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302 results on '"De Vargas, C."'

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

Author

Caputi, L, Carradec, Q, Eveillard, D, Kirilovsky, A, Pelletier, E, Pierella Karlusich, JJ, Rocha Jimenez Vieira, F, Villar, E, Chaffron, S, Malviya, S, Scalco, E, Acinas, SG, Alberti, A, Aury, JM, Benoiston, AS, Bertrand, A, Biard, T, Bittner, L, Boccara, M, Brum, JR, Brunet, C, Busseni, G, Carratalà, A, Claustre, H, Coelho, LP, Colin, S, D'Aniello, S, Da Silva, C, Del Core, M, Doré, H, Gasparini, S, Kokoszka, F, Jamet, JL, Lejeusne, C, Lepoivre, C, Lescot, M, Lima-Mendez, G, Lombard, F, Lukeš, J, Maillet, N, Madoui, MA, Martinez, E, Mazzocchi, MG, Néou, MB, Paz-Yepes, J, Poulain, J, Ramondenc, S, Romagnan, JB, Roux, S, Salvagio Manta, D, Sanges, R, Speich, S, Sprovieri, M, Sunagawa, S, Taillandier, V, Tanaka, A, Tirichine, L, Trottier, C, Uitz, J, Veluchamy, A, Veselá, J, Vincent, F, Yau, S, Kandels-Lewis, S, Searson, S, Dimier, C, Picheral, M, Bork, P, Boss, E, de Vargas, C, Follows, MJ, Grimsley, N, Guidi, L, Hingamp, P, Karsenti, E, Sordino, P, Stemmann, L, Sullivan, MB, Tagliabue, A, Zingone, A, Garczarek, L, d'Ortenzio, F, Testor, P, Not, F, d'Alcalà, MR, Wincker, P, Bowler, C, and Iudicone, D

Subjects
Genetics, Atmospheric Sciences, Geochemistry, Meteorology & Atmospheric Sciences, Oceanography
Abstract

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.

Published
2019

2. Marine Aerosols : Measurements by the Tara Pacific Expedition

Author

Flores, J. M., Bourdin, G., Altaratz, O., Trainic, M., Lang-Yona, N., Dzimban, E., Steinau, S., Tettich, F., Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Douville, E., Forcioli, D., Furla, P., Galand, P. E., Sullivan, M., Gilson, É., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sunagawa, S., Thomas, O. P., Troublé, R., de Vargas, C., Thurber, R. Vega, Voolstra, C. R., Wincker, P., Zoccola, D., Bowler, C., Gorsky, G., Rudich, Y., Vardi, A., and Koren, I.

Published
2020

3. Tara Pacific Expedition’s Atmospheric Measurements of Marine Aerosols across the Atlantic and Pacific Oceans : Overview and Preliminary Results

Author

Flores, J. M., Bourdin, G., Altaratz, O., Trainic, M., Lang-Yona, N., Dzimban, E., Steinau, S., Tettich, F., Planes, S., Allemand, D., Agostini, S., Banaigs, B., Boissin, E., Boss, E., Douville, E., Forcioli, D., Furla, P., Galand, P. E., Sullivan, M. B., Gilson, É., Lombard, F., Moulin, C., Pesant, S., Poulain, J., Reynaud, S., Romac, S., Sunagawa, S., Thomas, O. P., Troublé, R., de Vargas, C., Thurber, R. Vega, Voolstra, C. R., Wincker, P., Zoccola, D., Bowler, C., Gorsky, G., Rudich, Y., Vardi, A., and Koren, I.

Published
2020

6. Rethinking the ocean: conceptual engineering for the next 10000 years.

Author

Isaac, MG, Scharp, K, Koch, S, Bourgeois-Gironde, S, Flamme, E, Gallace, A, Hiernaux, Q, Malatesta, S, Squarcina, E, de Vargas, C, Wanek, E, Schmidt di Freidberg, M, Gallace, A., Malatesta, S., Squarcina, E., de Vargas, Colomban, Wanek, Eva, Schmidt di Freidberg, M., Isaac, MG, Scharp, K, Koch, S, Bourgeois-Gironde, S, Flamme, E, Gallace, A, Hiernaux, Q, Malatesta, S, Squarcina, E, de Vargas, C, Wanek, E, Schmidt di Freidberg, M, Gallace, A., Malatesta, S., Squarcina, E., de Vargas, Colomban, Wanek, Eva, and Schmidt di Freidberg, M.

Published
2023

8. Determinants of community structure in the global plankton interactome

Author

Tara Oceans Coordinators, Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., d'Ovidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sànchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J.

Published
2015

9. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Tara Oceans Coordinators, Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., d'Ortenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

11. Structure and function of the global ocean microbiome

Author

Tara Oceans Coordinators, Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., d'Ovidio, F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G., and Bork, P.

Published
2015

12. Eukaryotic plankton diversity in the sunlit ocean

Author

Tara Oceans Coordinators, de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

13. Patterns and ecological drivers of ocean viral communities

Author

Tara Oceans Coordinators, Brum, J. R., Ignacio-Espinoza, J. C., Doulcier, S. Roux G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., Gorsky, G., Gregory, A. C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B. T., Schwenck, S. M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E., and Sullivan, M. B.

Published
2015

14. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Author

Delmont, T.O., Gaia, M., Hinsinger, D.D., Frémont, P., Vanni, C., Fernandez-Guerra, A., Eren, A.M., Kourlaiev, A., d'Agata, L., Clayssen, Q., Villar, E., Labadie, K., Cruaud, C., Poulain, J., Da Silva, C., Wessner, M., Noel, B., Aury, J.M., de Vargas, C., Bowler, C., Karsenti, E., Pelletier, E., Wincker, P., and Jaillon, O.

Subjects
Cardiovascular and Metabolic Diseases, fungi
Abstract

Marine planktonic eukaryotes play critical roles 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, to our knowledge, 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 completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.

