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ABSTRACT: Cold seeps, located along the Sonora Margin transform fault in the Guaymas Basin, were extensively explored during the 'BIG' cruise in June 2010. They present a seafloor mosaic pattern consisting of different faunal assemblages and microbial mats. To investigate this mostly unknown cold and hydrocarbon-rich environment, geochemical and microbiological surveys of the sediments underlying two microbial mats and a surrounding macrofaunal habitat were analyzed in detail. The geochemical measurements suggest biogenic methane production and local advective sulfate-rich fluxes in the sediments. The distributions of archaeal communities, particularly those involved in the methane cycle, were investigated at different depths (surface to 18 cm below the sea floor (cmbsf)) using complementary molecular approaches, such as Automated method of Ribosomal Intergenic Spacer Analysis (ARISA), 16S rRNA libraries, fluorescence in situ hybridization and quantitative polymerase chain reaction with new specific primer sets targeting methanogenic and anaerobic methanotrophic lineages. Molecular results indicate that metabolically active archaeal communities were dominated by known clades of anaerobic methane oxidizers (archaeal anaerobic methanotroph (ANME)-1, -2 and -3), including a novel 'ANME-2c Sonora' lineage. ANME-2c were found to be dominant, metabolically active and physically associated with syntrophic Bacteria in sulfate-rich shallow sediment layers. In contrast, ANME-1 were more prevalent in the deepest sediment samples and presented a versatile behavior in terms of syntrophic association, depending on the sulfate concentration. ANME-3 were concentrated in small aggregates without bacterial partners in a restricted sediment horizon below the first centimetres. These niche specificities and syntrophic behaviors, depending on biological surface assemblages and environmental availability of electron donors, acceptors and carbon substrates, suggest that ANME could support alternative metabolic pathways than syntrophic anaerobic oxidation of methane.
The ISME Journal 02/2013; · 7.38 Impact Factor
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ABSTRACT: Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active
fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the
Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well. The vertical distribution of the archaeal community
assessed by PCR-DGGE highlighted the presence of ANME-2 in surface sediments, and ANME-1 in deeper sediments. Enrichments
of methanogens showed the presence of hydrogenotrophic methanogens of the Methanogenium genus in surface sediment layers as well. The active fraction of the archaeal community was uniquely composed of ANME-2 in
the shallow sulfate-rich sediments. Functional methyl coenzyme M reductase gene libraries showed that sequences affiliated
with the ANME-1 and ANME-3 groups appeared in the deeper sediments but ANME-2 dominated both surface and deeper layers. Finally,
dissimilatory sulfite reductase gene libraries revealed a high SRB diversity (i.e. Desulfobacteraceae, Desulfobulbaceae, Syntrophobacteraceae and Firmicutes) in the shallow sulfate-rich sediments. The SRB diversity was much lower in the deeper section. Overall, these results show
that the microbial community in sediments associated with a pockmark harbour classical cold seep ANME and SRB communities.
KeywordsPockmark–Cold seeps–
Archaea
–ANME–SRB
Antonie van Leeuwenhoek 04/2012; 100(4):639-653. · 2.09 Impact Factor
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ABSTRACT: Pockmarks are seabed geological structures sustaining methane seepage in cold seeps. Based on RNA-derived sequences the active fraction of the archaeal community was analysed in sediments associated with the G11 pockmark, in the Nyegga region of the Norwegian Sea. The anaerobic methanotrophic Archaea (ANME) and sulfate-reducing bacteria (SRB) communities were studied as well. The vertical distribution of the archaeal community assessed by PCR-DGGE highlighted the presence of ANME-2 in surface sediments, and ANME-1 in deeper sediments. Enrichments of methanogens showed the presence of hydrogenotrophic methanogens of the Methanogenium genus in surface sediment layers as well. The active fraction of the archaeal community was uniquely composed of ANME-2 in the shallow sulfate-rich sediments. Functional methyl coenzyme M reductase gene libraries showed that sequences affiliated with the ANME-1 and ANME-3 groups appeared in the deeper sediments but ANME-2 dominated both surface and deeper layers. Finally, dissimilatory sulfite reductase gene libraries revealed a high SRB diversity (i.e. Desulfobacteraceae, Desulfobulbaceae, Syntrophobacteraceae and Firmicutes) in the shallow sulfate-rich sediments. The SRB diversity was much lower in the deeper section. Overall, these results show that the microbial community in sediments associated with a pockmark harbour classical cold seep ANME and SRB communities.
