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A Holistic Approach to Marine Eco-Systems Biology ArchiMer
Karsenti, Eric; Acinas, Silvia G.; Bork, Peer; Bowler, Chris; De Vargas, Colomban; Raes, Jeroen; Sullivan, Matthew; Arendt, Detlev; Benzoni, Francesca; Claverie, Jean-michel; Follows, Mick; Gorsky, Gaby; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Kandels-lewis, Stefanie; Krzic, Uros; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Reynaud, Emmanuel Georges; Sardet, Christian; Sieracki, Michael E.; Speich, Sabrina; Velayoudon, Didier; Weissenbach, Jean; Wincker, Patrick.
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Ano: 2011 URL: http://archimer.ifremer.fr/doc/00051/16224/13748.pdf
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Benthic protists: the under-charted majority ArchiMer
Forster, Dominik; Dunthorn, Micah; Mahe, Frederic; Dolan, John R.; Audic, Stephane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-michel; Decelle, Johan; Edvardsen, Bente; Egge, Elianne; Eikrem, Wenche; Gobet, Angelique; Kooistra, Wiebe H. C. F.; Logares, Ramiro; Massana, Ramon; Montresor, Marina; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-tabrizi, Kamran; Simon, Nathalie; Richards, Thomas A.; Santini, Sebastien; Sarno, Diana; Siano, Raffaele; Vaulot, Daniel; Wincker, Patrick; Zingone, Adriana; De Vargas, Colomban; Stoeck, Thorsten.
Marine protist diversity inventories have largely focused on planktonic environments, while benthic protists have received relatively little attention. We therefore hypothesize that current diversity surveys have only skimmed the surface of protist diversity in marine sediments, which may harbour greater diversity than planktonic environments. We tested this by analyzing sequences of the hypervariable V4 18S rRNA from benthic and planktonic protist communities sampled in European coastal regions. Despite a similar number of OTUs in both realms, richness estimations indicated that we recovered at least 70% of the diversity in planktonic protist communities, but only 33% in benthic communities. There was also little overlap of OTUs between planktonic and...
Tipo: Text Palavras-chave: Benthic microbial communities; Coastal environments; Protist diversity; High-throughput sequencing.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00341/45233/44658.pdf
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Community-Level Responses to Iron Availability in Open Ocean Planktonic Ecosystems ArchiMer
Caputi, Luigi; Carradec, Quentin; Eveillard, Damien; Kirilovsky, Amos; Pelletier, Eric; Karlusich, Juan J. Pierella; Vieira, Fabio Rocha Jimenez; Villar, Emilie; Chaffron, Samuel; Malviya, Shruti; Scalco, Eleonora; Acinas, Silvia G.; Alberti, Adriana; Aury, Jean-marc; Benoiston, Anne-sophie; Bertrand, Arnaud; Biard, Tristan; Bittner, Lucie; Boccara, Martine; Brum, Jennifer R.; Brunet, Cedric; Busseni, Greta; Carratala, Anna; Claustre, Herve; Coelho, Luis Pedro; Colin, Sbastien; D'Aniello, Salvatore; Da Silva, Corinne; Del Core, Marianna; Dore, Hugo; Gasparini, Stephane; Kokoszka, Florian; Jamet, Jean-louis; Lejeusne, Christophe; Lepoivre, Cyrille; Lescot, Magali; Lima-mendez, Gipsi; Lombard, Fabien; Lukes, Julius; Maillet, Nicolas; Madoui, Mohammed-amin; Martinez, Elodie; Mazzocchi, Maria Grazia; Neou, Mario B.; Paz-yepes, Javier; Poulain, Julie; Ramondenc, Simon; Romagnan, Jean-baptiste; Roux, Simon; Manta, Daniela Salvagio; Sanges, Remo; Speich, Sabrina; Sprovieri, Mario; Sunagawa, Shinichi; Taillandier, Vincent; Tanaka, Atsuko; Tirichine, Leila; Trottier, Camille; Uitz, Julia; Veluchamy, Alaguraj; Vesela, Jana; Vincent, Flora; Yau, Sheree; Kandels-lewis, Stefanie; Searson, Sarah; Dimier, Cline; Picheral, Marc; Bork, Peer; Boss, Emmanuel; De Vargas, Colomban; Follows, Michael J.; Grimsley, Nigel; Guidi, Lionel; Hingamp, Pascal; Karsenti, Eric; Sordino, Paolo; Stemmann, Lars; Sullivan, Matthew B.; Tagliabue, Alessandro; Zingone, Adriana; Garczarek, Laurence; D'Ortenzio, Fabrizio; Testor, Pierre; Not, Fabrice; D'Alcala, Maurizio Ribera; Wincker, Patrick; Bowler, Chris; Iudicone, Daniele; Gorsky, Gabriel; Jaillon, Olivier; Karp-boss, Lee; Krzic, Uros; Ogata, Hiroyuki; Pesant, Stephane; Raes, Jeroen; Reynaud, Emmanuel G.; Sardet, Christian; Sieracki, Mike; Velayoudon, Didier; Weissenbach, Jean.
