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Registros recuperados: 27 | |
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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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Henneke, Ghislaine; Gueguen, Yannick; Flament, Didier; Azam, Philippe; Querellou, Joel; Dietrich, Jacques; Hubscher, Ulrich; Raffin, Jean-paul. |
The molecular organization of the replication complex in archaea is similar to that in eukaryotes. Only two proteins homologous to subunits of eukaryotic replication factor C (RFC) have been detected in Pyrococcus abyssi (Pab). The genes encoding these two proteins are arranged in tandem. We cloned these two genes and co-expressed the corresponding recombinant proteins in Escherichia coli. Two inteins present in the gene encoding the small subunit (Pab RFC-small) were removed during cloning. The recombinant protein complex was purified by anion-exchange and hydroxyapatite chromatography. Also, the Pab RFC-small subunit could be purified, while the large subunit (Pab RFC-large) alone was completely insoluble. The highly purified Pab RFC complex possessed an... |
Tipo: Text |
Palavras-chave: PCNA binding domain; Pyrococcus abyssi; Hyperthermophile; Archaea; Replication factor C. |
Ano: 2002 |
URL: https://archimer.ifremer.fr/doc/2002/publication-675.pdf |
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Alain, Karine; Pignet, Patricia; Zbinden, M; Quillevere, M; Duchiron, F; Donval, Jean-pierre; Lesongeur, Francoise; Raguenes, Gerard; Crassous, Philippe; Querellou, Joel; Cambon-bonavita, Marie-anne. |
A novel thermophilic, anaerobic, strictly chemoorganoheterotrophic bacterium, designated as AM1114(T), was isolated from a deep-sea hydrothermal vent sample from the East-Pacific Rise (EPR 13degrees N). The cells were long (3-10 mum) rods, motile with peritrichous flagella, and exhibited a Gram-negative cell wall ultrastructure. In the late stationary phase of growth, cells formed an ovoid, refractile, terminal endospore. They grew at 45-65 degreesC inclusive (optimum 55-60 degreesC; doubling time approx. 45 min), at pH 4.5-8.0 inclusive (optimum pH 7.5-8.0) and at sea salt concentrations of 20-60 g l(-1) inclusive (optimum 25-30 g l(-1)). Strain AM1114(T) was an obligately heterotrophic bacterium able to ferment a mixture of 20 amino acids, complex... |
Tipo: Text |
Palavras-chave: Caminicella sporogenes; Clostridiales; Thermophile; Deep sea hydrothermal vent. |
Ano: 2002 |
URL: http://archimer.ifremer.fr/doc/2002/publication-528.pdf |
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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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Postec, Anne; Le Breton, Claire; Fardeau, Marie-laure; Lesongeur, Francoise; Pignet, Patricia; Querellou, Joel; Ollivier, Bernard; Godfroy, Anne. |
A novel, thermophilic, anaerobic bacterium that is able to tolerate hydrogen was isolated from a deep-sea hydrothermal chimney collected at the Rainbow field on the Mid-Atlantic Ridge. Cells were rod-shaped and surrounded by a sheath-like outer structure (toga); they were weakly motile by means of a polar flagellum. They appeared singly, in pairs or in short chains. They grew at 35-65 degrees C (optimum 60 degrees C), pH 4.5-8.5 (optimum pH 6.0) and 10-65 g sea salts l(-1) (optimum 30-40 g l(-1)). The isolate was organotrophic, and able to grow on various carbohydrates or complex proteinaceous substrates. Growth was not inhibited under 100% hydrogen or in the presence of 2% oxygen in the gas phase. The isolate reduces sulfur, although sulfur reduction is... |
Tipo: Text |
Palavras-chave: Anaerobic bacterium; Marinitoga hydrogenitolerans; Thermotogales; Thermophile; Deep sea vent. |
Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-363.pdf |
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Henneke, Ghislaine; Flament, Didier; Hubscher, Ulrich; Querellou, Joel; Raffin, Jean-paul. |
DNA polymerases carry out DNA synthesis during DNA replication, DNA recombination and DNA repair. During the past five years, the number of DNA polymerases in both eukarya and bacteria has increased to at least 19 and multiple biological roles have been assigned to many DNA polymerases. Archaea, the third domain of life, on the other hand, have only a subset of the eukaryotic-like DNA polymerases. The diversity among the archaeal DNA polymerases poses the intriguing question of their functional tasks. Here, we focus on the two identified DNA polymerases, the family B DNA polymerase B (PabpolB) and the family D DNA polymerase D (PabpolD) from the hyperthermophilic euryarchaeota Pyrococcus abyssi. Our data can be summarized as follows: (i) both Pabpols are... |
