: Biological sciences, Ectotherm, fungi, Environmental science, Climate model, Ecosystem, Plankton, Zooplankton, Copepod, Latitude
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump, This article is contribution number 121 of Tara Oceans.-- 19 pages, 6 figures, 2 tables, supplementary information https://doi.org/10.1038/s41598-021-94615-5.-- Data availability: Median ESD and abundance values by zooplankton groups are available at https://doi.org/10.17632/nwvjwccgvh.1. Zooplankton imaging datasets from the Tara Oceans expeditions are available through the collaborative web Ecotaxa application and repository under the addresses: https://ecotaxa.obs-vlfr.fr/prj/377, https://ecotaxa.obs-vlfr.fr/prj/2245, https://ecotaxa.obs-vlfr.fr/prj/378 for the WP2 net; https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for the Bongo net; https://ecotaxa.obs-vlfr.fr/prj/415, https://ecotaxa.obs-vlfr.fr/prj/409, https://ecotaxa.obs-vlfr.fr/prj/408, https://ecotaxa.obs-vlfr.fr/prj/411, https://ecotaxa.obs-vlfr.fr/prj/412 for the Régent net. Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582, Tara Oceans (which 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 (http://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). M.C.B. acknowledges postdoc fellowships from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES) (99999.000487/2016-03) and the Fonds Français pour l'Environnement Mondial (FFEM). F.B. received support from ETH Zürich and from the European Union’s Horizon 2020 research and innovation program under grant agreement n°SEP-210591007, With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)
Published: 2021

5. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Stemmann, Lars, and Lombard, Fabien
Subjects: Ocean sciences, Ecology, fungi, Article
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump.
Published: 2021

6. Complex Response of the Chlorarachniophyte Bigelowiella natans to Iron Availability

Author: Kotabova, Eva, Malych, Ronald, Pierella Karlusich, Juan José, Kazamia, Elena, Eichner, Meri, Mach, Jan, Lesuisse, Emmanuel, Bowler, Chris, Prášil, Ondřej, and Sutak, Robert
Subjects: Molecular Biology and Physiology, metagenomics, iron, metatranscriptomics, photosynthesis, proteomics, fungi, phytoplankton, Microbiology, QR1-502, Bigelowiella natans, Research Article
Abstract: Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes., The productivity of the ocean is largely dependent on iron availability, and marine phytoplankton have evolved sophisticated mechanisms to cope with chronically low iron levels in vast regions of the open ocean. By analyzing the metabarcoding data generated from the Tara Oceans expedition, we determined how the global distribution of the model marine chlorarachniophyte Bigelowiella natans varies across regions with different iron concentrations. We performed a comprehensive proteomics analysis of the molecular mechanisms underpinning the adaptation of B. natans to iron scarcity and report on the temporal response of cells to iron enrichment. Our results highlight the role of phytotransferrin in iron homeostasis and indicate the involvement of CREG1 protein in the response to iron availability. Analysis of the Tara Oceans metagenomes and metatranscriptomes also points to a similar role for CREG1, which is found to be widely distributed among marine plankton but to show a strong bias in gene and transcript abundance toward iron-deficient regions. Our analyses allowed us to define a new subfamily of the CobW domain-containing COG0523 putative metal chaperones which are involved in iron metabolism and are restricted to only a few phytoplankton lineages in addition to B. natans. At the physiological level, we elucidated the mechanisms allowing a fast recovery of PSII photochemistry after resupply of iron. Collectively, our study demonstrates that B. natans is well adapted to dynamically respond to a changing iron environment and suggests that CREG1 and COG0523 are important components of iron homeostasis in B. natans and other phytoplankton. IMPORTANCE Despite low iron availability in the ocean, marine phytoplankton require considerable amounts of iron for their growth and proliferation. While there is a constantly growing knowledge of iron uptake and its role in the cellular processes of the most abundant marine photosynthetic groups, there are still largely overlooked branches of the eukaryotic tree of life, such as the chlorarachniophytes. In the present work, we focused on the model chlorarachniophyte Bigelowiella natans, integrating physiological and proteomic analyses in culture conditions with the mining of omics data generated by the Tara Oceans expedition. We provide unique insight into the complex responses of B. natans to iron availability, including novel links to iron metabolism conserved in other phytoplankton lineages.
Published: 2021

7. Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics

Author: Delmont, Tom O., Gaia, Morgan, Hinsinger, Damien D., Fremont, Paul, Vanni, Chiara, Fernandez Guerra, Antonio, Eren, A. Murat, Kourlaiev, Artem, d'Agata, Leo, Clayssen, Quentin, Villar, Emilie, Labadie, Karine, Cruaud, Corinne, Poulain, Julie, Da Silva, Corinne, Wessner, Marc, Noel, Benjamin, Aury, Jean-Marc, de Vargas, Colomban, Bowler, Chris, Karsenti, Eric, Pelletier, Eric, Wincker, Patrick, and Jaillon, Olivier
Subjects: fungi
Abstract: Marine planktonic eukaryotes play a critical role in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years. Cover Navigating on the map of plankton genomics with Tara Oceans and anvi'o: a comprehensive genome-resolved metagenomic survey dedicated to eukaryotic plankton. ![Figure][1] Competing Interest Statement The authors have declared no competing interest. [1]: pending:yes
Published: 2021

8. Environmental vulnerability of the global ocean epipelagic plankton community interactome

Author: Chaffron, Samuel, Delage, Erwan, Budinich, Marko, Vintache, Damien, Henry, Nicolas, Nef, Charlotte, Ardyna, Mathieu, Zayed, Ahmed A., Junger, Pedro C., Galand, Pierre E., Lovejoy, Connie, Murray, Alison E., Sarmento, Hugo, Acinas, Silvia G., Babin, Marcel, Iudicone, Daniele, Jaillon, Olivier, Karsenti, Eric, Wincker, Patrick, Karp-Boss, Lee, Sullivan, Matthew B., Bowler, Chris, de Vargas, Colomban, Eveillard, Damien, Galand, Pierre, 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, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID, 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Earth System Science [Stanford] (ESS), Stanford EARTH, Stanford University-Stanford University, Federal University of São Carlos (UFSCar), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), 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 de Biologie Intégrative et des Systèmes [Québec] (IBIS), Division of Earth and Ecosystem Sciences (DEES), Desert Research Institute (DRI), 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), Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Takuvik Joint International Laboratory ULAVAL-CNRS, Université Laval [Québec] (ULaval)-Centre National de la Recherche Scientifique (CNRS), 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), Université de Nantes (UN), 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 Microbiology [Columbus], Ohio State University [Columbus] (OSU), Department of Marine Biology and Oceanography, 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), 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), University of Maine, Adaptation et diversité en milieu marin (AD2M), 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), European Project: 862923,AtlantECO, European Project: 835067,DIATOMIC, IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-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), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Adaptation et diversité en milieu marin (ADMM), and Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR)
Subjects: [SDE] Environmental Sciences, changement climatique, Ecology, Systems Biology, fungi, SciAdv r-articles, réseau écologique, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], plancton océanique, [SDE]Environmental Sciences, Bio-informatique, sense organs, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, Research Articles, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, ComputingMilieux_MISCELLANEOUS, Research Article, modélisation
Abstract: A global photic-ocean plankton ecological network predicts distinct vulnerabilities to environmental change across marine biomes., Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network—the community interactome—and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
Published: 2021

9. Evolutionary analysis of DNA methyltransferases in microeukaryotes: Insights from the model diatom Phaeodactylum tricornutum

Author: Hoguin, Antoine, Ait, Ouardia, Bowler, Chris, Genovesio, Auguste, Rocha Jimenez Vieira, Fabio, TIRICHINE, LEILA, Unité de fonctionnalité et ingénierie de protéines (UFIP), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), and Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], fungi, ComputingMilieux_MISCELLANEOUS
Abstract: Cytosine DNA methylation is an important epigenetic mark in eukaryotes that is involved in the transcriptional control of mainly transposable elements in mammals, plants, and fungi. Eukaryotes encode a diverse set of DNA methyltransferases that were iteratively acquired and lost during evolution. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes that include the main phytoplankton classes such as diatoms and dinoflagellates. However, little is known about the diversity of DNA methyltransferases and their role in the deposition and maintenance of DNA methylation in microalgae. We performed a phylogenetic analysis of DNA methyltransferase families found in marine microeukaryotes and show that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes family revisiting previously established phylogenies. Furthermore, we reveal a novel group of DNMTs with three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrate that the loss of the DNMT5 gene correlates with a global depletion of DNA methylation and overexpression of transposable elements in the model diatom Phaeodactylum tricornutum . The study provides a pioneering view of the structure and function of a DNMT family in the SAR supergroup.
Published: 2021

10. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author: Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, de Vargas, Colomban, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie, European Commission, and Ministerio de Economía y Competitividad (España)
Subjects: Geography, Oceans and Seas, fungi, temperature, Tara Oceans, high-throughput sequencing, Biodiversity, Models, Theoretical, Plankton, Article, climate warming, latitudinal diversity gradient, plankton functional groups, trans-kingdom diversity, macroecology, high-throughput imaging, Seawater, human activities, Phylogeny
Abstract: 35 pages, 18 figures, 1 table, supplementary information https://doi.org/10.1016/j.cell.2019.10.008.-- Raw reads of Tara Oceans are deposited at the European Nucleotide Archive (ENA). In particular, newly released 18S rRNA gene metabarcoding reads are available under the number ENA: PRJEB9737. ENA references for the metagenomics reads corresponding to the size fraction < 0.22 μm (for prokaryotic viruses) analyzed in this study are included in Gregory et al. (2019); see their Table S3. ENA references for the metagenomics reads corresponding to the size fraction 0.22-1.6/3 μm (for prokaryotes and giruses) correspond to Salazar et al. (2019) (see https://zenodo.org/record/3473199). Imaging datasets from the nets are available through the collaborative web application and repository EcoTaxa (Picheral et al., 2017) under the address https://ecotaxa.obs-vlfr.fr/prj/412 for regent data, within the 3 projects https://ecotaxa.obs-vlfr.fr/prj/397, https://ecotaxa.obs-vlfr.fr/prj/398, https://ecotaxa.obs-vlfr.fr/prj/395 for bongo data, and within the 2 projects https://ecotaxa.obs-vlfr.fr/prj/377 and https://ecotaxa.obs-vlfr.fr/prj/378 for WP2 data. A table with Shannon values and multiple samples identifiers, plus a table with flow cytometry data split in six groups are available (https://doi.org/10.17632/p9r9wttjkm.1). Contextual data from the Tara Oceans expedition, including those that are newly released from the Arctic Ocean, are available at https://doi.org/10.1594/PANGAEA.875582, The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation, Tara Oceans (which includes both the Tara Oceans and Tara Oceans Polar Circle expeditions) would not exist without the leadership of the Tara Ocean 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), the European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Ministry of Research, and the French Government “Investissements d’Avenir” programs OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), the PSL∗ Research University (ANR-11-IDEX-0001-02), as well as EMBRC-France (ANR-10-INBS-02). Funding for the collection and processing of the Tara Oceans data set was provided by NASA Ocean Biology and Biogeochemistry Program under grants NNX11AQ14G, NNX09AU43G, NNX13AE58G, and NNX15AC08G (to the University of Maine); the Canada Excellence research chair on remote sensing of Canada’s new Arctic frontier; and the Canada Foundation for Innovation. We also thank agnès b. and Etienne Bourgois, the Prince Albert II de Monaco Foundation, the Veolia Foundation, Region Bretagne, Lorient Agglomeration, Serge Ferrari, Worldcourier, and KAUST for support and commitment. The global sampling effort was enabled by countless scientists and crew who sampled aboard the Tara from 2009–2013, and we thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expeditions. We are also grateful to the countries who graciously granted sampling permission. We thank Stephanie Henson for providing ocean carbon export data and are also grateful to the other researchers who kindly made their data available. We thank Juan J. Pierella-Karlusich for advice regarding single-copy genes. C.d.V. and N.H. thank the Roscoff Bioinformatics platform ABiMS (http://abims.sb-roscoff.fr) for providing computational resources. C.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program (grant agreement 835067) as well as the Radcliffe Institute of Advanced Study at Harvard University for a scholar’s fellowship during the 2016-2017 academic year. M.B.S. thanks the Gordon and Betty Moore Foundation (award 3790) and the National Science Foundation (awards OCE#1536989 and OCE#1829831) as well as the Ohio Supercomputer for computational support. S.G.A. thanks the Spanish Ministry of Economy and Competitiveness (CTM2017-87736-R), and J.M.G. is grateful for project RT2018-101025-B-100. F.L. thanks the Institut Universitaire de France (IUF) as well as the EMBRC platform PIQv for image analysis. M.C.B., D.S., and J.R. received financial support from the French Facility for Global Environment (FFEM) as part of the “Ocean Plankton, Climate and Development” project. M.C.B. also received financial support from the Coordination for the Improvement of Higher Education Personnel of Brazil (CAPES 99999.000487/2016-03)
Published: 2019

11. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author: Ibarbalz, Federico M, Henry, Nicolas, Brandao, Manoela C, Martini, Verine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M, Gregory, Ann C, Mahe, Frederic, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Saez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A, Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Celine, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stephane, Acinas, Silvia G, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy, de Vargas, Colomban, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Bopp, Laurent, Lombard, Fabien, and Zinger, Lucie
Subjects: Biochemistry & Molecular Biology, Science & Technology, CLIMATE-CHANGE, fungi, Cell Biology, ECOLOGY, LATITUDINAL GRADIENTS, OCEAN, PHYTOPLANKTON, PATTERNS, DISTRIBUTIONS, BIODIVERSITY, Life Sciences & Biomedicine, TEMPERATURE, human activities, MICROBIAL DIVERSITY
Abstract: The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. VIDEO ABSTRACT. ispartof: CELL vol:179 issue:5 pages:1084-+ ispartof: location:United States status: published
Published: 2019

12. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

Author: Rastogi, Achal, Maheswari, Uma, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Maumus, Florian, Kustka, Adam, McCarthy, James, Allen, Andy E., Kersey, Paul, Bowler, Chris, Tirichine, Leila, TIRICHINE, LEILA, 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), Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, ERC Advanced Award 'Diatomite', Louis D Foundation of the Institut de France, Gordon and Betty Moore Foundation, French Government 'Investissements d'Avenir' programmes MEMO LIFE [ANR-10-LABX-54], PSL Research University [ANR-1253 11-IDEX-0001-02], and OCEANOMICS [ANR-11-BTBR-0008] : Radcliffe Institute of Advanced Study at Harvard University, National Science Foundation [NSF-OCE-0727997] : United States Department of Energy [DE-SC00006719, DE-SC0008593], Gordon and Betty Moore Foundation [GBMF3828], CNRS, MEMO LIFE PhD scholarship, EMBO Long-Term Fellowship [ALTF 1124-2014], 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)-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 Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris
Subjects: Diatoms, Proteomics, [SDE] Environmental Sciences, Models, Genetic, Gene Expression Profiling, [SDV]Life Sciences [q-bio], Science, fungi, Terminal Repeat Sequences, Molecular Sequence Annotation, [INFO] Computer Science [cs], Article, Introns, Evolution, Molecular, [SDV] Life Sciences [q-bio], [SDE]Environmental Sciences, Medicine, [INFO]Computer Science [cs], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract: International audience; Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
Published: 2018

13. A global ocean atlas of eukaryotic genes

Author: Carradec, Quentin, Pelletier, Eric, da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel, Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew, Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Weissenbach, Jean, Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut de Génomique d'Evry (IG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute for Chemical Research, Kyoto University, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Hasso Plattner Institute [Potsdam, Germany], European Molecular Biology Laboratory [Heidelberg] (EMBL), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Hawai'i [Honolulu] (UH), Ohio State University [Columbus] (OSU), European Molecular Biology Laboratory [Grenoble] (EMBL), Diversité et Interactions au sein du Plancton Océanique (DIPO), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Kyoto University [Kyoto], Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Stazione Zoologica Anton Dohrn (SZN), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-BLAN-1709,PHYTBACK,Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton(2010), ANR-09-BLAN-0348,POSEIDON(2009), ANR-09-GENM-0031,PROMETHEUS,Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans.(2009), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), European Project: 294823,EC:FP7:ERC,ERC-2011-ADG_20110310,DIATOMITE(2012), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Kyoto University, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Savelli, Bruno, Biotech - Bioressources - Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques - - OCEANOMICS2011 - ANR-11-BTBR-0008 - BTBR - VALID, Initiative d'excellence - Paris Sciences et Lettres - - PSL2010 - ANR-10-IDEX-0001 - IDEX - VALID, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, BLANC - Rétroactions écologie-climat dues à l'évolution de la taille et de la forme du phytoplancton - - PHYTBACK2010 - ANR-10-BLAN-1709 - BLANC - VALID, Blanc - - POSEIDON2009 - ANR-09-BLAN-0348 - Blanc - VALID, Génomique et biotechnologies végétales - Approches génomiques pour l?analyse de la biodiversité fonctionnelle des protistes océaniques de l?expédition Tara-Oceans. - - PROMETHEUS2009 - ANR-09-GENM-0031 - GENOM-BTV - VALID, Marine Microbial Biodiversity, Bioinformatics and Biotechnology - MICRO B3 - - EC:FP7:KBBE2012-01-01 - 2015-12-31 - 287589 - VALID, and Genome-enabled dissection of marine diatom ecophysiology - DIATOMITE - - EC:FP7:ERC2012-06-01 - 2017-05-31 - 294823 - VALID
Subjects: [SDV] Life Sciences [q-bio], [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Science, [SDV]Life Sciences [q-bio], fungi, lcsh:Q, [SDV.BID]Life Sciences [q-bio]/Biodiversity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, lcsh:Science, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: International audience; While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
Published: 2018

14. Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Author: Karp‐Boss, Lee, Wincker, Patrick, Kandels‐Lewis, Stefanie, Jaillon, Olivier, Iudicone, Daniele, Hingamp, Pascal, Grimsley, Nigel, Gorsky, Gabriel, Follows, Michael J., Vargas, Colomban, Bowler, Chris, Boss, Emmanuel, Bork, Peer, Acinas, Silvia G., Karsenti, Eric, Weissenbach, Jean, Velayoudon, Didier, Sunagawa, Shinichi, Sullivan, Matthew B., Stemmann, Lars, Speich, Sabrina, Sieracki, Mike, Sardet, Christian, Reynaud, Emmanuel G., Raes, Jeroen, Pesant, Stéphane, Ogata, Hiroyuki, Not, Fabrice, Krzic, Uros, Caputi, Luigi, Carradec, Quentin, Eveillard, Damien, Kirilovsky, Amos, Pelletier, Eric, Pierella Karlusich, Juan J., Rocha Jimenez Vieira, Fabio, Villar, Emilie, Chaffron, Samuel, Malviya, Shruti, Scalco, Eleonora, Alberti, Adriana, Aury, Jean‐Marc, Benoiston, Anne‐Sophie, Bertrand, Alexis, Biard, Tristan, Bittner, Lucie, Boccara, Martine, Brum, Jennifer R., Brunet, Christophe, Busseni, Greta, Carratalà, Anna, Claustre, Hervé, Coelho, Luis Pedro, Colin, Sébastien, D'Aniello, Salvatore, Da Silva, Corinne, Del Core, Marianna, Doré, Hugo, Gasparini, Stéphane, Kokoszka, Florian, Jamet, Jean‐Louis, Lejeusne, Christophe, Lepoivre, Cyrille, Lescot, Magali, Lima‐Mendez, Gipsi, Lombard, Fabien, Lukeš, Julius, Maillet, Nicolas, Madoui, Mohammed‐Amin, Martinez, Elodie, Mazzocchi, Maria Grazia, Néou, Mario B., Paz‐Yepes, Javier, Poulain, Julie, Ramondenc, Simon, Romagnan, Jean‐Baptiste, Roux, Simon, Salvagio Manta, Daniela, Sanges, Remo, Sprovieri, Mario, Taillandier, Vincent, Tanaka, Atsuko, Tirichine, Leila, Trottier, Camille, Uitz, Julia, Veluchamy, Alaguraj, Veselá, Jana, Vincent, Flora, Yau, Sheree, Searson, Sarah, Dimier, Céline, Picheral, Marc, Guidi, Lionel, Sordino, Paolo, Tagliabue, Alessandro, Zingone, Adriana, Garczarek, Laurence, d'Ortenzio, Fabrizio, Testor, Pierre, d'Alcalà, Maurizio Ribera, Stazione Zoologica Anton Dohrn (SZN), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Combinatoire et Bioinformatique (LS2N - équipe COMBI), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (ADMM), Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne = University of Lausanne (UNIL), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Istituto per la Microelettronica e Microsistemi [Catania] (IMM), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Department of Oceanography and Coastal Sciences, Louisiana State University (LSU), Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Instituto de Engenharia de Sistemas e Computadores (INESC), Departament de Genetica, Facultat de Biologia, Universitat de Barcelona (UB), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Czech Academy of Sciences [Prague] (CAS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Istituto per l'Ambiente Marino Costiero, Sezione Ecologia Marina Integrata, European Molecular Biology Laboratory [Heidelberg] (EMBL), National Cardiovascular Center, Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography [Honolulu], University of Hawai‘i [Mānoa] (UHM), University of Maine, Department of Earth and Environment [Boston], Boston University [Boston] (BU), Department of Earth Ocean and Ecological Sciences [Liverpool], University of Liverpool, Variabilité de l'Océan et de la Glace de mer (VOG), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, National Science Foundation [Arlington] (NSF), DVIPC, ANR-17-CE02-0014,CINNAMON,Analyse multi-échelle de l'adaptation à la carence en Fer chez un organisme clé du phytoplancton marin, dans un contexte de changement global(2017), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Combinatoire et Bioinformatique (COMBI), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Lausanne (UNIL), Consiglio Nazionale delle Ricerche (CNR), Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Consiglio Nazionale delle Ricerche [Roma] (CNR), Observatoire océanologique de Villefranche-sur-mer (OOVM), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), ECOlogy of MArine Plankton (ECOMAP), Vrije Universiteit Brussel (VUB), Department of Structural Biology, Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Gordon and Betty Moore Foundation, Fondation Prince Albert II de Monaco, National Science Foundation (US), Stazione Zoologica Anton Dohrn, National Fund for Scientific Research (Belgium), Centre National de la Recherche Scientifique (France), Région Bretagne, and JAMET, Jean-Louis
Subjects: 0106 biological sciences, Atmospheric Science, PROCHLOROCOCCUS, 010504 meteorology & atmospheric sciences, Iron fertilization, species networks, DIVERSITY, PROTEIN, Oceanography, 01 natural sciences, CARBON, Settore BIO/13 - Biologia Applicata, oxidative stress, Meteorology & Atmospheric Sciences, Geosciences, Multidisciplinary, OXIDATIVE STRESS, ComputingMilieux_MISCELLANEOUS, GENE-EXPRESSION, General Environmental Science, Global and Planetary Change, LIMITATION, Ecology, IN-SITU, system biology, Geology, Plankton, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], iron response, meta-omics, MARINE-PHYTOPLANKTON, in-situ, limitation, Physical Sciences, Life Sciences & Biomedicine, Biogeochemical cycle, PACIFIC, Environmental Sciences & Ecology, Context (language use), prochlorococcus, Biology, Zooplankton, marine-phytoplankton, diversity, Atmospheric Sciences, Phytoplankton, pacific, Genetics, Environmental Chemistry, Ecosystem, 14. Life underwater, Life Below Water, 0105 earth and related environmental sciences, Science & Technology, 010604 marine biology & hydrobiology, carbon, fungi, Pelagic zone, gene-expression, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, Geochemistry, Cardiovascular and Metabolic Diseases, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, protein, Environmental Sciences, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 29 pages, 9 figures, supporting information https://doi.org/10.1029/2018GB006022, Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio‐oceanographic and bio‐omics data sets from Tara Oceans in the context of the iron products from two state‐of‐the‐art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large‐scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular Groupement de Recherche GDR3280, the Mission Pour l'Interdisciplinarité – Project MEGALODOM, and the Fédération de Recherche GO‐SEE FR2022), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, the French Government “Investissements d'Avenir” programs Oceanomics (ANR‐11‐BTBR‐0008), MEMO LIFE (ANR‐10‐LABX‐54), PSL* Research University (ANR‐11‐IDEX‐0001‐02), and FRANCE GENOMIQUE (ANR‐10‐INBS‐09), Fund for Scientific Research – Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects “PHYTBACK/ANR‐2010‐1709‐01,” POSEIDON/ANR‐09‐BLAN‐0348, PROMETHEUS/ANR‐09‐PCS‐GENM‐217, TARA‐GIRUS/ANR‐09‐PCS‐GENM‐218, SAMOSA/ANR‐13‐ADAP‐0010, CINNAMON/ANR‐17‐CE02‐0014‐01), EU FP7 (MicroB3/No. 287589), ERC Advanced Grant Award (Diatomite: 294823), the LouisD foundation of the Institut de France, a Radcliffe Institute Fellowship from Harvard University to C. B., JSPS/MEXT KAKENHI (26430184, 16H06437, and 16KT0020), The Canon Foundation (203143100025), Gordon and Betty Moore Foundation (award #3790) and the US National Science Foundation (awards OCE#1536989 and OCE#1829831) to MBS, agnès b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L'Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Fonds Français pour l'Environnement Mondial, the TARA schooner and its captain and crew.
Published: 2019

15. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author: Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis P., Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar Guiral, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Acinas, Silvia G., Tara Oceans Coordinators, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy R., de Vargas, Colomban, Follows, Michael J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Pelletier, Eric, Bopp, Laurent, Lombard, Fabien, and Zinger, Lucie
Subjects: fungi, human activities
Abstract: The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation. ISSN:0092-8674 ISSN:1097-4172
Published: 2019

16. 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

17. Progressive and Biased Divergent Evolution Underpins the Origin and Diversification of Peridinin Dinoflagellate Plastids

Author: Dorrell, Richard G, Klinger, Christen M, Newby, Robert J, Butterfield, Erin R, Richardson, Elisabeth, Dacks, Joel B, Howe, Christopher J, Nisbet, Ellen R, Bowler, Chris, Howe, Christopher [0000-0002-6975-8640], Nisbet, Ellen [0000-0003-4487-196X], and Apollo - University of Cambridge Repository
Subjects: algae, fungi, Genome, Plastid, food and beverages, Genetic Variation, Sequence Analysis, DNA, chloroplast genomes, Biological Evolution, Carotenoids, MMETSP, poly(U) tail, Evolution, Molecular, DNA, Algal, alveolates, Dinoflagellida, Plastids, Codon, Phylogeny
Abstract: Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons. Understanding the extent of this divergent evolution has been hampered by the lack of characterized peridinin plastid sequences. We have identified over 300 previously unannotated peridinin plastid mRNAs from published transcriptome projects, vastly increasing the number of sequences available. Using these data, we have produced a well-resolved phylogeny of peridinin plastid lineages, which uncovers several novel relationships within the dinoflagellates. This enables us to define changes to plastid sequences that occurred early in dinoflagellate evolution, and that have contributed to the subsequent diversification of individual dinoflagellate clades. We find that the origin of the peridinin dinoflagellates was specifically accompanied by elevations both in the overall number of substitutions that occurred on plastid sequences, and in the Ka/Ks ratio associated with plastid sequences, consistent with changes in selective pressure. These substitutions, alongside other changes, have accumulated progressively in individual peridinin plastid lineages. Throughout our entire dataset, we identify a persistent bias toward non-synonymous substitutions occurring on sequences encoding photosystem I subunits and stromal regions of peridinin plastid proteins, which may have underpinned the evolution of this unusual organelle.
Published: 2018
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18. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author: Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis Pedro, Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Dimier, Céline, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Babin, Marcel, Boss, Emmanuel, Iudicone, Daniele, Jaillon, Olivier, Acinas, Silvia G., Ogata, Hiroyuki, Pelletier, Eric, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Bopp, Laurent, de Vargas, Colomban, Karp-Boss, Lee, Wincker, Patrick, Lombard, Fabien, Bowler, Chris, Zinger, Lucie, Bork, Peer, Cochrane, Guy, Follows, Mick, Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Karsenti, Eric, Not, Fabrice, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, and Speich, Sabrina
Subjects: latitudinal diversity gradient, fungi, plankton functional groups, trans-kingdom diversity, macroecology, high-throughput imaging, temperature, Tara Oceans, put sequencing, high-through, human activities, climate warming
Abstract: The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.
Published: 2019