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 ‐omics datasets 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 towards iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole sub‐communities co‐varying with...
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00475/58680/61184.pdf
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Comparative Transcriptome of Wild Type and Selected Strains of the Microalgae Tisochrysis lutea Provides Insights into the Genetic Basis, Lipid Metabolism and the Life Cycle ArchiMer
Carrier, Gregory; Garnier, Matthieu; Le Cunff, Loic; Bougaran, Gael; Probert, Ian; De Vargas, Colomban; Corre, E; Cadoret, Jean-paul; Saint-jean, Bruno.
The applied exploitation of microalgae cultures has to date almost exclusively involved the use of wild type strains, deposited over decades in dedicated culture collections. Concomitantly, the concept of improving algae with selection programs for particular specific purposes is slowly emerging. Studying since a decade an economically and ecologically important haptophyte Tisochrysis lutea (Tiso), we took advantage of the availability of wild type (Tiso-Wt) and selected (Tiso-S2M2) strains to conduct a molecular variations study. This endeavour presented substantial challenges: the genome assembly was not yet available, the life cycle unknown and genetic diversity of Tiso-Wt poorly documented. This study brings the first molecular data in order to set up...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00175/28662/27089.pdf
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Coupling between taxonomic and functional diversity in protistan coastal communities ArchiMer
Ramond, Pierre; Sourisseau, Marc; Simon, Nathalie; Romac, Sarah; Schmitt, Sophie; Rigaut-jalabert, Fabienne; Henry, Nicolas; De Vargas, Colomban; Siano, Raffaele.
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait‐based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size‐classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the Operational Taxonomic Units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade‐offs) in order to build the best functional groups....
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00478/58964/61554.pdf
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Eukaryotic plankton diversity in the sunlit ocean ArchiMer
De Vargas, Colomban; Audic, Stephane; Henry, Nicolas; Decelle, Johan; Mahe, Frederic; Logares, Ramiro; Lara, Enrique; Berney, Cedric; Le Bescot, Noan; Probert, Ian; Carmichael, Margaux; Poulain, Julie; Romac, Sarah; Colin, Sebastien; Aury, Jean-marc; Bittner, Lucie; Chaffron, Samuel; Dunthorn, Micah; Engelen, Stefan; Flegontova, Olga; Guidi, Lionel; Horak, Ales; Jaillon, Olivier; Lima-mendez, Gipsi; Lukes, Julius; Malviya, Shruti; Morard, Raphael; Mulot, Matthieu; Scalco, Eleonora; Siano, Raffaele; Vincent, Flora; Zingone, Adriana; Dimier, Celine; Picheral, Marc; Searson, Sarah; Kandels-lewis, Stefanie; Acinas, Silvia G.; Bork, Peer; Bowler, Chris; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Raes, Jeroen; Sieracki, Michael E.; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Weissenbach, Jean; Wincker, Patrick; Karsenti, Eric.