Published
2022

15. Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Author

Cordier, T., Barrenechea-Angeles, I., Henry, N., Lejzerowicz, F., Berney, C., Morard, R., Brandt, A., Cambon-Bonavita, M.A., Guidi, L., Lombard, F., Martinez-Arbizu, P., Massana, R., Orejas, Covadonga, Poulain, J., Smith, C.R., Wincker, P., Arnaud-Haond, S., Gooday, A.J., de Vargas, C., Pawlowski, J., Cordier, T., Barrenechea-Angeles, I., Henry, N., Lejzerowicz, F., Berney, C., Morard, R., Brandt, A., Cambon-Bonavita, M.A., Guidi, L., Lombard, F., Martinez-Arbizu, P., Massana, R., Orejas, Covadonga, Poulain, J., Smith, C.R., Wincker, P., Arnaud-Haond, S., Gooday, A.J., de Vargas, C., and Pawlowski, J.

Abstract

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump.

Published
2022

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

Author

Emilie Villar, Corinne Cruaud, de Vargas C, Patrick Wincker, Chiara Vanni, Da Silva C, Chris Bowler, Karine Labadie, Julie Poulain, Clayssen Q, Eric Karsenti, Leo d’Agata, Guerra Af, Eric Pelletier, Olivier Jaillon, Eren Am, Kourlaiev A, Paul Frémont, Jean-Marc Aury, Morgan Gaia, Damien Daniel Hinsinger, Tom O. Delmont, Bernard Noël, Wessner M, 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), The Globe Institute, The University of Chicago Medicine [Chicago], Station biologique de Roscoff, Centre National de la Recherche Scientifique (CNRS), 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), European Molecular Biology Laboratory (EMBL), 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-09-GENM-0032,TARA-GIRUS,Inventaire et ressources génétiques de virus géants à ADN dans les milieux marins sur Tara-Oceans(2009), ANR-14-CE23-0001,HydroGen,Metagenomique comparative comme instrument de mesure pour la biodiversité. Application à l'étude de la vie dans les océans(2014), 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), ANR-10-INBS-0002,EMBRC-France,CENTRE NATIONAL DE RESSOURCES BIOLOGIQUES MARINES(2010), ANR-17-CE02-0012,ALGALVIRUS,Adaptations Génomique des Algues Marines aux Virus(2017), 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: 261376,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,IHMS(2011), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), 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), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)

Subjects
Marine eukaryotes, Tara Oceans, single-cellgenomics, Marine life, Genomics, Biology, phylogeny, Genome, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, evolution, genomics, 14. Life underwater, 030304 developmental biology, open ocean, functions, 0303 health sciences, metagenomics, Phylogenetic tree, fungi, plankton, 15. Life on land, Plankton, Multicellular organism, Metagenomics, Evolutionary biology, [SDE]Environmental Sciences, anvi’o, ecology, 030217 neurology & neurosurgery
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 metagenomic reads from 143 Tara Oceans stations to reconstruct and manually curate more than 700 abundant and widespread eukaryotic metagenome-assembled genomes ranging from 10 Mbp to up to 1.3 Gbp. The resulting non-redundant genomic resource of 25 billion nucleotides that describe 10 million genes covers a wide range of poorly characterized unicellular and multicellular eukaryotic lineages that complement the long-standing contributions of culture efforts to survey the tree of marine life while better representing plankton from the open ocean. Phylogeny of the DNA-dependent RNA polymerase placed this genomic resource in a comprehensive evolutionary framework that provided insights into the relationships of eukaryotic supergroups. From there, classification of unicellular eukaryotic plankton based on functions encoded in their genes revealed four major groups connecting distantly related lineages such as the diatoms and green algae. There has been a recurrent problem in understanding the interplay between eukaryotes’ vertical evolution and their phenotype. By disentangling phylogenetic signals from functional trends with genomics, we found that neither the classical trophic mode of plankton nor its vertical evolutionary history could fully explain the genomic functional landscape of marine eukaryotes that coexisted 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.

Published
2021

18. Eukaryotic plankton diversity in the sunlit ocean

Author

de Vargas, C., Audic, S., Henry, N., Decelle, J., Mahé, F., Logares, R., Lara, E., Berney, C., Le Bescot, N., Probert, I., Carmichael, M., Poulain, J., Romac, S., Colin, S., Aury, J.-M., Bittner, L., Chaffron, S., Dunthorn, M., Engelen, S., Flegontova, O., Guidi, L., Horák, A., Jaillon, O., Lima-Mendez, G., Lukeš, J., Malviya, S., Morard, R., Mulot, M., Scalco, E., Siano, R., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Bowler, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Raes, J., Sieracki, M. E., Speich, S., Stemmann, L., Sunagawa, S., Weissenbach, J., Wincker, P., and Karsenti, E.

Published
2015

19. Determinants of community structure in the global plankton interactome

Author

Lima-Mendez, G., Faust, K., Henry, N., Decelle, J., Colin, S., Carcillo, F., Chaffron, S., Ignacio-Espinosa, J. C., Roux, S., Vincent, F., Bittner, L., Darzi, Y., Wang, J., Audic, S., Berline, L., Bontempi, G., Cabello, A. M., Coppola, L., Cornejo-Castillo, F. M., dʼOvidio, F., De Meester, L., Ferrera, I., Garet-Delmas, M.-J., Guidi, L., Lara, E., Pesant, S., Royo-Llonch, M., Salazar, G., Sánchez, P., Sebastian, M., Souffreau, C., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Gorsky, G., Not, F., Ogata, H., Speich, S., Stemmann, L., Weissenbach, J., Wincker, P., Acinas, S. G., Sunagawa, S., Bork, P., Sullivan, M. B., Karsenti, E., Bowler, C., de Vargas, C., and Raes, J.