Tipo: Text |
Palavras-chave: DNA polymerase; Strand displacement; Gap filling; Euryarchaea; DNA replication. |
Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-423.pdf |
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Postec, Anne; Pignet, Patricia; Cueff-gauchard, Valerie; Schmitt, Anne; Querellou, Joel; Godfroy, Anne. |
The hyperthermophilic archaeon Thermococcus hydrothermalis was cultivated in continuous culture in a gas-lift bioreactor in the absence of elemental sulphur on both proteinaceous and maltose-containing media. Optimal conditions (pH, temperature and gas flow rate), determined on complex media that yielded maximal growth rate and maximal steady state cell density, were obtained at 80degreesC, pH 6 and gas sparging at 0.2 v v(-1) min(-1). Higher steady state cell densities were obtained on a medium containing maltose and yeast extract. In order to design a defined and minimal media, the nutritional requirements of T hydrothermalis were then investigated using continuous culture in the absence of elemental sulphur in the gas-lift bioreactor. First, the complex... |
Tipo: Text |
Palavras-chave: Bioreactor; Defined and minimal media; Culture optimisation; Gas lift bioreactor; Thermococcus hydrothermalis. |
Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-365.pdf |
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Postec, Anne; Urios, Laurent; Lesongeur, Francoise; Ollivier, Bernard; Querellou, Joel; Godfroy, Anne. |
The microflora developing during a continuous enrichment culture from a hydrothermal chimney sample was investigated by molecular methods. The culture was performed in a gas-lift bioreactor under anaerobic conditions, at 90 degrees C and pH 6.5, on a complex medium containing sulfur as the terminal electron acceptor. Archaeal and bacterial diversity was studied. Microorganisms affiliated with the genera Pyrococcus, Marinitoga, and Bacillus were detected through DGGE analysis of 16S rDNA. Additional sequences phylogenetically related to Thermococus and epsilon-Proteobacteria were detected by cloning and sequencing of 16S rDNA from two samples of the enrichment culture. In comparison, the sequences retrieved from cloning analysis from an enrichment culture... |
Tipo: Text |
Palavras-chave: Sequence alignment; Anaerobic digester; Thermotogales; Thermophile; Deep sea vent. |
Ano: 2005 |
URL: http://archimer.ifremer.fr/doc/2005/publication-364.pdf |
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Ishibashi, Jun-ichiro; Lupton, John E.; Yamaguchi, Toshiyuki; Querellou, Joel; Nunoura, Takuro; Takai, Ken. |
TheValu Fa Ridge (VFR) in the southern Lau Basin—located behind the westward‐dipping Tonga‐Kerrnadec subduction zone—was one of the earliest targets to b e explored for hydrothermal activity in the southwestern Pacific Ocean (Figure l).In 1989, the French‐German dive program NAUTILAU (Nautile‐lan) discovered active hydrothermal fields venting high‐temperature fluids with high acidity accompanied by massive ore deposits in this area [Fbuquet et al., 1993]. In September–October 2004, the SWEEP VENTS (Southwestern Edge of Pacific hydrothermal vents) expedition explored and sampled the hydrothermal systems of the VFR using the deep submergence research vehicle (DSRV) Shinkai 6500. The 2004 Shinkai dives focused on the geobiological and geochemical character of... |
Tipo: Text |
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Ano: 2006 |
URL: http://archimer.ifremer.fr/doc/00451/56261/57831.pdf |
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Rouillon, Christophe; Henneke, Ghislaine; Flament, Didier; Querellou, Joel; Raffin, Jean-paul. |
DNA replication in Archaea, as in other organisms, involves large protein complexes called replisomes. In the Euryarchaeota subdomain, only two putative replicases have been identified, and their roles in leading and lagging strand DNA synthesis are still poorly understood. In this study, we focused on the coupling of proliferating cell nuclear antigen (PCNA)loading mechanisms with DNA polymerase function in the Euryarchaea Pyrococcus abyssi. PCNA spontaneously loaded onto primed DNA, and replication factor C dramatically increased this loading. Surprisingly, the family B DNA polymerase (Pol B) also increased PCNA loading, probably by stabilizing the clamp on primed DNA via an essential motif. In contrast, on an RNA-primed DNA template, the PCNA/Pol B... |
Tipo: Text |