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, > 0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at similar to 150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups....
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Ano: 2015 URL: http://archimer.ifremer.fr/doc/00270/38135/37217.pdf
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Expanding Tara Oceans Protocols for Underway, Ecosystemic Sampling of the Ocean-Atmosphere Interface During Tara Pacific Expedition (2016-2018) ArchiMer
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.; Douville, Eric; 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..
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...
Tipo: Text Palavras-chave: Neuston/plankton genomics/taxonomy/imaging; Aerosols; NCP; IOP; Trace metals; Microplastic.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00599/71083/69390.pdf
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Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome ArchiMer
Salazar, Guillem; Paoli, Lucas; Alberti, Adriana; Huerta-cepas, Jaime; Cuenca, Miguelangel; Field, Christopher M.; Coelho, Luis Pedro; Cruaud, Corinne; Engelen, Stefan; Gregory, Ann C.; Labadie, Karine; Marec, Claudie; Pelletier, Eric; Royo-llonch, Marta; Roux, Simon; Sánchez, Pablo; Uehara, Hideya; Zayed, Ahmed A.; Zeller, Georg; Carmichael, Margaux; Dimier, Céline; Ferland, Joannie; Kandels, Stefanie; Picheral, Marc; Pisarev, Sergey; Poulain, Julie; Acinas, Silvia G.; Babin, Marcel; Bork, Peer; Bowler, Chris; De Vargas, Colomban; Guidi, Lionel; Hingamp, Pascal; Iudicone, Daniele; Karp-boss, Lee; Karsenti, Eric; Ogata, Hiroyuki; Pesant, Stephane; Speich, Sabrina; Sullivan, Matthew B.; Wincker, Patrick; Sunagawa, Shinichi.
Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes....
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00591/70339/68396.pdf
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Genetic and morphological divergence in the warm-water planktonic foraminifera genus Globigerinoides ArchiMer
Morard, Raphaël; Füllberg, Angelina; Brummer, Geert-jan A.; Greco, Mattia; Jonkers, Lukas; Wizemann, André; Weiner, Agnes K. M.; Darling, Kate; Siccha, Michael; Ledevin, Ronan; Kitazato, Hiroshi; De Garidel-thoron, Thibault; De Vargas, Colomban; Kucera, Michal.
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...
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00595/70719/68946.pdf
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Global Trends in Marine Plankton Diversity across Kingdoms of Life ArchiMer
Ibarbalz, Federico M.; Henry, Nicolas; Costa Brandao, Manoela; Martini, Verine; Busseni, Greta; Byrne, Hannah; Coelho, Luis Pedro; Endo, Hisashi; Gasol, Josep M.; Gregory, Ann C.; Mahe, Frederic; Rigonato, Janaina; Royo-llonch, Marta; Salazar, Guillem; Sanz-saez, Isabel; Scalco, Eleonora; Soviadan, Dodji; Zayed, Ahmed A.; Zingone, Adriana; Labadie, Karine; Ferland, Joannie; Marec, Claudie; Kandels, Stefanie; Picheral, Marc; Dimier, Celine; Poulain, Julie; Pisarev, Sergey; Carmichael, Margaux; Pesant, Stephane; Acinas, Silvia G.; Babin, Marcel; Bork, Peer; Boss, Emmanuel; Bowler, Chris; Cochrane, Guy; De Vargas, Colomban; Follows, Mick; Gorsky, Gabriel; Grimsley, Nigel; Guidi, Lionel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Kandels, Stefanie; Karp-boss, Lee; Karsenti, Eric; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Poulton, Nicole; Raes, Jeroen; Sardet, Christian; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew B.; Sunagawa, Shinichi; Wincker, Patrick; Bopp, Laurent; Lombard, Fabien; Zinger, Lucie.
The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus Glades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21st century could lead to tropicalization of the diversity of most planktonic...