Published
2015

20. Structure and function of the global ocean microbiome

Author

Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., Cornejo-Castillo, F. M., Costea, P. I., Cruaud, C., dʼOvidio, F., Engelen, S., Ferrera, I., Gasol, J. M., Guidi, L., Hildebrand, F., Kokoszka, F., Lepoivre, C., Lima-Mendez, G., Poulain, J., Poulos, B. T., Royo-Llonch, M., Sarmento, H., Vieira-Silva, S., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Bowler, C., de Vargas, C., Gorsky, G., Grimsley, N., Hingamp, P., Iudicone, D., Jaillon, O., Not, F., Ogata, H., Pesant, S., Speich, S., Stemmann, L., Sullivan, M. B., Weissenbach, J., Wincker, P., Karsenti, E., Raes, J., Acinas, S. G., and Bork, P.

Published
2015

21. Environmental characteristics of Agulhas rings affect interocean plankton transport

Author

Villar, E., Farrant, G. K., Follows, M., Garczarek, L., Speich, S., Audic, S., Bittner, L., Blanke, B., Brum, J. R., Brunet, C., Casotti, R., Chase, A., Dolan, J. R., dʼOrtenzio, F., Gattuso, J.-P., Grima, N., Guidi, L., Hill, C. N., Jahn, O., Jamet, J.-L., Le Goff, H., Lepoivre, C., Malviya, S., Pelletier, E., Romagnan, J.-B., Roux, S., Santini, S., Scalco, E., Schwenck, S. M., Tanaka, A., Testor, P., Vannier, T., Vincent, F., Zingone, A., Dimier, C., Picheral, M., Searson, S., Kandels-Lewis, S., Oceans Coordinators, Tara, Acinas, S. G., Bork, P., Boss, E., de Vargas, C., Gorsky, G., Ogata, H., Pesant, S., Sullivan, M. B., Sunagawa, S., Wincker, P., Karsenti, E., Bowler, C., Not, F., Hingamp, P., and Iudicone, D.

Published
2015

22. Patterns and ecological drivers of ocean viral communities

Author

Brum, J. R., Ignacio-Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., Gorsky, G., Gregory, A. C., Guidi, L., Hingamp, P., Iudicone, D., Not, F., Ogata, H., Pesant, S., Poulos, B. T., Schwenck, S. M., Speich, S., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Oceans Coordinators, Tara, Bork, P., Bowler, C., Sunagawa, S., Wincker, P., Karsenti, E., and Sullivan, M. B.

Published
2015

23. A robust approach to estimate relative phytoplankton cell abundance from metagenomes

Author

Patrick Wincker, Sébastien Colin, Chris Bowler, Pierella Karlusich Jj, Richard G. Dorrell, de Vargas C, Josep M. Gasol, Adriana Zingone, Eleonora Scalco, Fabien Lombard, Lucie Zinger, Eric Pelletier, and Silvia G. Acinas

Subjects
0303 health sciences, Biomass (ecology), Phototroph, 030306 microbiology, fungi, 15. Life on land, Ribosomal RNA, Biology, Genome, 03 medical and health sciences, 13. Climate action, Evolutionary biology, Abundance (ecology), Metagenomics, Phytoplankton, 14. Life underwater, Relative species abundance, 030304 developmental biology
Abstract

Phytoplankton account for >45% of primary production on Earth, and hence have an enormous impact on aquatic food webs and on the entire Earth System. Their members are found across many of the major clades of the tree of life, including prokaryotes (cyanobacteria) and multiple eukaryotic lineages. Phytoplankton communities are generally studied by PCR amplification of rRNA marker genes from the DNA extracted from environmental samples and high-throughput sequencing of the amplicons. However, our appreciation of phytoplankton abundance or biomass is limited by PCR-amplification biases, rRNA gene copy number variations across taxa and the fact that rRNA do not provide insights into metabolic traits such as photosynthesis (i.e., it is sometimes difficult to distinguish an rRNA sequence of a phytoplanktonic species from a phylogenetically close non-photosynthetic species). In addition, rRNA marker genes fail to capture both cyanobacteria and photosynthetic eukaryotes simultaneously, thus hampering assessment of the entire phytoplankton community. Here, we propose to use the core single-copy photosynthetic gene psbO extracted from metagenomes to circumvent these limitations: the method is PCR-free, and the gene is present in both prokaryotes and eukaryotes, mainly in one copy per genome. We applied and validated this new strategy with the Tara Oceans datasets, and showed in most cases improved correlations with flow cytometry and microscopy than when based on rRNA genes. Furthermore, we revealed unexpected features of the ecology of these organisms, such as the high abundance of picocyanobacterial aggregates and symbionts in the ocean, and the decrease in relative abundance of phototrophs towards the larger size classes of marine communities of dinoflagellates. To facilitate the incorporation of psbO in future molecular-based surveys, we released a curated database including >20,000 unique sequences. Overall, psbO appears to be a promising new gene marker for improving molecular-based evaluations of phytoplankton communities.

Published
2021

24. Phytoplankton taxonomic and functional diversity patterns across a coastal tidal front

Author

Ramond, P., Siano, R., Schmitt, S., de Vargas, C., Marié, L., Memery, L., Sourisseau, M., Ramond, P., Siano, R., Schmitt, S., de Vargas, C., Marié, L., Memery, L., and Sourisseau, M.

