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| Registros recuperados: 30 | |
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| Alain, Karine; Rolland, Sophie; Crassous, Philippe; Lesongeur, Francoise; Zbinden, Magali; Le Gall, Christian; Godfroy, Anne; Page, Antoine; Juniper, S Kim; Cambon-bonavita, Marie-anne; Duchiron, Francis; Querellou, Joel. |
| A novel thermophilic, chemolithoautotrophic T bacterium, designated as NE1206(T), was isolated from a Juan de Fuca Ridge hydrothermal vent sample (tubes of the annelid polychaete Paralvinella sulfincola attached to small pieces of hydrothermal chimney). The cells were rod-shaped (1.2-3.5x0.4-0.7 mum), occurring as single motile rods or forming macroscopic aggregates visible as pinkish to brownish streamers. The new isolate was anaerobic. It grew between 50 and 70 degreesC (optimum 60-65 degreesC doubling time approximately 1 h 15 min at 60 degreesC), between pH 5.0 and 7.5 (optimum pH around 6.0-6.5) and at sea salts concentrations between 20 and 40 g l(-1) (optimum 30 g l(-1)). Cells grew chemolithoautotrophically in an H-2/CO2 atmosphere (80/20, v/v; 200... |
| Tipo: Text |
Palavras-chave: Thermophile; Nitrate reducing; Lithotroph; Desulfurobacterium crinifex; Deep sea hydrothermal vent; Cell networks. |
| Ano: 2003 |
URL: https://archimer.ifremer.fr/doc/2003/publication-663.pdf |
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| Cozannet, Marc; Borrel, Guillaume; Roussel, Erwan; Moalic, Yann; Allioux, Maxime; Sanvoisin, Amandine; Toffin, Laurent; Alain, Karine. |
| Members of the archaeal order Methanomassiliicoccales are methanogens mainly associated with animal digestive tracts. However, environmental members remain poorly characterized as no representatives not associated with a host have been cultivated so far. In this study, metabarcoding screening combined with quantitative PCR analyses on a collection of diverse non-host-associated environmental samples revealed that Methanomassiliicoccales were very scarce in most terrestrial and aquatic ecosystems. Relative abundance of Methanomassiliicoccales and substrates/products of methanogenesis were monitored during incubation of environmental slurries. A sediment slurry enriched in Methanomassiliicoccales was obtained from a freshwater sample. It allowed the... |
| Tipo: Text |
Palavras-chave: Methanomassiliicoccales; Cultivation; Methyl-compounds; Environmental cluster; Networks. |
| Ano: 2021 |
URL: https://archimer.ifremer.fr/doc/00665/77716/79808.pdf |
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| 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... |
| Tipo: Text |
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| Ano: 2012 |
URL: http://archimer.ifremer.fr/doc/00090/20171/17826.pdf |
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| 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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| Alain, Karine. |
| Cultural and molecular approaches were used to analyse the microbial assemblages associated to the deep-sea hydrothermal vent polychaete worms of the family Alvinellidae. In a first part of the work, the populations associated to three alvinellid species from the Juan de Fuca Ridge (Paralvinella palmiformis, Paralvinella pandorae and Paralvinella sulfincola) were identified by phylogenetic analyses. A wide microbial diversity was detected, like a great number of new sequences or of sequences belonging to species previously unidentified at deep-sea hydrothermal vents. All the libraries were found to be dominated by sequences affiliated to the epsilon-Proteobacteria. In other respects, fermentative micro-organisms belonging to the Thermococcales, the... |
| Tipo: Text |
Palavras-chave: Paralvinella; Alvinella; 16S rRNA; Thermophile; Hydrothermal vent; Paralvinella; Alvinella; ARNr 16S; Thermophile; Source hydrothermale. |
| Ano: 2003 |
URL: http://archimer.ifremer.fr/doc/2005/these-332.pdf |
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| 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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| Gaboyer, Frederic; Vandenabeele-trambouze, Odile; Cao, Junwei; Ciobanu, Maria-cristina; Jebbar, Mohamed; Le Romancer, Marc; Alain, Karine. |