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Ano: 2019 URL: https://archimer.ifremer.fr/doc/00597/70911/69146.pdf
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Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing ArchiMer
Massana, Ramon; Gobet, Angelique; Audic, Stephane; Bass, David; Bittner, Lucie; Boutte, Christophe; Chambouvet, Aurelie; Christen, Richard; Claverie, Jean-michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Forn, Irene; Forster, Dominik; Guillou, Laure; Jaillon, Olivier; Kooistra, Wiebe H. C. F.; Logares, Ramiro; Mahe, Frederic; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Probert, Ian; Romac, Sarah; Richards, Thomas; Santini, Sebastien; Shalchian-tabrizi, Kamran; Siano, Raffaele; Simon, Nathalie; Stoeck, Thorsten; Vaulot, Daniel; Zingone, Adriana; De Vargas, Colomban.
Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant European coastal sites. Environmental deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) from three size fractions (pico-, nano- and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta-diversity analyses split the protist community structure into three main clusters: picoplankton-nanoplankton-dissolved DNA, micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together,...
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Ano: 2015 URL: http://archimer.ifremer.fr/doc/00275/38594/37190.pdf
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Methodology for Single-Cell Genetic Analysis of Planktonic Foraminifera for Studies of Protist Diversity and Evolution ArchiMer
Weiner, Agnes K. M.; Morard, Raphael; Weinkauf, Manuel F. G.; Darling, Kate F.; André, Aurore; Quillévéré, Frédéric; Ujiie, Yurika; Douady, Christophe J.; De Vargas, Colomban; Kucera, Michal.
Single-cell genetic analysis is an essential method to investigate the biodiversity and evolutionary ecology of marine protists. In protist groups that do not reproduce under laboratory conditions, this approach provides the only means to directly associate molecular sequences with cell morphology. The resulting unambiguous taxonomic identification of the DNA sequences is a prerequisite for barcoding and analyses of environmental metagenomic data. Extensive single-cell genetic studies have been carried out on planktonic foraminifera over the past 20 years to elucidate their phylogeny, cryptic diversity, biogeography, and the relationship between genetic and morphological variability. In the course of these investigations, it has become evident that genetic...
Tipo: Text Palavras-chave: Foraminifera; Protists; Single-cell genetics; Cryptic diversity; Comparability; Methods; Laboratory protocols; Standardization.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00383/49460/49938.pdf
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Patterns of Rare and Abundant Marine Microbial Eukaryotes ArchiMer
Logares, Ramiro; Audic, Stephane; Bass, David; Bittner, Lucie; Boutte, Christophe; Christen, Richard; Claverie, Jean-michel; Decelle, Johan; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Gobet, Angelique; Kooistra, Wiebe H. C. F.; Mahe, Frederic; Not, Fabrice; Ogata, Hiroyuki; Pawlowski, Jan; Pernice, Massimo C.; Romac, Sarah; Shalchian-tabrizi, Kamran; Simon, Nathalie; Stoeck, Thorsten; Santini, Sebastien; Siano, Raffaele; Wincker, Patrick; Zingone, Adriana; Richards, Thomas A.; De Vargas, Colomban; Massana, Ramon.
Background Biological communities are normally composed of a few abundant and many rare species. This pattern is particularly prominent in microbial communities, in which most constituent taxa are usually extremely rare. Although abundant and rare subcommunities may present intrinsic characteristics that could be crucial for understanding community dynamics and ecosystem functioning, microbiologists normally do not differentiate between them. Here, we investigate abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere. We surveyed surface waters of six separate coastal locations in Europe, independently considering the picoplankton,...