Palavras-chave: RF C; PCNA loading; DNA polymerase switching; DNA replication; Archaea. |
Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-2638.pdf |
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Le Breton, Magali; Henneke, Ghislaine; Norais, C; Flament, Didier; Myllykallio, H; Querellou, Joel; Raffin, Jean-paul. |
We report on the characterization of the DNA primase complex of the hyperthermophilic archaeon Pyrococcus abyssi (Pab). The Pab DNA primase complex is composed of the proteins Pabp41 and Pabp46, which show sequence similarities to the p49 and p58 subunits, respectively, of the eukaryotic polymerase alpha-primase complex. Both subunits were expressed, purified, and characterized. The Pabp41 subunit alone had no RNA synthesis activity but could synthesize long (up to 3 kb) DNA strands. Addition of the Pabp46 subunit increased the rate of DNA synthesis but decreased the length of the DNA fragments synthesized and conferred RNA synthesis capability. Moreover, in our experimental conditions, Pab DNA primase had comparable affinities for ribonucleotides and... |
Tipo: Text |
Palavras-chave: Strand displacement; Gap filling; DNA primase; Archaea; DNA replication. |
Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-3520.pdf |
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Desbruyere, D; Arnaud-haond, Sophie; Fabri, Marie-claire; Guezennec, Jean; Querellou, Joel. |
Two third of our Planet are covered by oceans more than 3,000m deep (~ 307 millions km2) and the mean depth of the sea is approximately 3,800m. The volume of the deep ocean (aphotic) is about 1,280 Millions of km3 while the volume of terrestrial ecosystems is only 125 Millions of km3. Therefore, the deep-sea ecosystem is by far the largest complex biome on the Earth. However, it suffers from a general disinterest of the public and decision makers due to its remoteness and inaccessibility. Edward Forbes "azoic theory" is still deeply rooted in most people brains and during public conferences, a large part of the audience being still amazed to hear that macroscopic life does exist in the deepest part of the sea floor (11,000m depth). |
Tipo: Text |
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Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/00153/26452/24558.pdf |
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Postec, Anne; Lesongeur, Francoise; Pignet, Patricia; Ollivier, B; Querellou, Joel; Godfroy, Anne. |
The prokaryotic diversity of culturable thermophilic communities of deep-sea hydrothermal chimneys was analysed using a continuous enrichment culture performed in a gas-lift bioreactor, and compared to classical batch enrichment cultures in vials. Cultures were conducted at 60 degrees C and pH 6.5 using a complex medium containing carbohydrates, peptides and sulphur, and inoculated with a sample of a hydrothermal black chimney collected at the Rainbow field, Mid-Atlantic Ridge, at 2,275 m depth. To assess the relevance of both culture methods, bacterial and archaeal diversity was studied using cloning and sequencing, DGGE, and whole-cell hybridisation of 16S rRNA genes. Sequences of heterotrophic microorganisms belonging to the genera Marinitoga,... |
Tipo: Text |
Palavras-chave: Metabolic interactions; 16S rRNA gene; Thermophiles; Bioreactor; Continuous enrichment cultures; Deep sea hydrothermal vent; Microbial diversity. |
Ano: 2007 |
URL: http://archimer.ifremer.fr/doc/2007/publication-3885.pdf |
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Roussel, Erwan; Cambon-bonavita, Marie-anne; Querellou, Joel; Cragg, B; Webster, G; Prieur, D; Parkes, R. |
Sub-sea-floor sediments may contain two-thirds of Earth's total prokaryotic biomass. However, this has its basis in data extrapolation from ~500-meter to 4-kilometer depths, whereas the deepest documented prokaryotes are from only 842 meters. Here, we provide evidence for low concentrations of living prokaryotic cells in the deepest (1626 meters below the sea floor), oldest (111 million years old), and potentially hottest (~100°C) marine sediments investigated. These Newfoundland margin sediments also have DNA sequences related to thermophilic and/or hyperthermophilic Archaea. These form two unique clusters within Pyrococcus and Thermococcus genera, suggesting unknown, uncultured groups are present in deep, hot, marine sediments (~54° to 100°C). Sequences... |
Tipo: Text |
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Ano: 2008 |
URL: http://archimer.ifremer.fr/doc/2008/publication-4209.pdf |
