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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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| Bellec, Laure; Clerissi, Camille; Edern, Roseline; Foulon, Elodie; Simon, Nathalie; Grimsley, Nigel; Desdevises, Yves. |
| Background: Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from... |
| Tipo: Text |
Palavras-chave: Cophylogeny; Prasinovirus; Phycodnaviridae; Mamiellale; Chlorophyta; Specificity. |
| Ano: 2014 |
URL: https://archimer.ifremer.fr/doc/00374/48497/48827.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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| Hummel, Herman; Van Avesaath, Pim; Wijnhoven, Sander; Kleine-schaars, Loran; Degraer, Steven; Kerckhof, Francis; Bojanic, Natalia; Skejic, Sanda; Vidjak, Olja; Rousou, Maria; Orav-kotta, Helen; Kotta, Jonne; Jourde, Jerome; Pedrotti, Maria Luiza; Leclerc, Jean-charles; Simon, Nathalie; Rigaut-jalabert, Fabienne; Bachelet, Guy; Lavesque, Nicolas; Arvanitidis, Christos; Pavloudi, Christina; Faulwetter, Sarah; Crowe, Tasman; Coughlan, Jennifer; Benedetti-cecchi, Lisandro; Dal Bello, Martina; Magni, Paolo; Como, Serena; Coppa, Stefania; Ikauniece, Anda; Ruginis, Tomas; Jankowska, Emilia; Weslawski, Jan Marcin; Warzocha, Jan; Gromisz, Slawomira; Witalis, Bartosz; Silva, Teresa; Ribeiro, Pedro; Fernandes De Matos, Valentina Kirienko; Sousa-pinto, Isabel; Veiga, Puri; Troncoso, Jesus; Guinda, Xabier; Juanes De La Pena, Jose Antonio; Puente, Araceli; Espinosa, Free; Perez-ruzafa, Angel; Frost, Matt; Mcneill, Caroline Louise; Peleg, Ohad; Rilov, Gil. |
| Within the COST action EMBOS (European Marine Biodiversity Observatory System) the degree and variation of the diversity and densities of soft-bottom communities from the lower intertidal or the shallow subtidal was measured at 28 marine sites along the European coastline (Baltic, Atlantic, Mediterranean) using jointly agreed and harmonized protocols, tools and indicators. The hypothesis tested was that the diversity for all taxonomic groups would decrease with increasing latitude. The EMBOS system delivered accurate and comparable data on the diversity and densities of the soft sediment macrozoobenthic community over a large-scale gradient along the European coastline. In contrast to general biogeographic theory, species diversity showed no linear... |
| Tipo: Text |
Palavras-chave: Soft sediment; Benthos; Species diversity; Densities; Harmonization of methods; European cline; Biogeography; Latitudinal diversity gradient (LDG). |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00376/48675/49010.pdf |
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| Blanchard, Michel; Goulletquer, Philippe; Hamon, Dominique; Le Mao, Patrick; Nezan, Elizabeth; Gentil, Franck; Simon, Nathalie; Viard, Frédérique; Ar Gall, Erwan; Grall, Jacques; Hily, Christian; Le Duff, Michel; Stiger-pouvreau, Valérie; Acou, Anthony; Derrien-courtel, Sandrine; Feunteun, Eric; D'Hondt, Jean-loup; Canard, Alain; Ysnel, Frédéric; Perrin, Bertrand. |
| Tipo: Text |
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| Ano: 2010 |
URL: http://archimer.ifremer.fr/doc/00026/13737/10865.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,... |
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| Ano: 2015 |
URL: http://archimer.ifremer.fr/doc/00275/38594/37190.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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