Abstract

Oceanic physics at fine scale; e.g. eddies, fronts, filaments; are notoriously difficult to sample. However, an increasing number of theoretical approaches hypothesize that these processes affect phytoplankton diversity which have cascading effects on regional ecosystems. In 2015, we targeted the Iroise Sea (France) and evidenced the setting up of the Ushant tidal front from the beginning of spring to late summer. Seawater samples were taken during three sampling cruises and DNA-barcoding allowed us to investigate patterns of eukaryotic phytoplankton diversity across this front. First focusing on patterns of taxonomic richness, we evidenced that the front harbored a hotspot of eukaryotic phytoplankton diversity sustained throughout summer. We then detail the ecological processes leading to the formation of this hotspot by studying shifts in community composition across the Iroise Sea. Physical mixing mingled the communities surrounding the front, allowing the formation of a local ecotone, but it was cycles of disturbances and nutrient inputs over the front that allowed a decrease in competitive exclusion, which maintained a higher diversity of rare phytoplankton taxa. These processes did not select a specific ecological strategy as inferred by a trait approach coupled to our taxonomic approach. Instead the front favored higher richness within widespread strategies, resulting in functional redundancy. We detail how fine-scale ocean physics affect phytoplankton diversity and suppose that this interplay is a major control on regional ecosystems.

Published
2021

25. Sensitivity of coccolithophores to carbonate chemistry and ocean acidification

Author

Beaufort, L., Probert, I., de Garidel-Thoron, T., Bendif, E.M., Ruiz-Pino, D., Metzl, N., Goyet, C., Buchet, N., Coupel, P., Grelaud, M., Rost, B., Rickaby, R.E.M., and de Vargas, C.

Subjects
Water acidification -- Environmental aspects, Carbonates -- Chemical properties -- Environmental aspects, Coccolithophorids -- Chemical properties, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

About one-third of the carbon dioxide (C[O.sub.2]) released into the atmosphere as a result of human activity has been absorbed by the oceans (1), where it partitions into the constituent ions of carbonic acid. This leads to ocean acidification, one of the major threats to marine ecosystems (2) and particularly to calcifying organisms such as corals (3,4), foraminifera (5-7) and coccolithophores (8). Coccolithophores are abundant phytoplankton that are responsible for a large part of modern oceanic carbonate production. Culture experiments investigating the physiological response of coccolithophore calcification to increased C[O.sub.2] have yielded contradictory results between and even within species (8-11). Here we quantified the calcite mass of dominant coccolithophores in the present ocean and over the past forty thousand years, and found a marked pattern of decreasing calcification with increasing partial pressure of C[O.sub.2] and concomitant decreasing concentrations of C[O.sub.3.sup.2-]. Our analyses revealed that differentially calcified species and morphotypes are distributed in the ocean according to carbonate chemistry. A substantial impact on the marine carbon cycle might be expected upon extrapolation of this correlation to predicted ocean acidification in the future. However, our discovery of a heavily calcified Emiliania huxleyi morphotype in modern waters with low pH highlights the complexity of assemblage-level responses to environmental forcing factors., To assess the influence of the environment on coccolithophore calcification, we investigated 180 surface-water and 555 sediment-core samples encompassing a wide spectrum of present and past oceanic conditions (Fig. 1). [...]

Published
2011
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26. An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities

Author

Brandt M, Trouche B, Henry N, Liautard-Haag C, Maignien L, de Vargas C, Wincker P, Poulain J, Zeppilli D, and Arnaud-Haond S

Abstract

The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNAfor logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.

Published
2020

27. Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016–2018)

Author

Gorsky, Gabriel, Bourdin, Guillaume, Lombard, Fabien, Pedrotti, Maria Luiza, Audrain, Samuel, Bin, Nicolas, Boss, Emmanuel, Bowler, Chris, Cassar, Nicolas, Caudan, Loic, Chabot, Genevieve, Cohen, Natalie R., Cron, Daniel, De Vargas, Colomban, Dolan, John R., Douville, Eric, Elineau, Amanda, Flores, J. Michel, Ghiglione, Jean Francois, Haentjens, Nils, Hertau, Martin, John, Seth G., Kelly, Rachel L., Koren, Ilan, Lin, Yajuan, Marie, Dominique, Moulin, Clementine, Moucherie, Yohann, Pesant, Stephane, Picheral, Marc, Poulain, Julie, Pujo-pay, Mireille, Reverdin, Gilles, Romac, Sarah, Sullivan, Mathew B., Trainic, Miri, Tressol, Marc, Trouble, Romain, Vardi, Assaf, Voolstra, Christian R., Wincker, Patrick, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Gilson, Eric, Reynaud, Stephanie, Sunagawa, Shinichi, Thomas, Olivier P., Thurber, Rebecca Lisette Vega, Zoccola, Didier, Planes, Serge, Allemand, Denis, Karsenti, Eric, Planes, S., Banaig, B., Boissin, E., Iwankow, G., Allemand, D., Zoccola, D., Reynaud, S., Beraud, E., Djerbi, N., Forcioli, D., Furla, P., Gilson, E., Mcmind, R., Ottaviani, A., Rottinger, E., Rouan, A., Zamoum, T., Flume, B. C. C., Pogoreutz, C., Voolstra, C. R., Rothig, T., Ziegler, M., Paoli, L., Ruscheweyh, H-j, Salazar, G., Sunagawa, S., Flores, J. M., Koren, I, Trainic, M., Lang-yona, N., Vardi, A., Conan, P., Ghiglione, J-f, Pujo-pay, M., Galand, P. E., Hochart, C., Audrain, S., Bourgois, E., Hertau, M., Lancelot, J., Monmarche, D., Moulin, C., Moucherie, Y., Trouble, R., Boss, E., Bourdin, G., Haentjens, N., Karp-boss, L., Agostini, S., Mitsuhashi, G., Kitano, Y., Da Silva, O., Dolan, J. R., Gorsky, G., Lemee, R., Lombard, F., Pedrotti, M-l, Cronin, D., Sullivan, M., Armstrong, E., Aury, J-m, Barbe, V, Belser, C., Carradec, Q., Labadie, K., Le-hoang, J., Noel, B., Poulain, J., Wincker, P., Klinges, G., Vega-thunder, R., Bonnival, E., De Vargas, C., Henry, N., Marie, D., Romac, S., Pesant, S., Miguel-gorda, M., Thomas, O. P., Bowler, C., Friedrich, R., Cassar, N., Lin, Y., John, S. G., Kelly, R. L., Cohen, N. R., Reverdin, G., Filee, J., Pedrotti, Maria Luiza, Organisation et montée en puissance d'une Infrastructure Nationale de Génomique - - France-Génomique2010 - ANR-10-INBS-0009 - INBS - VALID, Laboratoires d'excellence - LabexMER Marine Excellence Research: a changing ocean - - LabexMER2010 - ANR-10-LABX-0019 - LABX - OLD, Laboratoire d'océanographie de Villefranche (LOV), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), University of Maine, Tara Expéditions, Institut de biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Nicholas School of the Environment, Duke University [Durham], Mercator Océan, Société Civile CNRS Ifremer IRD Météo-France SHOM, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Woods Hole Oceanographic Institution (WHOI), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Laboratoire d'Océanographie Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-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), University of Southern California (USC), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, 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), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), 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), Department of Civil, Environmental and Geodetic Engineering [Columbus], Ohio State University [Columbus] (OSU), Laboratoire d'aérologie (LAERO), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Universität Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Symbiose Marine (SM), Evolution Paris Seine, Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Dpt génétique médicale [CHU Nice], Centre Hospitalier Universitaire de Nice (CHU Nice), Laboratoire d'Ecogéochimie des environnements benthiques (LECOB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), Centre Scientifique de Monaco (CSM), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), European Molecular Biology Laboratory [Heidelberg] (EMBL), TARA, ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-10-LABX-0019,LabexMER,LabexMER Marine Excellence Research: a changing ocean(2010), 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), Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles et de la Guyane (UAG)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Nice Sophia Antipolis (... - 2019) (UNS), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées

Subjects
0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, [SDE.MCG]Environmental Sciences/Global Changes, trace metals, Ocean Engineering, neuston, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, Oceanography, 01 natural sciences, Pacific ocean, taxonomy, neuston/plankton genomics/taxonomy/imaging, ddc:570, Ecosystem, 14. Life underwater, lcsh:Science, Reef, 0105 earth and related environmental sciences, Water Science and Technology, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Global and Planetary Change, geography, geography.geographical_feature_category, aerosols, NCP, IOP, microplastic, plankton genomics, [SDU.OCEAN] Sciences of the Universe [physics]/Ocean, Atmosphere, ACL, 010604 marine biology & hydrobiology, Community structure, imaging, Pelagic zone, Plankton, Inlet, neuston/plankton genomics/taxonomy/imaging, aerosols, NCP, IOP, trace metals, microplastic, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, [SDE.MCG] Environmental Sciences/Global Changes, 13. Climate action, lcsh:Q, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Neuston
Abstract

Interactions between the ocean and the atmosphere occur at the air-sea interface through the transfer of momentum, heat, gases and particulate matter, and through the impact of the upper-ocean biology on the composition and radiative properties of this boundary layer. The Tara Pacific expedition, launched in May 2016 aboard the schooner Tara, was a 29-month exploration with the dual goals to study the ecology of reef ecosystems along ecological gradients in the Pacific Ocean and to assess inter-island and open ocean surface plankton and neuston community structures. In addition, key atmospheric properties were measured to study links between the two boundary layer properties. A major challenge for the open ocean sampling was the lack of ship-time available for work at “stations”. The time constraint led us to develop new underway sampling approaches to optimize physical, chemical, optical, and genomic methods to capture the entire community structure of the surface layers, from viruses to metazoans in their oceanographic and atmospheric physicochemical context. An international scientific consortium was put together to analyze the samples, generate data, and develop datasets in coherence with the existing Tara Oceans database. Beyond adapting the extensive Tara Oceans sampling protocols for high-resolution underway sampling, the key novelties compared to Tara Oceans’ global assessment of plankton include the measurement of (i) surface plankton and neuston biogeography and functional diversity; (ii) bioactive trace metals distribution at the ocean surface and metal-dependent ecosystem structures; (iii) marine aerosols, including biological entities; (iv) geography, nature and colonization of microplastic; and (v) high-resolution underway assessment of net community production via equilibrator inlet mass spectrometry. We are committed to share the data collected during this expedition, making it an important resource important resource to address a variety of scientific questions. ISSN:2296-7745

Published
2019

29. Limits on the electromagnetic counterpart to S190814bv

Author

Watson, A M, primary, Butler, N R, additional, Lee, W H, additional, Becerra, R L, additional, Pereyra, M, additional, Angeles, F, additional, Farah, A, additional, Figueroa, L, additional, Gónzalez-Buitrago, D, additional, Quirós, F, additional, Ruíz-Díaz-Soto, J, additional, Tejada de Vargas, C, additional, Tinoco, S J, additional, and Wolfram, T, additional

Published
2020
Full Text
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31. The Tara Pacific expedition-A pan-ecosystemic approach of the '-omics' complexity of coral reef holobionts across the Pacific Ocean