19. Plastid Transcript Editing across Dinoflagellate Lineages Shows Lineage-Specific Application but Conserved Trends

Author: Klinger, Christen M, Paoli, Lucas, Newby, Robert J, Wang, Matthew Yu-Wei, Carroll, Hyrum D, Leblond, Jeffrey D, Howe, Christopher J, Dacks, Joel B, Bowler, Chris, Cahoon, Aubery Bruce, Dorrell, Richard G, Richardson, Elisabeth, Howe, Christopher [0000-0002-6975-8640], and Apollo - University of Cambridge Repository
Subjects: Evolution, Molecular, Genome, fungi, Dinoflagellida, Plastids, RNA Editing, Symbiosis, Conserved Sequence, Phylogeny
Abstract: Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.
Published: 2018
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20. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms

Author: Kazamia, Elena, Sutak, Robert, Paz-Yepes, Javier, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Mach, Jan, Morrissey, Joe, Leon, Sébastien, Lam, France, Pelletier, Eric, Camadro, Jean-Michel, Bowler, Chris, Lesuisse, Emmanuel, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Parasitology, Faculty of Science, Charles University in Prague, Faculty of Science, Charles University in Prague, Institut Jacques Monod (IJM (UMR_7592)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-11-BSV7-0018,PHYTOIRON,Mechanisms of iron assimilation in marine micro-algae(2011), ANR-16-CE01-0008,PHYTOMET,Étude métallomique du phytoplancton: effet de l'acidification des océans sur la séquestration du fer(2016), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011), European Project: 275289,EC:FP7:PEOPLE,FP7-PEOPLE-2010-IOF,GENMARPHYTO(2012), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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)-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)-École normale supérieure - Paris (ENS-PSL), 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), ANR-10-IDEX-0001-02/10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), and ANR-11-BTBR-0008/11-BTBR-0008,OCEANOMICS,Biotechnologies et bioressources pour la valorisation des écosystèmes marins planctoniques(2011)
Subjects: Diatoms, Aquatic Organisms, Chloroplasts, Iron, fungi, SciAdv r-articles, Siderophores, Oceanography, Microbiology, Endocytosis, Protein Transport, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Species Specificity, Gene Knockdown Techniques, Research Articles, Research Article
Abstract: We report a new strategy uncovered for iron acquisition in globally important unicellular photosynthetic organisms., Phytoplankton growth is limited in vast oceanic regions by the low bioavailability of iron. Iron fertilization often results in diatom blooms, yet the physiological underpinnings for how diatoms survive in chronically iron-limited waters and outcompete other phytoplankton when iron becomes available are unresolved. We show that some diatoms can use siderophore-bound iron, and exhibit a species-specific recognition for siderophore types. In Phaeodactylum tricornutum, hydroxamate siderophores are taken up without previous reduction by a high-affinity mechanism that involves binding to the cell surface followed by endocytosis-mediated uptake and delivery to the chloroplast. The affinity recorded is the highest ever described for an iron transport system in any eukaryotic cell. Collectively, our observations suggest that there are likely a variety of iron uptake mechanisms in diatoms besides the well-established reductive mechanism. We show that iron starvation–induced protein 1 (ISIP1) plays an important role in the uptake of siderophores, and through bioinformatics analyses we deduce that this protein is largely diatom-specific. We quantify expression of ISIP1 in the global ocean by querying the Tara Oceans atlas of eukaryotic genes and show a link between the abundance and distribution of diatom-associated ISIP1 with ocean provinces defined by chronic iron starvation.
Published: 2018

21. The epibiotic life of the cosmopolitan diatom Fragilariopsis doliolus on heterotrophic ciliates in the open ocean

Author: Vincent, Flora J., COLIN, Sébastien, Romac, Sarah, Scalco, Eleonora, Bittner, Lucie, Garcia, Yonara, Lopes, Rubens M., Dolan, John R., Zingone, Adriana, de Vargas, Colomban, Bowler, Chris, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Stazione Zoologica Anton Dohrn (SZN), Analyse des Données à Haut Débit en Génomique (ADHDG), Evolution Paris Seine, Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC), University of Sao Polo, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), and COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SDV]Life Sciences [q-bio], fungi
Abstract: International audience; Diatoms are a diverse and ecologically important group of phytoplankton. Although most species are considered free living, several are known to interact with other organisms within the plankton. Detailed imaging and molecular characterization of any such partnership is, however, limited, and an appraisal of the large-scale distribution and ecology of such consortia was never attempted. Here, observation of Tara Oceans samples from the Benguela Current led to the detection of an epibiotic association between a pennate diatom and a tintinnid ciliate. We identified the diatom as Fragilariopsis doliolus that possesses a unique feature to form barrel-shaped chains, associated with seven different genera of tintinnids including five previously undescribed associations. The organisms were commonly found together in the Atlantic and Pacific Ocean basins, and live observations of the interaction have been recorded for the first time. By combining confocal and scanning electron microscopy of individual consortia with the sequencing of high-resolution molecular markers, we analyzed their distribution in the global ocean, revealing morpho-genetically distinct tintinnid haplotypes and biogeographically structured diatom haplotypes. The diatom was among the most abundant in the global ocean. We show that the consortia were particularly prevalent in nutrient-replete conditions, rich in potential predators. These observations support the hypothesis of a mutualistic symbiosis, wherein diatoms acquire increased motility and tintinnids benefit from silicification through increased protection, and highlight that such associations may be more prevalent than currently appreciated.
Published: 2018

22. Neobodonids are dominant kinetoplastids in the global ocean

Author: Flegontova, Olga, Flegontov, Pavel, Malviya, Shruti, Poulain, Julie, de Vargas, Colomban, Bowler, Chris, Lukes, Julius, Horak, Ales, Czech Academy of Sciences [Prague] (CAS), University of South Bohemia, Technical University of Ostrava [Ostrava] (VSB), 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), Tata Institute for Fundamental Research (TIFR), 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), 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), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), ERC [CZ LL1601], Czech Grant Agency [15-17643S, 14-23986S], ERC, Foundation Prince Albert II de Monaco, Tara Foundation, Louis D Foundation, PSL* Research University [ANR-1253 11-IDEX-0001-02], Radcliffe Institute of Advanced Study at Harvard University, CNRS [GDR3280], European Molecular Biology Laboratory (EMBL), Agence Nationale de la Recherche, Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, Electricit e de France (EDF) Foundation, Fondation pour la recherche sur la biodiversite (FRB), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), 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), European Project: 287589,EC:FP7:KBBE,FP7-OCEAN-2011,MICRO B3(2012), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Oceans and Seas, [SDV]Life Sciences [q-bio], parasitic diseases, fungi, RNA, Ribosomal, 18S, Biodiversity, Kinetoplastida, Plankton, DNA, Ribosomal, Phylogeny
Abstract: International audience; Kinetoplastid flagellates comprise basal mostly free-living bodonids and derived obligatory parasitic trypanosomatids, which belong to the best-studied protists. Due to their omnipresence in aquatic environments and soil, the bodonids are of ecological significance. Here, we present the first global survey of marine kinetoplastids and compare it with the strikingly different patterns of abundance and diversity in their sister clade, the diplonemids. Based on analysis of 18S rDNA V9 ribotypes obtained from 124 sites sampled during the Tara Oceans expedition, our results show generally low to moderate abundance and diversity of planktonic kinetoplastids. Although we have identified all major kinetoplastid lineages, 98% of kinetoplastid reads are represented by neobodonids, namely specimens of the Neobodo and Rhynchomonas genera, which make up 59% and 18% of all reads, respectively. Most kinetoplastids have small cell size (0.8-5 mu m) and tend to be more abundant in the mesopelagic as compared to the euphotic zone. Some of the most abundant operational taxonomic units have distinct geographical distributions, and three novel putatively parasitic neobodonids were identified, along with their potential hosts.
Published: 2018

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

Author: Lombard, Vincent, Carradec, Quentin, Pelletier, Eric, Wessner, Marc, Leconte, Jade, Mangot, Jean-Francois, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Véronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Acinas, Silvia G., Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, Wincker, Patrick, Seeleuthner, Yoann, and Mondy, Samuel
Subjects: fungi, Oceanography, Océanographie
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.
Published: 2018

24. The SlCBL10 Calcineurin B-Like Protein Ensures Plant Growth under Salt Stress by Regulating Na+ and Ca2+ Homeostasis1

Author: Egea, Isabel, Pineda, Benito, Ortíz-Atienza, Ana, Plasencia, Félix A., Drevensek, Stéphanie, García-Sogo, Begoña, Yuste-Lisbona, Fernando J., Barrero-Gil, Javier, Atarés, Alejandro, Flores, Francisco B., Barneche, Fredy, Angosto, Trinidad, Capel, Carmen, Salinas, Julio, Vriezen, Wim, Esch, Elisabeth, Bowler, Chris, Bolarín, Maria C., Moreno, Vicente, and Lozano, Rafael
Subjects: Salinity, Sodium-Hydrogen Exchangers, Calcineurin, fungi, Sodium, food and beverages, Articles, Salt Tolerance, Salt Stress, Phenotype, Solanum lycopersicum, Mutation, Vacuoles, Homeostasis, Calcium, Plant Proteins
Abstract: Tomato CALCINEURIN B-LIKE PROTEIN 10 (SlCBL10) ensures plant growth by regulating proper distribution of Na+ and Ca2+ in the shoot apical meristem and developing organs under salt stress.
Published: 2017

