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| Registros recuperados: 30 | |
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| 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... |
| Tipo: Text |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00475/58680/61184.pdf |
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| 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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| 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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| 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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| 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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| 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. |
| Tipo: Text |
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| Ano: 2011 |
URL: http://archimer.ifremer.fr/doc/00051/16224/13748.pdf |
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| Carradec, Quentin; Pelletier, Eric; Da Silva, Corinne; Alberti, Adriana; Seeleuthner, Yoann; Blanc-mathieu, Romain; Lima-mendez, Gipsi; Rocha, Fabio; Tirichine, Leila; Labadie, Karine; Kirilovsky, Amos; Bertrand, Alexis; Engelen, Stefan; Madoui, Mohammed-amin; Meheust, Raphael; Poulain, Julie; Romac, Sarah; Richter, Daniel J.; Yoshikawa, Genki; Dimier, Celine; Kandels-lewis, Stefanie; Picheral, Marc; Searson, Sarah; Jaillon, Olivier; Aury, Jean-marc; Karsenti, Eric; Sullivan, Matthew B.; Sunagawa, Shinichi; Bork, Peer; Not, Fabrice; Hingamp, Pascal; Raes, Jeroen; Guidi, Lionel; Ogata, Hiroyuki; De Vargas, Colomban; Iudicone, Daniele; Bowler, Chris; Wincker, Patrick; Tara Oceans Coordinators,. |
| While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their... |
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| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00660/77232/79053.pdf |
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| 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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| Ramond, Pierre; Siano, Raffaele; Schmitt, Sophie; De Vargas, Colomban; Marié, Louis; Memery, Laurent; Sourisseau, Marc. |
| 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... |
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| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00677/78933/81307.pdf |
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| 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 |
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| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00186/29683/28098.pdf |
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| Del Campo, Javier; Mallo, Diego; Massana, Ramon; De Vargas, Colomban; Richards, Thomas A.; Ruiz-trillo, Inaki. |
| The opisthokonts are one of the major super groups of eukaryotes. It comprises two major clades: (i) the Metazoa and their unicellular relatives and (ii) the Fungi and their unicellular relatives. There is, however, little knowledge of the role of opisthokont microbes in many natural environments, especially among non-metazoan and non-fungal opisthokonts. Here, we begin to address this gap by analysing high-throughput 18S rDNA and 18S rRNA sequencing data from different European coastal sites, sampled at different size fractions and depths. In particular, we analyse the diversity and abundance of choanoflagellates, filastereans, ichthyosporeans, nucleariids, corallochytreans and their related lineages. Our results show the great diversity of... |
| Tipo: Text |
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| Ano: 2015 |
URL: https://archimer.ifremer.fr/doc/00374/48492/48863.pdf |
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| 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... |
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| Ano: 2013 |
URL: http://archimer.ifremer.fr/doc/00114/22492/20174.pdf |
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| 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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| Andre, Aurore; Quillevere, Frederic; Morard, Raphael; Ujiie, Yurika; Escarguel, Gilles; De Vargas, Colomban; De Garidel-thoron, Thibault; Douady, Christophe J.. |
| The use of planktonic foraminifera in paleoceanography requires taxonomic consistency and precise assessment of the species biogeography. Yet, ribosomal small subunit (SSUr) DNA analyses have revealed that most of the modern morphospecies of planktonic foraminifera are composed of a complex of several distinct genetic types that may correspond to cryptic or pseudo-cryptic species. These genetic types are usually delimitated using partial sequences located at the 3'end of the SSUrDNA, but typically based on empirical delimitation. Here, we first use patristic genetic distances calculated within and among genetic types of the most common morpho-species to show that intra-type and inter-type genetic distances within morpho-species may significantly overlap,... |
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| Ano: 2014 |
URL: https://archimer.ifremer.fr/doc/00290/40107/38859.pdf |
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| 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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| 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... |
| Tipo: Text |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00595/70719/68946.pdf |
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| Seeleuthner, Yoann; Mondy, Samuel; Lombard, Vincent; Carradec, Quentin; Pelletier, Eric; Wessner, Marc; Leconte, Jade; Mangot, Jean-francois; Poulain, Julie; Labadie, Karine; Logares, Ramiro; Sunagawa, Shinichi; De Berardinis, Veronique; Salanoubat, Marcel; Dimier, Celine; Kandels-lewis, Stefanie; Picheral, Marc; Searson, Sarah; Pesant, Stephane; Poulton, Nicole; Stepanauskas, Ramunas; Bork, Peer; Bowler, Chris; Hingamp, Pascal; Sullivan, Matthew B.; Iudicone, Daniele; Massana, Ramon; Aury, Jean-marc; Henrissat, Bernard; Karsenti, Eric; Jaillon, Olivier; Sieracki, Mike; De Vargas, Colomban; Wincker, Patrick; Tara Oceans Coordinators,. |
| Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy in the oceans. While their roles as primary producers and grazers are well appreciated, other aspects of their life histories remain obscure due to challenges in culturing and sequencing their natural diversity. Here, we exploit single-cell genomics and metagenomics data from the circumglobal Tara Oceans expedition to analyze the genome content and apparent oceanic distribution of seven prevalent lineages of uncultured heterotrophic stramenopiles. Based on the available data, each sequenced genome or genotype appears to have a specific oceanic distribution, principally correlated with water temperature and depth. The genome content provides... |
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| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00660/77234/79044.pdf |
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| 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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| Registros recuperados: 30 | |
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