Author

Planes, Serge, Allemand, Denis, Agostini, Sylvain, Banaigs, Bernard, Boissin, Emilie, Boss, Emmanuel, Bourdin, Guillaume, Bowler, Chris, Douville, Eric, Flores, J. Michel, Forcioli, Didier, Furla, Paola, Galand, Pierre E., Ghiglione, Jean-francois, Gilson, Eric, Lombard, Fabien, Moulin, Clementine, Pesant, Stephane, Poulain, Julie, Reynaud, Stephanie, Romac, Sarah, Sullivan, Matthew B., Sunagawa, Shinichi, Thomas, Olivier P., Trouble, Romain, De Vargas, Colomban, Thurber, Rebecca Vega, Voolstra, Christian R., Wincker, Patrick, Zoccola, Didier, Planes, S., Allemand, D., Agostini, S., Armstrong, E., Audrain, S., Aury, J-m, Banaig, B., Barbe, V, Belser, C., Beraud, E., Boissin, E., Bonnival, E., Boss, E., Bourdin, G., Bourgois, E., Bowler, C., Carradec, Q., Cassar, N., Cohen, N. R., Conan, P., Cronin, D. R., Da Silva, O., De Vargas, C., Djerbi, N., Dolan, J. R., Herta, Dominguez G., Du J, Filee, J., Flores, J. M., Forcioli, D., Friedrich, R., Furla, P., Galand, P. E., Ghiglione, J-f, Gilson, E., Gorsky, G., Guinther, M., Haentjens, N., Henry, N., Hertau, M., Hochart, C., Hume, B. C. C., Iwankow, G., John, S. G., Karp-boss, L., Kelly, R. L., Kitano, Y., Klinges, G., Koren, I, Labadie, K., Lancelot, J., Lang-yona, N., Le-hoang, J., Lemee, R., Lin, Y., Lombard, F., Marie, D., Mcmind, R., Miguel-gordo, M., Trainic, M., Monmarche, D., Moulin, C., Mucherie, Y., Noel, B., Ottaviani, A., Paoli, L., Pedrotti, M-l, Pesant, S., Pogoreutz, C., Poulain, J., Pujo-pay, M., Reverdin, G., Reynaud, S., Romac, S., Rothig, T., Rottinger, E., Rouan, A., Ruscheweyh, H-j, Salazar, G., Sullivan, M. B., Sunagawa, S., Thomas, O. P., Trouble, R., Vardi, A., Vega-thunder, R., Voolstra, C. R., Wincker, P., Zahed, A., Zamoum, T., Ziegler, M., Zoccola, D., Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre Scientifique de Monaco (CSM), Tara Expéditions, Shimoda Marine Research Center, Université de Tsukuba = University of Tsukuba, University of Maine, 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 (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 des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Géochrononologie Traceurs Archéométrie (GEOTRAC), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Earth and Planetary Science [Rehovot], Weizmann Institute of Science [Rehovot, Israël], Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), 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 Microbienne (LOMIC), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Observatoire océanologique de Banyuls (OOB), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, 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), ECOlogy of MArine Plankton (ECOMAP), 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), Ohio State University [Columbus] (OSU), Department of Biology [ETH Zürich] (D-BIOL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), National University of Ireland [Galway] (NUI Galway), Oregon State University (OSU), University of Konstanz, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Duke University [Durham], Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Chemistry and Geochemistry (WHOI), Woods Hole Oceanographic Institution (WHOI), Évolution, génomes, comportement et écologie (EGCE), Université Paris-Sud - Paris 11 (UP11)-IRD-Centre National de la Recherche Scientifique (CNRS), Department of Earth Sciences [USC Los Angeles], University of Southern California (USC), Martin Ryan Institute, 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), University of Derby [United Kingdom], Justus-Liebig-Universität Gießen = Justus Liebig University (JLU), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), ANR-17-CE02-0020,CORALGENE,Complexité génomique de l'holobionte ' corail ' à l'échelle du Pacifique(2017), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), 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), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire océanologique de Banyuls (OOB), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-IRD-Université Paris-Sud - Paris 11 (UP11), 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), Justus-Liebig-Universität Gießen (JLU), Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)

Subjects
0301 basic medicine, Topography, Coral reefs, Effects of global warming on oceans, Coral, Biodiversity, Marine and Aquatic Sciences, Ecosystem services, 0302 clinical medicine, Community Page, Oceans, Biology (General), Islands, [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, geography.geographical_feature_category, Ecology, Microbiota, General Neuroscience, Eukaryota, Coral reef, Anthozoa, Plankton, Holobiont, Corals, Expeditions, General Agricultural and Biological Sciences, Marine ecosystems, QH301-705.5, Climate change, Marine Biology, Biology, Ecosystems, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, ddc:570, Animals, Metabolomics, Marine ecosystem, 14. Life underwater, Symbiosis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, Landforms, geography, Pacific Ocean, General Immunology and Microbiology, ACL, Ecology and Environmental Sciences, Organisms, Biology and Life Sciences, Geomorphology, Bodies of Water, 15. Life on land, Invertebrates, 030104 developmental biology, 13. Climate action, Earth Sciences, Reefs, Metagenomics, Reef ecosystems, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery
Abstract

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects—in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the “-omics” complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016–2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east–west transect from Panama to Papua New Guinea and a south–north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene., This Community Page article presents the Tara Pacific expedition, which aims to shed light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs, and providing a reference of the biological state of modern reef systems.

Published
2019

32. Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides

Author

Morard, R., Füllberg, A., Brummer, G.-J. A., Greco, M., Jonkers, L., Wizemann, A., Weiner, A.K.M., Darling, K., Siccha, M., Ledevin, R., Kitazato, H., de Garidel-Thoron, T., de Vargas, C., Kucera, M., Morard, R., Füllberg, A., Brummer, G.-J. A., Greco, M., Jonkers, L., Wizemann, A., Weiner, A.K.M., Darling, K., Siccha, M., Ledevin, R., Kitazato, H., de Garidel-Thoron, T., de Vargas, C., and Kucera, M.

Abstract

The planktonic foraminifera genus Globigerinoides provides a prime example of a species-rich genus in which genetic and morphological divergence are uncorrelated. To shed light on the evolutionary processes that lead to the present-day diversity of Globigerinoides, we investigated the genetic, ecological and morphological divergence of its constituent species. We assembled a global collection of single-cell barcode sequences and show that the genus consists of eight distinct genetic types organized in five extant morphospecies. Based on morphological evidence, we reassign the species Globoturborotalita tenella to Globigerinoides and amend Globigerinoides ruber by formally proposing two new subspecies, G. ruber albus n.subsp. and G. ruber ruber in order to express their subspecies level distinction and to replace the informal G. ruber “white” and G. ruber “pink”, respectively. The genetic types within G. ruber and Globigerinoides elongatus show a combination of endemism and coexistence, with little evidence for ecological differentiation. CT-scanning and ontogeny analysis reveal that the diagnostic differences in adult morphologies could be explained by alterations of the ontogenetic trajectories towards final (reproductive) size. This indicates that heterochrony may have caused the observed decoupling between genetic and morphological diversification within the genus. We find little evidence for environmental forcing of either the genetic or the morphological diversification, which allude to biotic interactions such as symbiosis, as the driver of speciation in Globigerinoides.