25. A global ocean atlas of eukaryotic genes

Author: Carradec, Quentin, Pelletier, Eric, Da Silva, Corinne, Alberti, Adriana, Seeleuthner, Yoann, Blanc-Mathieu, Romain, Lima-Mendez, Gipsi, Rocha, Fabio, Tirichine, Leila, Labadie, Karine, Kirilovsky, Amos, Bertrand, Alexis, Engelen, Stefan, Madoui, Mohammed-Amin, Méheust, Raphaël, Poulain, Julie, Romac, Sarah, Richter, Daniel J., Yoshikawa, Genki, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Jaillon, Olivier, Aury, Jean-Marc, Karsenti, Eric, Sullivan, Matthew B., Sunagawa, Shinichi, Bork, Peer, Not, Fabrice, Hingamp, Pascal, Raes, Jeroen, Guidi, Lionel, Ogata, Hiroyuki, de Vargas, Colomban, Iudicone, Daniele, Bowler, Chris, Wincker, Patrick, Acinas, Silvia G., Boss, Emmanuel, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Pesant, Stephane, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Follows, Michael J, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, and Follows, Michael J
Subjects: fungi
Abstract: While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.
Published: 2017

26. 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, Frederick, Gas, Shahinaz, Guy, Julie, Haquelle, Maud, Jacoby, E'Krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaelle, Wessner, Mark, Acinas, Silvia G., Royo-llonch, Marta, Cornejo-castillo, Francisco M., Logares, Ramiro, Fernandez-gomez, Beatriz, Bowler, Chris, Cochrane, Guy, Amid, Clara, Ten Hoopen, Petra, De Vargas, Colomban, Grimsley, Nigel, Desgranges, Elodie, Kandels-lewis, Stefanie, Ogata, Hiroyuki, Poulton, Nicole, Sieracki, Michael E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stephane, Karsenti, Eric, Wincker, Patrick, Bork, Peer, Boss, Emmanuel, Follows, Michael, Gorsky, Gabriel, Hingamp, Pascal, Iudicone, Daniele, Karp-boss, Lee, Not, Fabrice, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Bazire, Pascal, Beluche, Odette, Besnard-gonnet, Marielle, Bordelais, Isabelle, Boutard, Magali, Dubois, Maria, Dumont, Corinne, Ettedgui, Evelyne, Fernandez, Patricia, Garcia, Esperance, Aiach, Nathalie Giordanenco, Guerin, Thomas, Hamon, Chadia, Brun, Elodie, Lebled, Sandrine, Lenoble, Patricia, Louesse, Claudine, Mahieu, Eric, Mairey, Barbara, Martins, Nathalie, Megret, Catherine, Milani, Claire, Muanga, Jacqueline, Orvain, Celine, Payen, Emilie, Perroud, Peggy, Petit, Emmanuelle, Robert, Dominique, Ronsin, Murielle, and Vacherie, Benoit
Subjects: fungi
Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www. ebi. ac. uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems.
Published: 2017

27. 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, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Acinas, Silvia G., Royo-Llonch, Marta, Cornejo-Castillo, Francisco M., 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 E., Stepanauskas, Ramunas, Sullivan, Matthew B., Brum, Jennifer R., Duhaime, Melissa B., Poulos, Bonnie T., Hurwitz, Bonnie L., Pesant, Stéphane, Karsenti, Eric, and Wincker, Patrick
Subjects: Water microbiology, Statistics and Probability, Data Descriptor, Molecular biology, Nucleotides, Oceans and Seas, fungi, Genomics, Library and Information Sciences, Plankton, Computer Science Applications, Education, Cardiovascular and Metabolic Diseases, Viruses, Metagenomics, Statistics, Probability and Uncertainty, Ecosystem, Information Systems
Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world’s planktonic ecosystems.
Published: 2017
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28. 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, Julie, Haquelle, Maud, Jacoby, E'krame, Jaillon, Olivier, Lemainque, Arnaud, Pelletier, Eric, Samson, Gaëlle, Wessner, Mark, Acinas, Silvia G, Royo-Llonch, Marta, Cornejo-Castillo, Francisco M, 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 E, Stepanauskas, Ramunas, Sullivan, Matthew B, Brum, Jennifer R, Duhaime, Melissa B, Poulos, Bonnie T, Hurwitz, Bonnie L, Tara Oceans Consortium Coordinators, Pesant, Stéphane, Karsenti, Eric, Wincker, Patrick, and Raes, Jeroen
Subjects: fungi
Abstract: A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems. ispartof: Scientific Data vol:4 pages:170093-170093 ispartof: location:England status: published
Published: 2017

29. 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, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., 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, Gorsky, Gabriel, Grimsley, Nigel, Karp-Boss, Lee, Krzic, Uros, Not, Fabrice, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Velayoudon, Didier, Weissenbach, Jean, Follows, Michael J, Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, and Follows, Michael J
Subjects: fungi
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.
Published: 2017

30. Plankton networks driving carbon export in the oligotrophic ocean

Author: Guidi, Lionel, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Chaffron, Samuel, Tara Oceans Consortium Coordinators, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Bittner, Lucie, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Eveillard, Damien, Gorsky, Gabriel, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), Department of Applied Biological Sciences (DBIT), Department of Microbiology and Immunology, Rega Institute, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Biological Oceanography Division, CSIR National Institute of Oceanography [India] (NIO), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Ohio State University [Columbus] (OSU), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Structural and Computational Biology, European Molecular Biology Laboratory [Heidelberg] (EMBL), Directors’ Research European Molecular Biology, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), School of Marine Sciences, University of Maine, Institute for Chemical Research, Kyoto University, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Max Delbrück Centre for Molecular Medicine, Stazione Zoologica Anton Dohrn (SZN), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Department of Bio-engineering Sciences, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), Department of Ecology and Evolutionary Biology, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École polytechnique (X)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Kyoto University [Kyoto], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0301 basic medicine, Chlorophyll, Aquatic Organisms, 010504 meteorology & atmospheric sciences, Genes, Viral, General Science & Technology, Oceans and Seas, chemistry.chemical_element, Biology, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 01 natural sciences, Deep sea, Article, 03 medical and health sciences, Ecosystem, Seawater, Viral, 14. Life underwater, Photosynthesis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Total organic carbon, Marine biology, Synechococcus, Deep chlorophyll maximum, Multidisciplinary, Geography, Ecology, Tara Oceans coordinators, fungi, Bacterial, 15. Life on land, Plankton, Carbon, 030104 developmental biology, Oceanography, Genes, chemistry, 13. Climate action, Ocean color, Genes, Bacterial, Dinoflagellida, Expeditions
Abstract: Guidi, Lionel ... et al.-- 16 pages, 4 figures, supplementary information https://dx.doi.org/10.1038/nature16942 .-- This article is contribution number 34 of Tara Oceans, The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions, We thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research – Flanders, Rega Institute, KU Leuven, The French Ministry of Research, the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ANR (projects POSEIDON/ANR-09-BLAN-0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218, SAMOSA, ANR-13-ADAP-0010), European Union FP7 (MicroB3/No.287589, ERC Advanced Grant Award to C.B. (Diatomite: 294823), Gordon and Betty Moore Foundation grant (#3790 and #2631) and the UA Technology and Research Initiative Fund and the Water, Environmental, and Energy Solutions Initiative to M.B.S., the Italian Flagship Program RITMARE to D.I., the Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d'Ajusts Universitaris i Reserca to S.G.A., JSPS KAKENHI grant number 26430184 to H.O., and FWO, BIO5, Biosphere 2 to M.B.S. We also thank the support and commitment of Agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, the Tara schooner and its captains and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions
Published: 2016

31. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author: Villar, Emilie, Farrant, Gregory K, Follows, Michael, Garczarek, Laurence, Speich, Sabrina, Audic, Stéphane, Bittner, Lucie, Blanke, Bruno, Brum, Jennifer R, Brunet, Christophe, Casotti, Raffaella, Chase, Alison, Dolan, John R, d'Ortenzio, Fabrizio, Gattuso, Jean-Pierre, Grima, Nicolas, Guidi, Lionel, Hill, Christopher N, Jahn, Oliver, Jamet, Jean-Louis, Le Goff, Hervé, Lepoivre, Cyrille, Malviya, Shruti, Pelletier, Eric, Romagnan, Jean-Baptiste, Roux, Simon, Santini, Sébastien, Scalco, Eleonora, Schwenck, Sarah M, Tanaka, Atsuko, Testor, Pierre, Vannier, Thomas, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans coordinators, Acinas, Silvia G, Bork, Peer, Boss, Emmanuel, de Vargas, Colomban, Gorsky, Gabriel, Ogata, Hiroyuki, Pesant, Stéphane, Sullivan, Matthew B, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, Bowler, Chris, Not, Fabrice, Hingamp, Pascal, and Iudicone, Daniele
Subjects: fungi
Abstract: Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.
Published: 2015

32. Patterns and ecological drivers of ocean viral communities

Author: Brum, Jennifer R, Ignacio-Espinoza, J Cesar, Roux, Simon, Doulcier, Guilhem, Acinas, Silvia G, Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, de Vargas, Colomban, Gasol, Josep M, Gorsky, Gabriel, Gregory, Ann C, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T, Schwenck, Sarah M, Speich, Sabrina, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Tara Oceans Coordinators, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Karsenti, Eric, and Sullivan, Matthew B
Subjects: viruses, fungi
Abstract: Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.
Published: 2015

33. Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean

Author: de Vargas, Colomban, Audic, Stéphane, Henry, Nicolas, Decelle, Johan, Mahé, Frédéric, Logares, Ramiro, Lara, Enrique, Berney, Cédric, Le Bescot, Noan, Probert, Ian, Carmichael, Margaux, Poulain, Julie, Romac, Sarah, Colin, Sébastien, Aury, Jean-Marc, Bittner, Lucie, Chaffron, Samuel, Dunthorn, Micah, Engelen, Stefan, Flegontova, Olga, Guidi, Lionel, Horak, Ales, Jaillon, Olivier, Lima-Mendez, Gipsi, Lukeš, Julius, Malviya, Shruti, Morard, Raphael, Mulot, Matthieu, Scalco, Eleonora, Siano, Raffaele, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Acinas, Silvia G, Bork, Peer, Bowler, Chris, Gorsky, Gabriel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Raes, Jeroen, Sieracki, Michael E, Speich, Sabrina, Stemmann, Lars, Tara Oceans coordinators, Department of Bio-engineering Sciences, and Microbiology
Subjects: Oceans and Seas, fungi, plankton, Sunlight, Animals, DNA Barcoding, Taxonomic, Eukaryota, natural sciences, Sequence Analysis, DNA, phylogeny, DNA, Ribosomal, Ribosomes, biodiversity
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.
Published: 2015

34. Patterns and ecological drivers of ocean viral communities

Author: Brum, Jennifer R., Gasol, Josep M., Gorsky, Gabriel, Gregory, Ann C., Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stéphane, Poulos, Bonnie T., Ignacio-Espinoza, J. Cesar, Schwenck, Sarah M., Speich, Sarah, Dimier, Celine, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Bork, Peer, Bowler, Chris, Sunagawa, Shinichi, Wincker, Patrick, Roux, Simon, Karsenti, Eric, Sullivan, Matthew B., Doulcier, Guilhem, Acinas, Silvia G., Alberti, Adriana, Chaffron, Samuel, Cruaud, Corinne, and de Vargas, Colomban
Subjects: viruses, fungi
Abstract: Viruses influence ecosystems by modulating microbial population size, diversity, metabolic outputs, and gene flow. Here, we use quantitative double-stranded DNA (dsDNA) viral-fraction metagenomes (viromes) and whole viral community morphological data sets from 43 Tara Oceans expedition samples to assess viral community patterns and structure in the upper ocean. Protein cluster cataloging defined pelagic upper-ocean viral community pan and core gene sets and suggested that this sequence space is well-sampled. Analyses of viral protein clusters, populations, and morphology revealed biogeographic patterns whereby viral communities were passively transported on oceanic currents and locally structured by environmental conditions that affect host community structure. Together, these investigations establish a global ocean dsDNA viromic data set with analyses supporting the seed-bank hypothesis to explain how oceanic viral communities maintain high local diversity.
Published: 2015

35. Ocean plankton. Determinants of community structure in the global plankton interactome

Author: Lima-Mendez, Gipsi, Faust, Karoline, Henry, Nicolas, Decelle, Johan, Colin, Sébastien, Carcillo, Fabrizio, Chaffron, Samuel, Ignacio-Espinosa, J Cesar, Roux, Simon, Vincent, Flora, Bittner, Lucie, Darzi, Youssef, Wang, Jun, Audic, Stéphane, Berline, Léo, Bontempi, Gianluca, Cabello, Ana M, Coppola, Laurent, Cornejo-Castillo, Francisco M, d'Ovidio, Francesco, De Meester, Luc, Ferrera, Isabel, Garet-Delmas, Marie-José, Guidi, Lionel, Lara, Elena, Pesant, Stéphane, Royo-Llonch, Marta, Salazar, Guillem, Sánchez, Pablo, Sebastian, Marta, Souffreau, Caroline, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Gorsky, Gabriel, Not, Fabrice, Ogata, Hiroyuki, Speich, Sabrina, Stemmann, Lars, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Sunagawa, Shinichi, Bork, Peer, Sullivan, Matthew B, Karsenti, Eric, Bowler, Chris, de Vargas, Colomban, Raes, Jeroen, Tara Oceans coordinators, Department of Bio-engineering Sciences, Faculty of Economic and Social Sciences and Solvay Business School, Faculty of Sciences and Bioengineering Sciences, Hydrology and Hydraulic Engineering, and Microbiology
Subjects: Food Chain, Platyhelminths, Oceans and Seas, fungi, plankton, Sunlight, Animals, viruses, phylogeny, Host Specificity, symbiosis
Abstract: Species interaction networks are shaped by abiotic and biotic factors. Here, as part of the Tara Oceans project, we studied the photic zone interactome using environmental factors and organismal abundance profiles and found that environmental factors are incomplete predictors of community structure. We found associations across plankton functional types and phylogenetic groups to be nonrandomly distributed on the network and driven by both local and global patterns. We identified interactions among grazers, primary producers, viruses, and (mainly parasitic) symbionts and validated network-generated hypotheses using microscopy to confirm symbiotic relationships. We have thus provided a resource to support further research on ocean food webs and integrating biological components into ocean models.
Published: 2015

36. Revealing and analyzing networks of marine microbial ecosystems

Author: Eveillard, Damien, Guidi, Lionel, Bittner, Lucie, Chaffron, Samuel, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Gorsky, Gaby, Laboratoire d'Informatique de Nantes Atlantique (LINA), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), 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), 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), European Molecular Biology Laboratory [Heidelberg] (EMBL), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), INSU, Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS-PSL), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL)
Subjects: fungi, [SDE]Environmental Sciences
Abstract: International audience; Understanding interactions between microbial communities and their environment well enough to be able to predict diversity or biotic response on the basis of physicochemical parameters is a fundamental pursuit of microbial ecology that still eludes us. Networks have become a key approach to understanding systems of interacting objects, and network based analysis recently shown great promises to decipher microbial interactions. However, modeling microbial communities is a complicated task, because (i) communities are complex, (ii) most are described qualitatively, and (iii) quantitative understanding of the way communities interacts with their surroundings remains incomplete.We propose herein a network analysis that aims to overcome these points while focusing on one open biological question: revealing and analyzing plankton networks driving carbon export in the global ocean.The biological carbon pump is the process by which photosynthesis transforms CO2 to organic carbon sinking to the deep-ocean as particles where it is sequestered. While the intensity of the pump correlate to plankton community composition, the underlying ecosystem structure and interactions driving this process remain largely uncharacterized Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve understanding of these drivers. We show that specific plankton communities correlate with carbon export and highlight unexpected and overlooked taxa such as Radiolaria, alveolate parasites and bacterial pathogens, as well as Synechococcus and their phages, as key players in the biological pump. Additionally, we show that the abundances of just a few bacterial and viral genes predict most of the global ocean carbon export’s variability. Together these findings help elucidate ecosystem drivers of the biological carbon pump and present a case study for scaling from genes-to-ecosystems.
Published: 2015

37. The Ectocarpus Genome and Brown Algal Genomics The Ectocarpus Genome Consortium

Author: Cock, J. Mark, Sterck, Lieven, Ahmed, Sophia, Allen, Andrew E., Amoutzias, Grigoris, Anthouard, Véronique, Artiguenave, Francois, Arun, Alok, Aury, Jean-Marc, Badger, Jonathan H., Beszteri, Bank, Billiau, Kenny, Bonnet, Eric, Bothwell, John H., Bowler, Chris, Boyen, Catherine, Brownlee, Colin, Carrano, Carl J., Charrier, Benedicte, Cho, Ga Youn, Coelho, Susana M., Collen, Jonas, Le Corguillé, Gildas, Corre, Erwan, Dartevelle, Laurence, da Silva, Corinne, Delage, Ludovic, Delaroque, Nicolas, Dittami, Simon, Doulbeau, Sylvie, Elias, Marek, Farnham, Garry, Gachon, Claire M. M., Godfroy, Olivier, Gschloessl, Bernhard, Heesch, Svenja, Jabbari, Kamel, Jubin, Claire, Kawai, Hiroshi, Kimura, Kei, Kloareg, Bernard, Kuepper, Frithjof C., Lang, Daniel, Le Bail, Aude, Luthringer, Rémy, Leblanc, Catherine, Lerouge, Patrice, Lohr, Martin, Lopez, Pascal J., Macaisne, Nicolas, Martens, Cindy, Maumus, Florian, Michel, Gurvan, Miranda-Saavedra, Diego, Morales, Julia, Moreau, Herve, Motomura, Taizo, Nagasato, Chikako, Napoli, Carolyn A., Nelson, David R., Nyvall-Collén, Pi, Peters, Akira F., Pommier, Cyril, Potin, Philippe, Poulain, Julie, Quesneville, Hadi, Read, Betsy, Rensing, Stefan A., Ritter, Andrés, Rousvoal, Sylvie, Samanta, Manoj, Samson, Gaelle, Schroeder, Declan C., Scornet, Delphine, Ségurens, Béatrice, Strittmatter, Martina, Tonon, Thierry, Tregear, James W., Valentin, Klaus, von Dassow, Peter, Yamagishi, Takahiro, Rouzé, Pierre, van de Peer, Yves, Wincker, Patrick, Université Pierre et Marie Curie - Paris 6 (UPMC), Signaux oligosaccharidiques et lipidiques (SOL), 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)-GOEMAR-Centre National de la Recherche Scientifique (CNRS), Dept Plant Syst Biol, Universiteit Gent = Ghent University [Belgium] (UGENT), Dept Plant Biotechnol & Bioinformat, J. Craig Venter Institute [La Jolla, USA] (JCVI), Inst Genom, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Partenaires INRAE, Queen's University [Belfast] (QUB), Marine Biological Association of the UK, École normale supérieure - Cachan (ENS Cachan), Stn Zool, and Universiteit Gent = Ghent University (UGENT)
Subjects: IRON-DEFICIENCY, EVOLUTIONARY HISTORY, PLANT MICRORNAS, SILICULOSUS PHAEOPHYCEAE, TOPOISOMERASE-VI, [SDV]Life Sciences [q-bio], fungi, food and beverages, DIATOM THALASSIOSIRA-PSEUDONANA, PROTEIN FAMILY, LAMINARIA-DIGITATA, CHLAMYDOMONAS-REINHARDTII, NORTH-ATLANTIC
Abstract: International audience; Brown algae are important organisms both because of their key ecological roles in coastal ecosystems and because of the remarkable biological features that they have acquired during their unusual evolutionary history. The recent sequencing of the complete genome of the filamentous brown alga Ectocarpus has provided unprecedented access to the molecular processes that underlie brown algal biology. Analysis of the genome sequence, which exhibits several unusual structural features, identified genes that are predicted to play key roles in several aspects of brown algal metabolism, in the construction of the multicellular bodyplan and in resistance to biotic and abiotic stresses. Information from the genome sequence is currently being used in combination with other genomic, genetic and biochemical tools to further investigate these and other aspects of brown algal biology at the molecular level. Here, we review some of the major discoveries that emerged from the analysis of the Ectocarpus genome sequence, with a particular focus on the unusual genome structure, inferences about brown algal evolution and novel aspects of brown algal metabolism.
Published: 2012