Antonie van Leeuwenhoek 07/2011; 100(4):639-53. · 2.09 Impact Factor
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ABSTRACT: Microbial mats in marine cold seeps are known to be associated with ascending sulfide- and methane-rich fluids. Hence, they could be visible indicators of anaerobic oxidation of methane (AOM) and methane cycling processes in underlying sediments. The Napoli mud volcano is situated in the Olimpi Area that lies on saline deposits; from there, brine fluids migrate upward to the seafloor. Sediments associated with a brine pool and microbial orange mats of the Napoli mud volcano were recovered during the Medeco cruise. Based on analysis of RNA-derived sequences, the "active" archaeal community was composed of many uncultured lineages, such as rice cluster V or marine benthic group D. Function methyl coenzyme M reductase (mcrA) genes were affiliated with the anaerobic methanotrophic Archaea (ANME) of the ANME-1, ANME-2a, and ANME-2c groups, suggesting that AOM occurred in these sediment layers. Enrichment cultures showed the presence of viable marine methylotrophic Methanococcoides in shallow sediment layers. Thus, the archaeal community diversity seems to show that active methane cycling took place in the hypersaline microbial mat-associated sediments of the Napoli mud volcano.
Applied and environmental microbiology 02/2011; 77(9):3120-31. · 3.69 Impact Factor
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ABSTRACT: Siboglinid tubeworms in cold seep sediments can locally modify the geochemical gradients of electron acceptors and donors, hence creating potential microhabitats for prokaryotic populations. The archaeal communities associated with sediments populated by Oligobrachia haakonmosbiensis and Sclerolinum contortum Siboglinid tubeworms in the Storegga Slide were examined in this study. Vertical distribution of archaeal communities was investigated using denaturing gradient gel electrophoresis based on 16S rRNA genes. The active fraction of the archaeal community was assessed by using reverse-transcribed rRNA. Archaeal communities associated with sediments colonized by tubeworms were affiliated with uncultivated archaeal lineages of the Crenarchaeota and Euryarchaeota. The composition of the active archaeal populations changed with depth indicating a reorganization of microbial communities. 16S rRNA gene libraries were dominated by sequences affiliated to the Rice Cluster V which are unusual in marine sediment samples. Moreover, this study provides the first evidence of living Crenarchaeota of the Rice Cluster V in cold seep sediments. Furthermore, the Storegga Slide sediments harbored a high diversity of other minor groups of uncultivated lineages including Terrestrial Miscellaneous Euryarchaeotal Group, Marine Benthic Group (MBG)-D, MBG-E, Deep-Sea Hydrothermal Vent Euryarchaeotal Group, Lake Dagow Sediment, Val Kotinen Lake clade III, and Sippenauer Moor 1. Thus, we hypothesize that the vertical geochemical imprint created by the tubeworms could support broad active archaeal populations in the Siboglinidae-populated Storegga Slide sediments.
Microbial Ecology 10/2010; 60(3):516-27. · 2.91 Impact Factor
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ABSTRACT: 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, Thermosipho, Caminicella (Bacteria) and Thermococcus (Archaea) were obtained from both batch and continuous enrichment cultures while sequences of the autotrophic bacterial genera Deferribacter and Thermodesulfatator were only detected in the continuous bioreactor culture. It is presumed that over time constant metabolite exchanges will have occurred in the continuous enrichment culture enabling the development of a more diverse prokaryotic community. In particular, CO(2) and H(2) produced by the heterotrophic population would support the growth of autotrophic populations. Therefore, continuous enrichment culture is a useful technique to grow over time environmentally representative microbial communities and obtain insights into prokaryotic species interactions that play a crucial role in deep hydrothermal environments.
Extremophiles 12/2007; 11(6):747-57. · 2.94 Impact Factor
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ABSTRACT: 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 not required for growth. The fermentation products identified on glucose were acetate, ethanol, formate, hydrogen and CO(2). The G + C content of the genomic DNA was 28 +/- 1 mol%. Phylogenetic analysis of the 16S rRNA gene placed the strain within the genus Marinitoga, order Thermotogales, in the bacterial domain. On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, the isolate is considered to represent a novel species, for which the name Marinitoga hydrogenitolerans sp. nov. is proposed. The type strain is AT1271(T) (=DSM 16785(T) = JCM 12826(T)).