| A novel halophilic bacterium, strain RHS90T, was isolated from marine sediments from the Gulf of Lions, in the Mediterranean Sea. Its metabolic and physiological characteristics were examined under various cultural conditions, including exposure to stressful ones (oligotrophy, high pressure and high concentrations of metals). Based on phylogenetic analysis of the 16S rRNA gene, the strain was found to belong to the genus Halomonas in the class Gammaproteobacteria. Its closest relatives are H. axialensis and H. meridiana (98% similarity). DNA-DNA hybridizations indicated that the novel isolate is genotypically distinct from these species. The DNA G+C content of the strain is 54.4 mol%. The main fatty acids (C18:1ω7c, 2-OH iso-C15:0, C16:0 and/or C19:0 cyclo... |
| Tipo: Text |
Palavras-chave: Halomonas; Taxonomy; Environmental adaptation; Metal tolerance; Poly-beta-hydroxyalkanoate; Compatible. |
| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00201/31253/29658.pdf |
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| Alain, Karine; Querellou, Joel. |
| Since the invention of the Petri dish, there have been continuous efforts to improve efficiency in microbial cultivation. These efforts were devoted to the attainment for diverse growth conditions, simulation of in situ conditions and achievement of high-throughput rates. As a result, prokaryotes catalysing novel redox reactions as well as representatives of abundant, but not-yet cultured taxa, were isolated. Significant insights into microbial physiology have been made by studying the small number of prokaryotes already cultured. However, despite these numerous breakthroughs, microbial cultivation is still a low-throughput process. The main hindrance to cultivation is likely due to the prevailing lack of knowledge on targeted species. In this review, we... |
| Tipo: Text |
Palavras-chave: High throughput cultivation; Cell cell communication; Microbial community; Metabolism; Isolation; Culture. |
| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6820.pdf |
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| Cao, Junwei; Birien, Tiphaine; Gayet, Nicolas; Huang, Zhaobin; Shao, Zongze; Jebbar, Mohamed; Alain, Karine. |
| A novel sulfur-reducing bacterium, strain K6013(T), was isolated from a sulfide sample collected at a depth of 2771 m from a high-temperature hydrothermal vent in the Indian Ocean. Cells were Gram-stain-negative, anaerobic, motile rods (0.92.2 x 0.4-0.6 mu m). The strain grew at NaCl concentrations ranging from 1 to 4.5% (w/v) (optimum 2.5 %), at pH 5 to 8 (optimum pH 6), and at temperatures between 40 and 75 degrees C (optimum 65 degrees C). K6013(T) was an obligate chemolithoautotroph, using thiosulfate, sulfur and nitrate as terminal electron acceptors in the presence of H-2 but not sulfate, sulfite nor nitrite. The major cellular fatty acids were C-16 : 0 (17.4 %), C-18 : 1 omega 7c/C-18 : 1 omega 6c (ummed feature 8, 37.91 %), C-18 : 0 (18.29 %) and... |
| Tipo: Text |
Palavras-chave: Desulfurobacterium; Thermophilic; Hydrothermal vent; Chemolithoautotroph; Sulfur-reducer. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00395/50637/53724.pdf |
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| Cao, Junwei; Gayet, Nicolas; Zeng, Xiang; Shao, Zongze; Jebbar, Mohamed; Alain, Karine. |
| A novel sulfate-reducing bacterium, strain J2(T), was isolated from a serpentinized peridotite sample from the Indian Ocean. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain J2(T) clustered with the genus Desulfovibrio within the family Desulfovibrionaceae, but it showed low similarity (87.95 %) to the type species Desulfovibrio desulfuricans DSM 642(T). It was most closely related to Desulfovibrio portus MSL79(T) (96.96 %), followed by Desulfovibrio aespoeensis Aspo-2(T) (96.11 %), Desulfovibrio piezophilus C1TLV30(T) (96.04 %) and Desulfovibrio profundus DSM 11384(T) (95.17 %). Other available sequences shared less than 93.33 % 16S rRNA gene sequence similarity. Cells were Gram-staining-negative, anaerobic, motile vibrios (2-6 x... |
| Tipo: Text |