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Palud, Adeline; Villani, Giuseppe; L'Haridon, Stephane; Querellou, Joel; Raffin, Jean-paul; Henneke, Ghislaine. |
Spontaneous and induced abasic sites in hyperthermophiles DNA have long been suspected to occur at high frequency. Here, Pyrococcus abyssi was used as an attractive model to analyse the impact of such lesions onto the maintenance of genome integrity. We demonstrated that endogenous AP sites persist at a slightly higher level in P. abyssi genome compared with Escherichia coli. Then, the two replicative DNA polymerases, PabpolB and PabpolD, were characterized in presence of DNA containing abasic sites. Both Pabpols had abortive DNA synthesis upon encountering AP sites. Under running start conditions, PabpolB could incorporate in front of the damage and even replicate to the full-length oligonucleotides containing a specific AP site, but only when present at... |
Tipo: Text |
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Ano: 2008 |
URL: http://archimer.ifremer.fr/doc/2008/publication-6113.pdf |
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Castrec, Benoit; Rouillon, Christophe; Henneke, Ghislaine; Flament, Didier; Querellou, Joel; Raffin, Jean-paul. |
Replicative DNA polymerases possess a canonical C-terminal proliferating cell nuclear antigen (PCNA)-binding motif termed the PCNA-interacting protein (PIP) box. We investigated the role of the PIP box on the functional interactions of the two DNA polymerases, PabPol B (family B) and PabPol D (family D), from the hyperthermophilic euryarchaeon Pyrococcus abyssi, with its cognate PCNA. The PIP box was essential for interactions of PabPol B with PCNA, as shown by surface plasmon resonance and primer extension studies. In contrast, binding of PabPol D to PCNA was affected only partially by removing the PIP motif. We identified a second palindromic PIP box motif at the N-terminus of the large subunit of PabPol D that was required for the interactions of PabPol... |
Tipo: Text |
Palavras-chave: Archaea; PIP box; PCNA binding motifs; DNA polymerases; DNA replication. |
Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-7317.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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Takai, Ken; Miyazaki, Masayuki; Hirayama, Hisako; Nakagawa, Satoshi; Querellou, Joel; Godfroy, Anne. |
P>Two novel, thermophilic piezophiles, capable of chemolithoautotrophic growth, are successfully cultivated and isolated from a black smoker chimney at the TAG field (Mid Atlantic Ridge: MAR) by using a piezophilic cultivation technique. Both strains (strains 106 and 108) represent dominant cultivated populations of the microbial communities in the chimney surface habitat. Strain 106 represents typically thin, long spiral cells under the piezophilic growth condition but short bent cells under the non-piezophilic condition. It is a strictly chemolithoautotrophic gammaproteobacterium using reduced sulfur compounds as the electron donors, and nitrate and O-2 as the electron acceptors. Based on the 16S rRNA gene sequence, strain 106 would represent a novel... |
Tipo: Text |
Palavras-chave: Sp. nov.; Ecological signifiance; Hydrostatic pressure; Subsurface biosphere; Base composition; High temperature; Membrane lipids; Gen. nov.; Microorganisms; Diversity. |
Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6652.pdf |
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Slobodkina, G. B.; Kolganova, T. V.; Querellou, Joel; Bonch-osmolovskaya, E. A.; Slobodkin, A. I.. |
A hyperthermophilic, anaerobic, dissimilatory Fe(III)-reducing, facultatively chemolithoautotrophic archaeon (strain SBH6(T)) was isolated from a hydrothermal sample collected from the deepest of the known World Ocean hydrothermal fields, Ashadze field (12 degrees 58' 21 '' N 44 degrees 51' 47 '' W) on the Mid-Atlantic Ridge, at a depth of 4100 m. The strain was enriched using acetate as the electron donor and Fe(III) oxide as the electron acceptor. Cells of strain SBH6(T) were irregular cocci, 0.3-0.5 mu m in diameter. The temperature range for growth was 50-85 degrees C, with an optimum at 81 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.8. Growth of SBH6(T) was observed at NaCl concentrations ranging from 1 to 6 % (w/v) with an... |
Tipo: Text |
Palavras-chave: Dissimilatory reduction; Microorganisms; Gradient. |
Ano: 2009 |
URL: http://archimer.ifremer.fr/doc/2009/publication-6977.pdf |
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Registros recuperados: 27 | |
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