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| Brandt, Angelika; Gutt, Julian; Hildebrandt, Marc; Pawlowski, Jan; Schwendner, Jakob; Soltwedel, Thomas; Thomsen, Laurenz. |
| Many countries are very active in marine research and operate their own research fleets. In this decade, a number of research vessels have been renewed and equipped with the most modern navigation systems and tools. However, much of the research gear used for biological sampling, especially in the deep-sea, is outdated and dependent on wired operations. The deployment of gear can be very time consuming and, thus, expensive. The present paper reviews wire-dependent, as well as autonomous research gear for biological sampling at the deep seafloor. We describe the requirements that new gear could fulfil, including the improvement of spatial and temporal sampling resolution, increased autonomy, more efficient sample conservation methodologies for morphological... |
| Tipo: Text |
Palavras-chave: Deep-sea; Autonomous sampling devices; Sampling efficiency; Benthic research; Wire times; Robotics. |
| Ano: 2016 |
URL: https://archimer.ifremer.fr/doc/00335/44589/44306.pdf |
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| Gooday, Andrew J.; Holzmann, Maria; Caulle, Clemence; Goineau, Aurelie; Jones, Daniel Ob; Kamenskaya, Olga; Simon-lledo, Erik; Weber, Alexandra A. -t.; Pawlowski, Jan. |
| We describe Aschemonella monile Gooday and Holzmann sp. nov. from the Clarion-Clipperton Zone (CCZ, abyssal eastern equatorial Pacific), a region characterized by commercially significant concentrations of polymetallic nodules. The new species is the most abundant xenophyophore (giant agglutinated foraminifera) in our main sampling area (12-14 degrees N; 116 degrees 30'-117 degrees 26'W). Additional specimens originate from the central CCZ, and from a third area, similar to 900 km NW of the main area, where A. monile numerically dominates the megabenthos in photographic surveys of the seafloor (average densities 1.54 individuals/m(2); peak densities > 3 individuals/m(2)). Aschemonella monile is much larger (>= 7 cm in length) than previously... |
| Tipo: Text |
Palavras-chave: Abyssal megafauna; Biodiversity; Clarion-Clipperton Zone; Deep-sea benthos; Deep-sea mining; Protist. |
| Ano: 2018 |
URL: https://archimer.ifremer.fr/doc/00435/54663/56099.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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| Sierra, Roberto; Canas-duarte, Silvia J.; Burki, Fabien; Schwelm, Arne; Fogelqvist, Johan; Dixelius, Christina; Gonzalez-garcia, Laura N.; Gile, Gillian H.; Slamovits, Claudio H.; Klopp, Christophe; Restrepo, Silvia; Arzul, Isabelle; Pawlowski, Jan. |
| The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that... |
| Tipo: Text |
Palavras-chave: Rhizaria; Parasites; Phylogenomics. |
| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00320/43156/44988.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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| 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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| 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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| Gooday, Andrew J.; Holzmann, Maria; Caulle, Clemence; Goineau, Aurelie; Kamenskaya, Olga; Weber, Alexandra A. -t.; Pawlowski, Jan. |
| Xenophyophores, giant, fragile, agglutinated foraminifera (protists), are major constituents of the abyssal megafauna in the equatorial Pacific Clarion-Clipperton Zone (Ca), a region where seabed mining of polymetallic nodules may occur in the future. As part of a baseline study of benthic communities We made extensive collections of xenophyophores in two areas (UK-1 and OMS) licensed for exploration by the International Seabed Authority. Based on test morphology, we distinguished 36 morphospecies (34 new to science) among 130 specimens. Twenty of these morphospecies yielded 184 DNA sequences, a 14-fold increase in genetic data for xenophyophores that confirms their high diversity in the eastern Ca. A further 15 morphospecies (8 new to science) were... |
| Tipo: Text |
Palavras-chave: Deep-sea mining; Deep-sea benthos; Biodiversity; Protist; Clarion-Clipperton Zone. |
| Ano: 2017 |
URL: https://archimer.ifremer.fr/doc/00381/49275/49680.pdf |
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