Published
2019

33. Plankton networks correlated to the biological carbon pump in the global ocean

Author

Benoiston, A.S., Bittner, L., Guidi, Lionel, Chaffron, S., Eveillard, D., Ayata, S.D., Jean, Géraldine, Pelletier, E., Pesant, S., de Vargas, C., Karsenti, E., Bowler, C., Gorsky, G., Consortium, Tara, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), 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), Combinatoire et Bioinformatique (LS2N - équipe COMBI), 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)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de la Mer de Villefranche (IMEV), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-École Centrale de Nantes (Nantes Univ - ECN), Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST), Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie, Nantes Université (Nantes Univ)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique), Nantes Université (Nantes Univ), 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), Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (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), 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)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography
Abstract

International audience

Published
2017

35. UniEuk : Time to Speak a Common Language in Protistology!

Author

Berney, C, Ciuprina, A, Bender, S, Brodie, J, Edgcomb, V, Kim, E, Rajan, J, Parfrey, LW, Adl, S, Audic, S, Bass, D, Caron, DA, Cochrane, G, Czech, L, Dunthorn, M, Geisen, S, Glöckner, FO, Mahé, F, Quast, C, Kaye, JZ, Simpson, AGB, Stamatakis, A, del Campo, J, Yilmaz, P, de Vargas, C, Berney, C, Ciuprina, A, Bender, S, Brodie, J, Edgcomb, V, Kim, E, Rajan, J, Parfrey, LW, Adl, S, Audic, S, Bass, D, Caron, DA, Cochrane, G, Czech, L, Dunthorn, M, Geisen, S, Glöckner, FO, Mahé, F, Quast, C, Kaye, JZ, Simpson, AGB, Stamatakis, A, del Campo, J, Yilmaz, P, and de Vargas, C

Abstract

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.

Published
2017

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

Author

Mordret, S., Romac, S., Henry, N., Colin, S., Carmichael, M., Berney, C., Audic, S., Richter, D.J., Pochon, X., de Vargas, C., Decelle, Johan, Mordret, S., Romac, S., Henry, N., Colin, S., Carmichael, M., Berney, C., Audic, S., Richter, D.J., Pochon, X., de Vargas, C., and Decelle, Johan

Abstract

Symbiotic partnerships between heterotrophic hosts and intracellular microalgae are common in tropical and subtropical oligotrophic waters of benthic and pelagic marine habitats. The iconic example is the photosynthetic dinoflagellate genus Symbiodinium that establishes mutualistic symbioses with a wide diversity of benthic hosts, sustaining highly biodiverse reef ecosystems worldwide. Paradoxically, although various species of photosynthetic dinoflagellates are prevalent eukaryotic symbionts in pelagic waters, Symbiodinium has not yet been reported in symbiosis within oceanic plankton, despite its high propensity for the symbiotic lifestyle. Here we report a new pelagic photosymbiosis between a calcifying ciliate host and the microalga Symbiodinium in surface ocean waters. Confocal and scanning electron microscopy, together with an 18S rDNA-based phylogeny, showed that the host is a new ciliate species closely related to Tiarina fusus (Colepidae). Phylogenetic analyses of the endosymbionts based on the 28S rDNA gene revealed multiple novel closely related Symbiodinium clade A genotypes. A haplotype network using the high-resolution internal transcribed spacer-2 marker showed that these genotypes form eight divergent, biogeographically structured, subclade types that do not seem to associate with any benthic hosts. Ecological analyses using the Tara Oceans metabarcoding data set (V9 region of the 18S rDNA) and contextual oceanographic parameters showed a global distribution of the symbiotic partnership in nutrient-poor surface waters. The discovery of the symbiotic life of Symbiodinium in the open ocean provides new insights into the ecology and evolution of this pivotal microalga and raises new hypotheses about coastal pelagic connectivity.

Published
2015

41. Global distribution and vertical patterns of a prymnesiophyte–cyanobacteria obligate symbiosis

Author

Cabello, Ana María, Cornejo-Castillo, Francisco, Raho, Nicolás, Blasco, Dolors, Vidal, M., Audic, S., de Vargas, C., Latasa, Mikel, Acinas, Silvia, Massana, R., Cabello, Ana María, Cornejo-Castillo, Francisco, Raho, Nicolás, Blasco, Dolors, Vidal, M., Audic, S., de Vargas, C., Latasa, Mikel, Acinas, Silvia, and Massana, R.

Abstract

A marine symbiosis has been recently discovered between prymnesiophyte species and the unicellular diazotrophic cyanobacterium UCYN-A. At least two different UCYN-A phylotypes exist, the clade UCYN-A1 in symbiosis with an uncultured small prymnesiophyte and the clade UCYN-A2 in symbiosis with the larger Braarudosphaera bigelowii. We targeted the prymnesiophyte–UCYN-A1 symbiosis by double CARD-FISH (catalyzed reporter deposition-fluorescence in situ hybridization) and analyzed its abundance in surface samples from the MALASPINA circumnavigation expedition. Our use of a specific probe for the prymnesiophyte partner allowed us to verify that this algal species virtually always carried the UCYN-A symbiont, indicating that the association was also obligate for the host. The prymnesiophyte–UCYN-A1 symbiosis was detected in all ocean basins, displaying a patchy distribution with abundances (up to 500 cells ml− 1) that could vary orders of magnitude. Additional vertical profiles taken at the NE Atlantic showed that this symbiosis occupied the upper water column and disappeared towards the Deep Chlorophyll Maximum, where the biomass of the prymnesiophyte assemblage peaked. Moreover, sequences of both prymnesiophyte partners were searched within a large 18S rDNA metabarcoding data set from the Tara-Oceans expedition around the world. This sequence-based analysis supported the patchy distribution of the UCYN-A1 host observed by CARD-FISH and highlighted an unexpected homogeneous distribution (at low relative abundance) of B. bigelowii in the open ocean. Our results demonstrate that partners are always in symbiosis in nature and show contrasted ecological patterns of the two related lineages.