38. The Phaeodactylum genome reveals the dynamic nature and multi-lineage evolutionary history of diatom genomes

Author: Bowler, Chris, Allen, Andrew E., Badger, Jonathan H., Grimwood, Jane, Jabbari, Kamel, Kuo, Alan, Maheswari, Uma, Martens, Cindy, Maumus, Florian, Otillar, Robert P., Rayko, Edda, Salamov, Asaf, Vandepoele, Klaas, Beszteri, Bank, Gruber, Ansgar, Heijde, Marc, Katinka, Michael, Mock, Thomas, Valentin, Klaus, Verret, Frederic, Berges, John A., Brownlee, Colin, Cadoret, Jean-Paul, Chiovitti, Anthony, Choi, Chang Jae, Coesel, Sacha, Martino, Alessandra De, Detter, J. Chris, Durkin, Colleen, Falciatore, Angela, Fournet, Jerome, Haruta, Miyoshi, Huysman, Marie, Jenkins, Bethany D., Jiroutova, Katerina, Jorgensen, Richard E., Joubert, Yolaine, Kaplan, Aaron, Kroeger, Nils, Kroth, Peter, Roche, Julie La, Lindquist, Erica, Lommer, Markus, Martin-Jezequel, Veronique, Lopez, Pascal J., Lucas, Susan, Mangogna, Manuela, McGinnis, Karen, Medlin, Linda K., Montsant, Anton, Secq, Marie-Pierre Oudot-Le, Napoli, Carolyn, Obornik, Miroslav, Petit, Jean-Louis, Porcel, Betina M., Poulsen, Nicole, Robison, Matthew, Rychlewski, Leszek, Rynearson, Tatiana A., Schmutz, Jeremy, Parker, Micaela Schnitzler, Shapiro, Harris, Siaut, Magali, Stanley, Michele, Sussman, Michael J., Taylor, Alison, Vardi, Assaf, Dassow, Peter von, Vyverman, Wim, Willis, Anusuya, Wyrwicz, Lucjan S., Rokhsar, Daniel S., Weissenbach, Jean, Armbrust, E. Virginia, Green, Beverley R., Peer, Yves Van de, and Grigoriev, Igor V.
Subjects: fungi, Phaeodactylum genome, diatom genomes
Abstract: Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (40percent) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans.
Published: 2008

39. Semi-quantitative RT-PCR analysis of photoregulated gene expression in marine diatoms

Author: LEBLANC, Catherine, FALCIATORE, Angela, WATANABE, Masakatsu, and BOWLER, Chris
Subjects: Diatoms, Light, Sequence Homology, Amino Acid, Reverse Transcriptase Polymerase Chain Reaction, fungi, Algal Proteins, Molecular Sequence Data, Photosynthetic Reaction Center Complex Proteins, Light-Harvesting Protein Complexes, DNA, Sequence Analysis, DNA, Actins, Gene Expression Regulation, Genes, Spectrophotometry, Amino Acid Sequence, RNA, Messenger, Sequence Alignment
Abstract: The low cell densities of diatoms and other phytoplankton in culture has precluded the use of classical RNA analysis techniques for routine studies of gene expression in large numbers of samples. This has seriously hampered studies of the basic biology of such organisms. To circumvent this problem, we have developed a high-throughput semi-quantitative RT-PCR-based protocol and used it to monitor expression of a gene encoding a fucoxanthin, chlorophyll a/c-binding protein (FCP) in the centric planktonic diatom Thalassiosira weissflogii. Analysis of FCP gene expression in dark-adapted diatom cultures revealed that mRNA levels increase 5- to 6-fold in response to white light irradiation and peak around 6 to 8 h. To determine the photoreceptors involved in this response action spectra of FCP gene expression were determined using the Okazaki large spectrograph. Responses consistent with the presence of cryptochrome-, rhodopsin- and phytochrome-type receptors could be detected. The apparent presence of phytochrome-mediated responses is of particular interest given the low fluences of red and far-red light wavelengths in the marine environment.
Published: 1999

40. Eukaryotic plankton diversity in the sunlit ocean

Author: de Vargas, Colomban, Audic, Stéphane, Henry, Nicolas, Decelle, Johan, Mahé, Frédéric, Logares, Ramiro, Lara, Enrique, Berney, Cédric, Le Bescot, Noan, Probert, Ian, Carmichael, Margaux, Poulain, Julie, Romac, Sarah, Colin, Sébastien, Aury, Jean-Marc, Bittner, Lucie, Chaffron, Samuel, Dunthorn, Micah, Engelen, Stefan, Flegontova, Olga, Guidi, Lionel, Horák, Aleš, Jaillon, Olivier, Lima-Mendez, Gipsi, Lukeš, Julius, Malviya, Shruti, Morard, Raphael, Mulot, Matthieu, Scalco, Eleonora, Siano, Raffaele, Vincent, Flora, Zingone, Adriana, Dimier, Céline, Picheral, Marc, Searson, Sarah, Kandels-Lewis, Stefanie, Tara Oceans Coordinators, Acinas, Silvia G, Bork, Peer, Bowler, Chris, Gorsky, Gabriel, Grimsley, Nigel, Hingamp, Pascal, Iudicone, Daniele, Not, Fabrice, Ogata, Hiroyuki, Pesant, Stephane, Raes, Jeroen, Sieracki, Michael E, Speich, Sabrina, Stemmann, Lars, Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, and Karsenti, Eric
Subjects: fungi, natural sciences
Abstract: Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at ~150, 000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the ~11, 200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts., プランクトンの世界 : 新しいフロンティア -タラ海洋探査からの最新情報-. 京都大学プレスリリース. 2015-05-22.

41. Macroscale patterns of oceanic zooplankton composition and size structure

Author: Brandão, Manoela C., Benedetti, Fabio, Martini, Séverine, Soviadan, Yawouvi Dodji, Irisson, Jean-Olivier, Romagnan, Jean-Baptiste, Elineau, Amanda, Desnos, Corinne, Jalabert, Laëtitia, Freire, Andrea S., Picheral, Marc, Guidi, Lionel, Gorsky, Gabriel, Bowler, Chris, Karp-Boss, Lee, Henry, Nicolas, de Vargas, Colomban, Sullivan, Matthew B., Tara Oceans Consortium Coordinators, Stemmann, Lars, and Lombard, Fabien
Subjects: Ocean sciences, Ecology, 13. Climate action, FOS: Biological sciences, fungi, 14. Life underwater, 15. Life on land
Abstract: Ocean plankton comprise organisms from viruses to fish larvae that are fundamental to ecosystem functioning and the provision of marine services such as fisheries and CO2 sequestration. The latter services are partly governed by variations in plankton community composition and the expression of traits such as body size at community-level. While community assembly has been thoroughly studied for the smaller end of the plankton size spectrum, the larger end comprises ectotherms that are often studied at the species, or group-level, rather than as communities. The body size of marine ectotherms decreases with temperature, but controls on community-level traits remain elusive, hindering the predictability of marine services provision. Here, we leverage Tara Oceans datasets to determine how zooplankton community composition and size structure varies with latitude, temperature and productivity-related covariates in the global surface ocean. Zooplankton abundance and median size decreased towards warmer and less productive environments, as a result of changes in copepod composition. However, some clades displayed the opposite relationships, which may be ascribed to alternative feeding strategies. Given that climate models predict increasingly warmed and stratified oceans, our findings suggest that zooplankton communities will shift towards smaller organisms which might weaken their contribution to the biological carbon pump., Scientific Reports, 11 (1), ISSN:2045-2322

42. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author: Read, Betsy A., Kegel, Jessica, Klute, Mary J., Kuo, Alan, Lefebvre, Stephane C., Maumus, Florian, Mayer, Christoph, Miller, John, Monier, Adam, Salamov, Asaf, Young, Jeremy, Aguilar, Maria, Claverie, Jean-Michel, Frickenhaus, Stephan, Gonzalez, Karina, Herman, Emily K., Lin, Yao-Cheng, Napier, Johnathan, Ogata, Hiroyuki, Sarno, Analissa F., Shmutz, Jeremy, Schroeder, Declan, De Vargas, Colomban, Verret, Frederic, Von Dassow, Peter, Valentin, Klaus, Van De Peer, Yves, Wheeler, Glen, Allen, Andrew E., Bidle, Kay, Borodovsky, Mark, Bowler, Chris, Brownlee, Colin, Cock, J. Mark, Elias, Marek, Gladyshev, Vadim N., Groth, Marco, Guda, Chittibabu, Hadaegh, Ahmad, Iglesias-Rodriguez, Maria Debora, Jenkins, Jerry, Jones, Bethan M., Lawson, Tracy, Leese, Florian, Lindquist, Erika, Lobanov, Alexei, Lomsadze, Alexandre, Malik, Shehre-Banoo, Marsh, Mary E., Mackinder, Luke, Mock, Thomas, Mueller-Roeber, Bernd, Pagarete, Ant��nio, Parker, Micaela, Probert, Ian, Quesneville, Hadi, Raines, Christine, Rensing, Stefan A., Ria��o-Pach��n, Diego Mauricio, Richier, Sophie, Rokitta, Sebastian, Shiraiwa, Yoshihiro, Van Der Giezen, Mark, Soanes, Darren M., Wahlund, Thomas M., Williams, Bryony, Wilson, Willie, Wolfe, Gordon, Wurch, Louie L., Dacks, Joel B., Delwiche, Charles F., Dyhrman, Sonya, Gl��ckner, Gernot, John, Uwe, Richards, Thomas, Worden, Alexandra Z., Zhang, Xiaoyu, and Grigoriev, Igor V.
Subjects: Marine biology, 13. Climate action, fungi, Paleontology, 14. Life underwater, 15. Life on land, Marine ecology
Abstract: Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 percent of total carbon fixation in some systems. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.

43. Global Trends in Marine Plankton Diversity across Kingdoms of Life

Author: Ibarbalz, Federico M., Henry, Nicolas, Brandão, Manoela C., Martini, Séverine, Busseni, Greta, Byrne, Hannah, Coelho, Luis P., Endo, Hisashi, Gasol, Josep M., Gregory, Ann C., Mahé, Frédéric, Rigonato, Janaina, Royo-Llonch, Marta, Salazar Guiral, Guillem, Sanz-Sáez, Isabel, Scalco, Eleonora, Soviadan, Dodji, Zayed, Ahmed A., Zingone, Adriana, Labadie, Karine, Ferland, Joannie, Marec, Claudie, Kandels, Stefanie, Picheral, Marc, Poulain, Julie, Pisarev, Sergey, Carmichael, Margaux, Pesant, Stéphane, Acinas, Silvia G., Tara Oceans Coordinators, Babin, Marcel, Bork, Peer, Boss, Emmanuel, Bowler, Chris, Cochrane, Guy R., de Vargas, Colomban, Follows, Michael J., Gorsky, Gabriel, Grimsley, Nigel, Guidi, Lionel, Hingamp, Pascal, Iudicone, Daniele, Jaillon, Olivier, Karp-Boss, Lee, Karsenti, Eric, Not, Fabrice, Ogata, Hiroyuki, Poulton, Nicole, Raes, Jeroen, Sardet, Christian, Speich, Sabrina, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Wincker, Patrick, Pelletier, Eric, Bopp, Laurent, Lombard, Fabien, and Zinger, Lucie
Subjects: 13. Climate action, fungi, 14. Life underwater, 15. Life on land, human activities
Abstract: The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation., Cell, 179 (5), ISSN:0092-8674, ISSN:1097-4172

44. 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-Francois, Poulain, Julie, Labadie, Karine, Logares, Ramiro, Sunagawa, Shinichi, de Berardinis, Veronique, Salanoubat, Marcel, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Searson, Sarah, Tara Oceans, Coordinators, Pesant, Stephane, Poulton, Nicole, Stepanauskas, Ramunas, Bork, Peer, Bowler, Chris, Hingamp, Pascal, Sullivan, Matthew B., Iudicone, Daniele, Massana, Ramon, Aury, Jean-Marc, Henrissat, Bernard, Karsenti, Eric, Jaillon, Olivier, Sieracki, Mike, de Vargas, Colomban, and Wincker, Patrick
Subjects: Marine biology, Microbial ecology, Water microbiology, 13. Climate action, fungi, 14. Life underwater, Genomics
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., Nature Communications, 9, ISSN:2041-1723

45. The SlCBL10 calcineurin B-like protein ensures plant growth under salt stress by regulating Na+ and Ca2+ homeostasis

Author: Julio Salinas, Vicente Moreno, Rafael Lozano, Javier Barrero-Gil, Carmen Capel, Maria C. Bolarin, Isabel Egea, Francisco B. Flores, Fernando J. Yuste-Lisbona, Benito Pineda, Begoña García-Sogo, Wim H. Vriezen, Ana Ortíz-Atienza, Felix A. Plasencia, Fredy Barneche, Stéphanie Drevensek, Alejandro Atarés, Elisabeth Esch, Chris Bowler, Trinidad Angosto, PLANT-KBBE, Ministerio de Economía y Competitividad (España), Agence Nationale de la Recherche (France), Egea, Isabel, Pineda, Benito, Ortíz-Atienza, Ana, Plasencia, Félix A., Drevensek, Stéphanie, Yuste-Lisbona, Fernando J., Barrero-Gil, J., Atarés Huerta, Alejandro, Flores, Francisco B., Barneche, Fredy, Angosto Trillo, Trinidad, Salinas, Julio, Vriezen, Wim, Esch, Elizabeth, Bowler, Chris, Bolarín, María C., Moreno Ferrero, Vicente, Lozano, Rafael, Egea, Isabel [0000-0002-1248-0297], Pineda, Benito [0000-0001-9176-701X], Ortíz-Atienza, Ana [0000-0003-1750-4785], Plasencia, Félix A. [0000-0001-9353-990X], Drevensek, Stéphanie [0000-0002-2356-7021], Yuste-Lisbona, Fernando J. [0000-0001-9222-7293], Barrero-Gil, J. [0000-0003-0878-7576], Atarés Huerta, Alejandro [0000-0003-1728-5471], Flores, Francisco B. [0000-0002-9883-9458], Barneche, Fredy [0000-0002-7014-7097], Angosto Trillo, Trinidad [0000-0003-0294-9255], Salinas, Julio [0000-0003-2020-0950], Vriezen, Wim [0000-0001-8189-201X], Esch, Elizabeth [0000-0002-8760-3247], Bowler, Chris [0000-0003-3835-6187], Bolarín, María C. [0000-0002-2662-4917], Moreno Ferrero, Vicente [0000-0002-0345-7300], and Lozano, Rafael [0000-0001-5458-2075]
Subjects: 0106 biological sciences, 0301 basic medicine, Arabidopsis thaliana, Physiology, Calcium sensor cbl10, Ion homeostasis, Mutant, Expression, Plant Science, Vacuole, 01 natural sciences, Tomato, 03 medical and health sciences, Arabidopsis, Gene expression, Genetics, biology, Chemistry, fungi, food and beverages, Compartmentalization (fire protection), biology.organism_classification, Salinity tolerance, Cell biology, Transporters, GENETICA, 030104 developmental biology, Vacuolar h+-atpase, Enhancer trap, SOS pathway, Homeostasis, 010606 plant biology & botany
Abstract: 18 p.-9 fig., Characterization of a new tomato (Solanum lycopersicum) T-DNA mutant allowed for the isolation of the CALCINEURIN B-LIKE PROTEIN 10 (SlCBL10) gene whose lack of function was responsible for the severe alterations observed in the shoot apex and reproductive organs under salinity conditions. Physiological studies proved that SlCBL10 gene is required to maintain a proper low Na+/Ca2+ ratio in growing tissues allowing tomato growth under salt stress. Expression analysis of the main responsible genes for Na+ compartmentalization (i.e. Na+/H+ EXCHANGERs, SALT OVERLY SENSITIVE, HIGH-AFFINITY K+ TRANSPORTER 1; 2, H+-pyrophosphatase AVP1 [SlAVP1] and V-ATPase [SlVHA-A1]) supported a reduced capacity to accumulate Na+ in Slcbl10 mutant leaves, which resulted in a lower uploading of Na+ from xylem, allowing the toxic ion to reach apex and flowers. Likewise, the tomato CATION EXCHANGER 1 and TWO-PORE CHANNEL 1 (SlTPC1), key genes for Ca2+ fluxes to the vacuole, showed abnormal expression in Slcbl10 plants indicating an impaired Ca2+ release from vacuole. Additionally, complementation assay revealed that SlCBL10 is a true ortholog of the Arabidopsis (Arabidopsis thaliana) CBL10 gene, supporting that the essential function of CBL10 is conserved in Arabidopsis and tomato. Together, the findings obtained in this study provide new insights into the function of SlCBL10 in salt stress tolerance. Thus, it is proposed that SlCBL10 mediates salt tolerance by regulating Na+ and Ca2+ fluxes in the vacuole, cooperating with the vacuolar cation channel SlTPC1 and the two vacuolar H+-pumps, SlAVP1 and SlVHA-A1, which in turn are revealed as potential targets of SlCBL10.
Published: 2018

46. Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms

Author: Rastogi, Achal, Maheswari, Uma, Dorrell, Richard G., Vieira, Fabio Rocha Jimenez, Maumus, Florian, Kustka, Adam, McCarthy, James, Allen, Andy E., Kersey, Paul, Bowler, Chris, and Tirichine, Leila
Subjects: Vegetal Biology, fungi, Biologie végétale
Abstract: Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
Published: 2018

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