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| Registros recuperados: 20 | |
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| Dittami, Simon M; Arboleda, Enrique; Auguet, Jean-christophe; Bigalke, Arite; Briand, Enora; Cardenas, Paco; Cardini, Ulisse; Decelle, Johan; Engelen, Aschwin; Eveillard, Damien; Gachon, Claire Mm; Griffiths, Sarah; Harder, Tilmann; Kayal, Ehsan; Kazamia, Elena; Lallier, François H; Media, Monica; Marzinelli, Ezequiel M; Morganti, Teresa; Nunez Pons, Laura; Prado, Soizik; Pintado, José; Saha, Mahasweta; Selosse, Marc-andré; Skillings, Derek; Stock, Willem; Sunagawa, Shinichi; Toulza, Eve; Vorobev, Alexey; Leblanc, Catherine; Not, Fabrice. |
| Host-microbe interactions play crucial roles in marine ecosystems, but we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help describe and understand these complex systems. It posits that a host and its associated microbiota, living together in a long-lasting relationship, form the holobiont, and have to be studied together, as a coherent biological and functional unit, in order to understand the biology, ecology and evolution of the organisms. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We... |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00480/59209/61904.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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| 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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| Meng, Arnaud; Corre, Erwan; Probert, Ian; Gutierrez-rodriguez, Andres; Siano, Raffaele; Annamale, Anita; Alberti, Adriana; Da Silva, Corinne; Wincker, Patrick; Le Crom, Stephane; Not, Fabrice; Bittner, Lucie. |
| Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional... |
| Tipo: Text |
Palavras-chave: Genomics; Proteomics; Microbial biology; Molecular evolution; Protists; Transcriptomics. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00444/55550/57209.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... |
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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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| Mansour, Joost Samir; Norlin, Andreas; Llopis Monferrer, Natalia; L'Helguen, Stéphane; Not, Fabrice. |
| Rhizaria are large protistan cells that have been shown to be a major component of the planktic community in the oceans and contribute significantly to major biogeochemical cycles such as carbon or silicon. However, unlike for many other protists, limited data is available on rhizarian cellular carbon (C) and nitrogen (N) content and cell volume. Here we present novel C and N mass to volume equations and ratios for nine Rhizaria taxa belonging to Radiolaria (i.e., Collozoum, Sphaerozoum, Collosphaeridae, Acantharia, Nassellaria, and Spumellaria) and Phaeodaria (i.e., Aulacantha, Protocystis, and Challengeria). The C and N content of collodarian cells was significantly correlated to cell volume as expressed by the mass : vol equations ng C cell−1 =... |
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| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00684/79596/82288.pdf |
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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... |
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| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00475/58680/61184.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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| 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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| Chust, Guillem; Vogt, Meike; Benedetti, Fabio; Nakov, Teofil; Villeger, Sebastien; Aubert, Anais; Vallina, Sergio M.; Righetti, Damiano; Not, Fabrice; Biard, Tristan; Bittner, Lucie; Benoiston, Anne-sophie; Guidi, Lionel; Villarino, Ernesto; Gaborit, Charlie; Cornils, Astrid; Buttay, Lucie; Irisson, Jean-olivier; Chiarello, Marlene; Vallim, Alessandra L.; Blanco-bercial, Leocadio; Basconi, Laura; Guilhaumon, Francois; Ayata, Sakina-dorothee. |
| With global climate change altering marine ecosystems, research on plankton ecology is likely to navigate uncharted seas. Yet, a staggering wealth of new plankton observations, integrated with recent advances in marine ecosystem modeling, may shed light on marine ecosystem structure and functioning. A EuroMarine foresight workshop on the “Impact of climate change on the distribution of plankton functional and phylogenetic diversity” (PlankDiv) identified five grand challenges for future plankton diversity and macroecology research: (1) What can we learn about plankton communities from the new wealth of high-throughput “omics” data? (2) What is the link between plankton diversity and ecosystem function? (3) How can species distribution models be adapted to... |
| Tipo: Text |
Palavras-chave: Plankton; Macroecology; Species distribution; Functional diversity; Climate change; Habitat modeling. |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00625/73739/74755.pdf |
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| 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,... |
| Tipo: Text |
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| Ano: 2015 |
URL: http://archimer.ifremer.fr/doc/00275/38594/37190.pdf |
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| Stern, Rowena; Kraberg, Alexandra; Bresnan, Eileen; Kooistra, Wiebe H. C. F.; Lovejoy, Connie; Montresor, Marina; Moran, Xose Anxelu G.; Not, Fabrice; Salas, Rafael; Siano, Raffaele; Vaulot, Daniel; Amaral-zettler, Linda; Zingone, Adriana; Metfies, Katja. |