Published
2015

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

Author

Read, B.A., Kegel, J., Klute, M.J., Kuo, A., Lefebvre, S.C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J.-M., Frickenhaus, S., Gonzalez, K., Herman, E.K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A.F., Schmutz, J., Schroeder, D., de Vargas, C., Verret, F., von Dassow, P., Valentin, K., Van de Peer, Y., Wheeler, G., Emiliania huxleyi Annotation Consortium, Dacks, J.B., Delwiche, C.F., Dyhrman, S.T., Glöckner, G., John, U., Richards, T., Worden, A.Z., Zhang, X., and Grigoriev, I.V.

Subjects
fungi
Abstract

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent 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.

Published
2013

43. Mortalidad total y morbilidad cardiovascular a largo plazo en pacientes con cardiopatía isquémica que han completado un programa de rehabilitación cardíaca y prevención secundaria

Author

Expósito-Tirado, J.A., primary, Aguilera-Saborido, A., additional, López-Lozano, A.M., additional, Vallejo-Carmona, J., additional, Praena-Fernández, J.M., additional, Cano-Plasencia, G., additional, Linares-Gago, M., additional, Martínez-Martínez, Á., additional, and Echevarría-Ruiz-de-Vargas, C., additional

Published
2014
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44. Pan genome of the phytoplankton Emiliania underpins its global distribution

Author

Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J.-M., Frickenhaus, S., Gonzalez, K., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Shmutz, J., Schroeder, D., De Vargas, C., Verret, F., Von Dassow, P., Valentin, K., Van De Peer, Y., Wheeler, G., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, Alexandra Z., Zhang, X., Grigoriev, I. V., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, M. D., Jenkins, J., Jones, B. M., Lawson, T., Leese, F., Lindquist, E., Lobanov, A., Lomsadze, A., Malik, S.-B., Marsh, M. E., MacKinder, L., Mock, T., Mueller-Roeber, B., Pagarete, A., Parker, M., Probert, I., Quesneville, H., Raines, C., Rensing, S. A., Riaño-Pachón, D. M., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., Van Der Giezen, M., Wahlund, T. M., Williams, B., Wilson, W., Wolfe, G., Wurch, L. L., Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., Salamov, A., Young, J., Aguilar, M., Claverie, J.-M., Frickenhaus, S., Gonzalez, K., Herman, E. K., Lin, Y.-C., Napier, J., Ogata, H., Sarno, A. F., Shmutz, J., Schroeder, D., De Vargas, C., Verret, F., Von Dassow, P., Valentin, K., Van De Peer, Y., Wheeler, G., Dacks, J. B., Delwiche, C. F., Dyhrman, S. T., Glöckner, G., John, U., Richards, T., Worden, Alexandra Z., Zhang, X., Grigoriev, I. V., Allen, A. E., Bidle, K., Borodovsky, M., Bowler, C., Brownlee, C., Mark Cock, J., Elias, M., Gladyshev, V. N., Groth, M., Guda, C., Hadaegh, A., Iglesias-Rodriguez, M. D., Jenkins, J., Jones, B. M., Lawson, T., Leese, F., Lindquist, E., Lobanov, A., Lomsadze, A., Malik, S.-B., Marsh, M. E., MacKinder, L., Mock, T., Mueller-Roeber, B., Pagarete, A., Parker, M., Probert, I., Quesneville, H., Raines, C., Rensing, S. A., Riaño-Pachón, D. M., Richier, S., Rokitta, S., Shiraiwa, Y., Soanes, D. M., Van Der Giezen, M., Wahlund, T. M., Williams, B., Wilson, W., Wolfe, G., and Wurch, L. L.

Abstract

Coccolithophores have influenced the global climate for over 200 million years. These marine phytoplankton can account for 20 per cent 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 CO 2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO 2 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. © 2013 Macmillan Publishers Limited. All rights reserved.

Published
2013
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45. A Holistic Approach to Marine Eco-Systems Biology

Author

Karsenti, E, Acinas, S, Bork, P, Bowler, C, De Vargas, C, Raes, J, Sullivan, M, Arendt, D, Benzoni, F, Claverie, J, Follows, M, Gorsky, G, Hingamp, P, Iudicone, D, Jaillon, O, Kandels-Lewis, S, Krzic, U, Not, F, Ogata, H, Pesant, S, Reynaud, E, Sardet, C, Sieracki, M, Speich, S, Velayoudon, D, Weissenbach, J, Wincker, P, Acinas, SG, Claverie, J-M, Reynaud, EG, Sieracki, ME, Karsenti, E, Acinas, S, Bork, P, Bowler, C, De Vargas, C, Raes, J, Sullivan, M, Arendt, D, Benzoni, F, Claverie, J, Follows, M, Gorsky, G, Hingamp, P, Iudicone, D, Jaillon, O, Kandels-Lewis, S, Krzic, U, Not, F, Ogata, H, Pesant, S, Reynaud, E, Sardet, C, Sieracki, M, Speich, S, Velayoudon, D, Weissenbach, J, Wincker, P, Acinas, SG, Claverie, J-M, Reynaud, EG, and Sieracki, ME

Published
2011

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