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| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00359/47018/47131.pdf |
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| Jiang, Lijing; L'Haridon, Stephane; Jebbar, Mohamed; Xu, Hongxiu; Alain, Karine; Shao, Zongze. |
| Kosmotoga pacifica strain SLHLJ1T is a thermophilic chemoorganoheterotrophic bacterium isolated from a deep-sea hydrothermal sediment. It belongs to the physiologically homogeneous Thermotogaceae family. Here, we describe the phenotypic features of K. pacifica together with its genome sequence and annotation. The chromosome has 2,169,170 bp, organized in one contig. A total of 1897 candidate protein-encoding genes and 177 RNA genes were identified. The 16S rRNA gene sequence of this strain is distantly related to sequences of some relatives classified in the same genus (K. olearia 7.02% and K. shengliensis 7.83%), with dissimilarity percentages close to the threshold generally described for genus delineation. Nevertheless, the percentage of conserved... |
| Tipo: Text |
Palavras-chave: Marine; Hydrothermal vent; Thermotogales; Chemoorganoheterotroph; Thermophile. |
| Ano: 2017 |
URL: http://archimer.ifremer.fr/doc/00371/48191/48324.pdf |
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| Slobodkin, Alexander; Slobodkina, Galina; Allioux, Maxime; Alain, Karine; Jebbar, Mohamed; Shadrin, Valerian; Kublanov, Ilya; Toshchakov, Stepan; Bonch-osmolovskaya, Elizaveta. |
| nformation on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence... |
| Tipo: Text |
Palavras-chave: Autotrophic; Thermophile; RoTCA cycle; CO oxidation; Fe(III)-reduction; Nitrate reduction. |
| Ano: 2019 |
URL: https://archimer.ifremer.fr/doc/00589/70078/68051.pdf |
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| 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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| Dalmasso, Cecile; Oger, Philippe; Selva, Gwendoline; Courtine, Damien; L'Haridon, Stephane; Garlaschelli, Alexandre; Roussel, Erwan; Miyazaki, Junichi; Reveillaud, Julie; Jebbar, Mohamed; Takai, Ken; Maignien, Lois; Alain, Karine. |
| A novel strictly anaerobic, hyperthermophilic archaeon, designated strain CDGST, was isolated from a deep-sea hydrothermal vent in the Cayman Trough at 4964 m water depth. The novel isolate is obligate anaerobe and grows chemoorganoheterotrophically with stimulation of growth by sulphur containing compounds. Its growth is optimal at 75 °C, pH 6.0 and under a pressure of 50 MPa. It possesses the broadest hydrostatic pressure range for growth that has ever been described for a microorganism. Its genomic DNA G + C content is 51.11 mol%. The novel isolate belongs to the genus Thermococcus. Phylogenetic analyses indicated that it is most closely related to Thermococcus barossii DSM17882T based on its 16S rRNA gene sequence, and to ‘Thermococcus onnurineus’ NA1... |
| Tipo: Text |
Palavras-chave: Thermococcus; Piezophile; Hydrothermal vent; Cayman Trough. |
| Ano: 2016 |
URL: http://archimer.ifremer.fr/doc/00348/45949/45655.pdf |
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| Alain, Karine; Callac, Nolwenn; Guegan, Marianne; Lesongeur, Francoise; Crassous, Philippe; Cambon-bonavita, Marie-anne; Querellou, Joel; Prieur, Daniel. |
| A novel strictly anaerobic, thermophilic, sulfur-reducing bacterium, designated PH1209(T), was isolated from an East Pacific Rise hydrothermal vent (13 degrees N) sample and studied using a polyphasic taxonomic approach. Cells were Gram-negative, motile rods (approx. 1.60x0.40 mu m) with a single polar flagellum. Strain PH1209(T) grew at temperatures between 33 and 65 degrees C (optimum 60 degrees C), from pH 5.0 to 8.0 (optimum 6.0-6.5), and between 2 and 4% (w/v) NaCl (optimum 3%). Cells grew chemolithoautotrophically with H-2 as an energy source, So as an electron acceptor and CO2 as a carbon source. Strain PH1209(T) was also able to use peptone and yeast extract as carbon sources. The G+C content of the genomic DNA was 35 mol%. Phylogenetic: analyses... |
| Tipo: Text |
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| Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6585.pdf |