| Protists (microbial eukaryotes) are diverse, major components of marine ecosystems, and are fundamental to ecosystem services. In the last 10 years, molecular studies have highlighted substantial novel diversity in marine systems including sequences with no taxonomic context. At the same time, many known protists remain without a DNA identity. Since the majority of pelagic protists are too small to identify by light microscopy, most are neither comprehensively or regularly taken into account, particularly in Long-term Ecological Research Sites. This potentially undermines the quality of research and the accuracy of predictions about biological species shifts in a changing environment. The ICES Working Group for Phytoplankton and Microbial Ecology conducted... |
| Tipo: Text |
Palavras-chave: Protists; Long-term Ecological Research Station; Molecular; Time-series; Questionnaire; Literature survey. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00455/56708/58470.pdf |
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| Decelle, Johan; Siano, Raffaele; Probert, Ian; Poirier, Camille; Not, Fabrice. |
| Acantharia (Radiolaria) are widespread and abundant heterotrophic marine protists, some of which can host endosymbiotic eukaryotic microalgae. Although this photosymbiotic association was first described at the end of the 19th century, the diversity of the symbiotic microalgae remains poorly characterized. Here, we examined the identity of the microalgae associated with the acantharian species Acanthochiasma sp. by sequencing partial 18S and internal transcribed spacer (ITS) ribosomal DNA genes from cultured symbionts and directly from isolated holobiont specimens. Single Acanthochiasma cells contained multiple symbiotic partners, including distantly related dinoflagellates (Heterocapsa sp., Pelagodinium sp., Azadinium sp. and Scrippsiella sp.) as well as... |
| Tipo: Text |
Palavras-chave: Photosymbiosis; Radiolaria; Acantharia; Protists; Microalgae; Plankton. |
| Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00114/22493/21497.pdf |
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| Pesant, Stephane; Not, Fabrice; Picheral, Marc; Kandels-lewis, Stefanie; Le Bescot, Noan; Gorsky, Gabriel; Iudicone, Daniele; Karsenti, Eric; Speich, Sabrina; Trouble, Romain; Dimier, Celine; Searson, Sarah. |
| The Tara Oceans expedition (2009-2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the... |
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| Ano: 2015 |
URL: https://archimer.ifremer.fr/doc/00600/71209/69583.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,... |
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| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00186/29683/28098.pdf |
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| Ishitani, Yoshiyuki; Ujiie, Yurika; De Vargas, Colomban; Not, Fabrice; Takahashi, Kozo. |
| Collodaria are the only group of Radiolaria that has a colonial lifestyle. This group is potentially the most important plankton in the oligotrophic ocean because of its large biomass and the high primary productivity associated with the numerous symbionts inside a cell or colony. The evolution of Collodaria could thus be related to the changes in paleo-productivity that have affected organic carbon fixation in the oligotrophic ocean. However, the fossil record of Collodaria is insufficient to trace their abundance through geological time, because most collodarians do not have silicified shells. Recently, molecular phylogeny based on nuclear small sub-unit ribosomal DNA (SSU rDNA) confirmed Collodaria to be one of five orders of Radiolaria, though the... |
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| Ano: 2012 |
URL: https://archimer.ifremer.fr/doc/00140/25108/23217.pdf |
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| Llopis Monferrer, Natalia; Leynaert, Aude; Tréguer, Paul; Gutiérrez‐rodríguez, Andrés; Moriceau, Brivaela; Gallinari, Morgane; Latasa, Mikel; L'Helguen, Stéphane; Maguer, Jean-francois; Safi, Karl; Pinkerton, Matthew H.; Not, Fabrice. |
| We examined biogenic silica production and elementary composition (biogenic Si, particulate organic carbon and particulate organic nitrogen) of Rhizaria and diatoms in the upper 200 m along a transect in the Southwest Pacific sector of the Southern Ocean during austral summer (January–February 2019). From incubations using the 32Si radioisotope, silicic acid uptake rates were measured at 15 stations distributed in the Polar Front Zone, the Southern Antarctic Circumpolar Current and the Ross Sea Gyre. Rhizaria cells are heavily silicified (up to 7.6 nmol Si cell−1), displaying higher biogenic Si content than similar size specimens found in other areas of the global ocean, suggesting a higher degree of silicification of these organisms in the silicic acid... |
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| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00692/80407/83515.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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| 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 |
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| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00600/71256/69634.pdf |
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| Registros recuperados: 20 | |
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