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Registros recuperados: 6
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DNA extractions from deep subseafloor sediments: Novel cryogenic-mill-based procedure and comparison to existing protocols ArchiMer
Alain, Karine; Callac, Nolwenn; Ciobanu, Maria Cristina; Reynaud, Yann; Duthoit, Frederique; Jebbar, Mohamed.
Extracting DNA from deep subsurface sediments is challenging given the complexity of sediments types, low bio-masses, resting structures (spores, cysts) frequently encountered in deep sediments, and the potential presence of enzymatic inhibitors. Promising results for cell lysis efficiency were recently obtained by use of a cryogenic mill (Lipp et al., 2008). These findings encouraged us to devise a DNA extraction protocol using this tool. Thirteen procedures involving a combination of grinding in liquid nitrogen (for various durations and beating rates) with different chemical solutions (phenol, chloroform, SDS, sarkosyl, proteinase, GTC), or with use of DNA recovery kits (MagExtractor (R)) were compared. Effective DNA extraction was evaluated in terms of...
Tipo: Text Palavras-chave: Sediment; DNA extraction; Deep subsurface biosphere.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00056/16691/14364.pdf
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In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths ArchiMer
Redou, Vanessa; Ciobanu, Maria Cristina; Pachiadaki, Maria G.; Edgcomb, Virginia; Alain, Karine; Barbier, Georges; Burgaud, Gaetan.
The deep subseafloor, extending from a few centimeters below the sediment surface to several hundred meters into sedimentary deposits, constitutes the deep biosphere and harbors an unexpected microbial diversity. Several studies have described the occurrence, turnover, activity and function of subseafloor prokaryotes; however, subsurface eukaryotic communities still remain largely underexplored. Ribosomal RNA surveys of superficial and near-surface marine sediments have revealed an unexpected diversity of active eukaryotic communities, but knowledge of the diversity of deep subseafloor microeukaryotes is still scarce. Here, we investigated the vertical distribution of DNA and RNA fungal signatures within subseafloor sediments of the Canterbury basin (New...
Tipo: Text Palavras-chave: 454 pyrotag; Canterbury basin; Deep subseafloor; Fungi; Microeukaryotes.
Ano: 2014 URL: https://archimer.ifremer.fr/doc/00247/35810/34418.pdf
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Microorganisms persist at record depths in the subseafloor of the Canterbury Basin ArchiMer
Ciobanu, Maria Cristina; Burgaud, Gaetan; Dufresne, Alexis; Breuker, Anja; Redou, Vanessa; Ben Maamar, Sarah; Gaboyer, Frederic; Vandenabeele-trambouze, Odile; Lipp, Julius Sebastian; Schippers, Axel; Vandenkoornhuyse, Philippe; Barbier, Georges; Jebbar, Mohamed; Godfroy, Anne; Alain, Karine.
The subsurface realm is colonized by microbial communities to depths of >1000 meters below the seafloor (m.b.sf.), but little is known about overall diversity and microbial distribution patterns at the most profound depths. Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. Representatives of some microbial taxa were also cultivated using methods mimicking in situ conditions. These results suggest that diverse microorganisms persist down to 1922 m.b.sf. in the seafloor of the Canterbury Basin and extend the previously known depth limits of...
Tipo: Text Palavras-chave: Deep biosphere; Subsurface life; Eukaryote; Record depth.
Ano: 2014 URL: http://archimer.ifremer.fr/doc/00201/31243/29895.pdf
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Phaeobacter leonis sp nov., an alphaproteobacterium from Mediterranean Sea sediments ArchiMer
Gaboyer, Frederic; Tindall, Brian J.; Ciobanu, Maria Cristina; Duthoit, Frederique; Le Romancer, Marc; Alain, Karine.
A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306(T), was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306(T) grew at temperatures between 4 and 32 degrees C (optimum 17-22 degrees C), from pH 6.5 to 9.0 (optimum 8.0-9.0) and between 0.5 and 6.0% (w/v) NaCl (optimum 2.0%). Its DNA G+C content was 58.8 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the class Alphaproteobacteria and is related to the genus Phaeobacter. It shares 98.7% 16S rRNA sequence identity with Phaeobacter arcticus, its closest phylogenetic relative. It contained Q-10 as the only respiratory quinone, C-18:1 omega 7c and C-16:0 as major...
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Ano: 2013 URL: http://archimer.ifremer.fr/doc/00166/27750/25981.pdf
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Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin ArchiMer
Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan; Pignet, Patricia; Caprais, Jean-claude; Callac, Nolwenn; Ciobanu, Maria Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent.
Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00203/31408/29801.pdf
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Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments ArchiMer
Ciobanu, Maria Cristina; Rabineau, Marina; Droz, Laurence; Revillon, Sidonie; Ghiglione, J. -f.; Dennielou, Bernard; Jorry, Stephan; Kallmeyer, J.; Etoubleau, Joel; Pignet, Patricia; Crassous, Philippe; Vandenabeele-trambouze, Odile; Laugier, J.; Guegan, Matthieu; Godfroy, Anne; Alain, Karine.
An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine...
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Ano: 2012 URL: http://archimer.ifremer.fr/doc/00090/20171/17826.pdf
Registros recuperados: 6
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