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| Alain, Karine; Olagnon, Michel; Desbruyeres, Daniel; Page, Antoine; Barbier, Georges; Juniper, Kim; Querellou, Joel; Cambon-bonavita, Marie-anne. |
| As part of an ongoing examination of microbial diversity associated with hydrothermal vent polychaetes of the family Alvinellidae, we undertook a culture-independent molecular analysis of the bacterial assemblage associated with mucous secretions of the Northeastern Pacific vent polychaete Paralvinella palmiformis. Using a molecular 16S rDNA-based phylogenetic approach, clone libraries were constructed from two samples collected from active sulfide edifices in two hydrothermal vent fields. In both cases, clone libraries were largely dominated by epsilon-Proteobacteria. Phylotypes belonging to the Cytophaga-Flavobacteria and to the Verrucomicrobia were also largely represented within the libraries. The remaining sequences were related to the taxonomic... |
| Tipo: Text |
Palavras-chave: Proteobacteria; 16S rRNA; Microbial diversity; Phylogeny; Hydrothermal vent; Paralvinella palmiformis. |
| Ano: 2002 |
URL: https://archimer.ifremer.fr/doc/2002/publication-661.pdf |
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| L'Haridon, Stephane; Jiang, Lijing; Alain, Karine; Chalopin, Morgane; Rouxel, Ouafae; Beauverger, Mikael; Xu, Hongxiu; Shao, Zongze; Jebbar, Mohamed. |
| A novel strictly anaerobic thermophilic heterotrophic bacterium, strain SLHLJ1T, was isolated from a Pacific hydrothermal sediment. Cells were Gram-negative coccobacilli (approximately 1.0 × 0.6 μm) with a toga. It grew at temperatures between 33 and 78 °C (optimum 70 °C). Elemental sulphur and l-cystine stimulated its growth. It contained C16:0, C16:1 ω11c, C18:0 and C18:1 ω9c as major fatty acids (>5 %), 3 phospholipids and 2 glycolipids as polar lipids. Its DNA G+C content was 43.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLHLJ1T within the family Thermotogaceae. The novel isolate was most closely related to Kosmotoga arenicorallina (97.93 % 16S rRNA gene sequence similarity), K. olearia (92.43 %) and K. shengliensis... |
| Tipo: Text |
Palavras-chave: Thermotogales; Kosmotoga; Kosmotoga pacifica; Hydrothermal sediment. |
| Ano: 2014 |
URL: http://archimer.ifremer.fr/doc/00171/28204/26509.pdf |
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| Cao, Junwei; Maignien, Lois; Shao, Zongze; Alain, Karine; Jebbar, Mohamed. |
| The complete genome sequence of Desulfovibrio indicus J2(T), a member of the family Desulfovibrionaceae, consists of 3,966,573-bp in one contig and encodes 3,461 predicted genes, 5 noncoding RNAs, 3 rRNAs operons, and 52 tRNA-encoding genes. The genome is consistent with a heterotrophic, anaerobic lifestyle including the sulfate reduction pathway. |
| Tipo: Text |
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| Ano: 2016 |
URL: https://archimer.ifremer.fr/doc/00601/71311/69740.pdf |
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| Allioux, Maxime; Yvenou, Steven; Slobodkina, Galina; Slobodkin, Alexander; Shao, Zongze; Jebbar, Mohamed; Alain, Karine. |
| Marine hydrothermal systems are characterized by a pronounced biogeochemical sulfur cycle with the participation of sulfur-oxidizing, sulfate-reducing and sulfur-disproportionating microorganisms. The diversity and metabolism of sulfur disproportionators are studied to a much lesser extent compared with other microbial groups. Dissulfurirhabdus thermomarina SH388T is an anaerobic thermophilic bacterium isolated from a shallow sea hydrothermal vent. D. thermomarina is an obligate chemolithoautotroph able to grow by the disproportionation of sulfite and elemental sulfur. Here, we present the results of the sequencing and analysis of the high-quality draft genome of strain SH388T. The genome consists of a one circular chromosome of 2,461,642 base pairs, has a... |
| Tipo: Text |
Palavras-chave: Genome annotation; Dissulfurirhabdus; Shallow sea hydrothermal vents; Inorganic sulfur compound disproportionation. |
| Ano: 2020 |
URL: https://archimer.ifremer.fr/doc/00651/76270/77245.pdf |
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| Registros recuperados: 30 | |
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