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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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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,...
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00275/38594/37190.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
Registros recuperados: 4
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