Tipo: Text
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00186/29683/28098.pdf
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The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy ArchiMer
Guillou, Laure; Bachar, Dipankar; Audic, S; Bass, David; Berney, Cedric; Bittner, Lucie; Boutte, Christophe; Burgaud, Gaetan; De Vargas, Colomban; Decelle, Johan; Del Campo, Javier; Dolan, John R.; Dunthorn, Micah; Edvardsen, Bente; Holzmann, Maria; Kooistra, Wiebe H. C. F.; Lara, Enrique; Le Bescot, Noan; Logares, Ramiro; Mahe, F; Massana, Ramon; Montresor, Marina; Morard, Raphael; Not, Fabrice; Pawlowski, Jan; Probert, Ian; Sauvadet, Anne-laure; Siano, Raffaele; Stoeck, Thorsten; Vaulot, Daniel; Zimmermann, Pascal; Christen, Richard.
The interrogation of genetic markers in environmental meta-barcoding studies is currently seriously hindered by the lack of taxonomically curated reference data sets for the targeted genes. The Protist Ribosomal Reference database (PR2, http://ssurrna. org/) provides a unique access to eukaryotic small sub-unit (SSU) ribosomal RNA and DNA sequences, with curated taxonomy. The database mainly consists of nuclear-encoded protistan sequences. However, metazoans, land plants, macrosporic fungi and eukaryotic organelles (mitochondrion, plastid and others) are also included because they are useful for the analysis of hightroughput sequencing data sets. Introns and putative chimeric sequences have been also carefully checked. Taxonomic assignation of sequences...
Tipo: Text
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00114/22492/20174.pdf
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The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean ArchiMer
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.; Douville, Eric; 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..
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...
Tipo: Text
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00593/70500/68650.pdf
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Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition ArchiMer
Alberti, Adriana; Poulain, Julie; Engelen, Stefan; Labadie, Karine; Romac, Sarah; Ferrera, Isabel; Albini, Guillaume; Aury, Jean-marc; Belser, Caroline; Bertrand, Alexis; Cruaud, Corinne; Da Silva, Corinne; Dossat, Carole; Gavory, Frederick; Gas, Shahinaz; Guy, Julie; Haquelle, Maud; Jacoby, E'Krame; Jaillon, Olivier; Lemainque, Arnaud; Pelletier, Eric; Samson, Gaelle; Wessner, Mark; Acinas, Silvia G.; Royo-llonch, Marta; Cornejo-castillo, Francisco M.; Logares, Ramiro; Fernandez-gomez, Beatriz; Bowler, Chris; Cochrane, Guy; Amid, Clara; Ten Hoopen, Petra; De Vargas, Colomban; Grimsley, Nigel; Desgranges, Elodie; Kandels-lewis, Stefanie; Ogata, Hiroyuki; Poulton, Nicole; Sieracki, Michael E.; Stepanauskas, Ramunas; Sullivan, Matthew B.; Brum, Jennifer R.; Duhaime, Melissa B.; Poulos, Bonnie T.; Hurwitz, Bonnie L.; Pesant, Stephane; Karsenti, Eric; Wincker, Patrick; Bork, Peer; Boss, Emmanuel; Follows, Michael; Gorsky, Gabriel; Hingamp, Pascal; Iudicone, Daniele; Karp-boss, Lee; Not, Fabrice; Raes, Jeroen; Sardet, Christian; Speich, Sabrina; Stemmann, Lars; Sunagawa, Shinichi; Bazire, Pascal; Beluche, Odette; Besnard-gonnet, Marielle; Bordelais, Isabelle; Boutard, Magali; Dubois, Maria; Dumont, Corinne; Ettedgui, Evelyne; Fernandez, Patricia; Garcia, Esperance; Aiach, Nathalie Giordanenco; Guerin, Thomas; Hamon, Chadia; Brun, Elodie; Lebled, Sandrine; Lenoble, Patricia; Louesse, Claudine; Mahieu, Eric; Mairey, Barbara; Martins, Nathalie; Megret, Catherine; Milani, Claire; Muanga, Jacqueline; Orvain, Celine; Payen, Emilie; Perroud, Peggy; Petit, Emmanuelle; Robert, Dominique; Ronsin, Murielle; Vacherie, Benoit.
A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the...
Tipo: Text
Ano: 2017 URL: https://archimer.ifremer.fr/doc/00600/71256/69634.pdf
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