International journal of systematic and evolutionary microbiology 06/2005; 55(Pt 3):1217-21. · 2.27 Impact Factor
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ABSTRACT: A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20T) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaCl concentration range for growth was 0-120 g l(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at pH 7.0 was 4-50 degrees C, with the optimum at 37-40 degrees C. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %); phosphatidylethanolamines (9 %) were minor components. The fatty acid composition was dominated by side chains of 16 : 0, 14 : 0 and 16 : 1. The G+C content of the genomic DNA was 42 mol%. On the basis of 16S rRNA gene sequence analysis and the secondary structure of the V6 region, this organism was found to belong to the genus Marinilactibacillus and was closely related to Marinilactibacillus psychrotolerans M13-2(T) (99 %), Marinilactibacillus sp. strain MJYP.25.24 (99 %) and Alkalibacterium olivapovliticus strain ww2-SN4C (97 %). Despite the high similarity between their 16S rRNA gene sequences (99 %), the DNA-DNA hybridization levels were less than 20 %. On the basis of physiological and genetic characteristics, it is proposed that this organism be classified as a novel species, Marinilactibacillus piezotolerans sp. nov. The type strain is LT20T (=DSM 16108T=JCM 12337T).
International journal of systematic and evolutionary microbiology 02/2005; 55(Pt 1):345-51. · 2.27 Impact Factor
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ABSTRACT: A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140(T), was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1.8 microm long and 0.4 microm wide, surrounded by an outer sheath-like structure (toga). They grew at 45-80 degrees C (optimum 65 degrees C), pH 5.0-9.0 (optimum pH 6.0) and at sea salt concentrations of 20-60 g l(-1) (optimum 30 g l(-1)). Strain DV1140(T) was able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genus Thermosipho in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the name Thermosipho atlanticus sp. nov. is proposed. The type strain is DV1140(T) (=CIP 108053(T)=DSM 15807(T)).
International journal of systematic and evolutionary microbiology 12/2004; 54(Pt 6):1953-7. · 2.27 Impact Factor
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ABSTRACT: A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16 : 1omega7c, 15 : 0 iso, 16 : 0 and 13 : 0 iso. The G+C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98 %), Shewanella oneidensis (97 %) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were <20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella. Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (=DSM 15900(T)=JCM 12080(T)) as the type strain.
International journal of systematic and evolutionary microbiology 11/2004; 54(Pt 6):1943-9. · 2.27 Impact Factor
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ABSTRACT: A novel anaerobic, Gram-positive, sporulating and strictly chemoorganoheterotrophic bacterium, designated strain DV1184(T), was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were short, straight rods (4 micro m long and 0.8 micro m wide) and were motile with peritrichous flagella. They grew between 35 and 55 degrees C (optimum, 45 degrees C), between pH 5.0 and 8.0 (optimum, 6.0) and at 20-60 g sea salts l(-1) (optimum sea salts concentration, 30 g l(-1)). Strain DV1184(T) was able to ferment yeast extract, tryptone, peptone, glucose, sucrose, maltose and pyruvate. The main fermentation products from glucose were (in decreasing order) formate, acetate and ethanol. The genomic DNA G+C content was 29 mol%. Phylogenetic analysis of the 16S rRNA gene located the strain within cluster XI of the lineage that encompasses the genus Clostridium and related genera in the bacterial domain. On the basis of 16S rDNA sequence comparison and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel species, Tepidibacter formicigenes sp. nov. The type strain is DV1184(T) (=CIP 107893(T)=DSM 15518(T)).
International journal of systematic and evolutionary microbiology 04/2004; 54(Pt 2):439-43. · 2.27 Impact Factor
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ABSTRACT: An extremely thermophilic archaeon, strain MA898, was isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. This strain is a strictly anaerobic coccus of approximately 0.7-1.2 microm in diameter. Optimal temperature, pH, and NaCl concentration for growth are around 85 degrees C, pH 7, and 3%, respectively. Strain MA898 grows preferentially in the presence of elemental sulfur, polysulfur, cystine, or L-cysteine. The microorganism requires rich proteinaceous substrates. BHI-S medium supports rapid growth, with a final concentration of more than 1.2 x 10(9) cells ml(-1), but strain MA898 exhibits poor growth on 2216S medium (yeast/peptone) and poor growth on starch. Growth is inhibited by rifampicin and chloramphenicol at a concentration of 100 microg/ml. The DNA G+C content is 50 mol%. Sequencing of the 16S rRNA gene indicates that strain MA898 belongs to the Thermococcusgenus, and from DNA/DNA hybridization data it is proposed as a new species: Thermococcus atlanticus. The deposition numbers are CIP-107420T and DSM15226.
Extremophiles 05/2003; 7(2):101-9. · 2.94 Impact Factor
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ABSTRACT: An extremely thermophilic archaeon, strain MA898, was isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge. This strain is a strictly anaerobic coccus of approximately 0.7-1.2 m in diameter. Optimal temperature, pH, and NaCl concentration for growth are around 85 C, pH 7, and 3%, respectively. Strain MA898 grows preferentially in the presence of elemental sulfur, polysulfur, cystine, or L-cysteine. The microorganism requires rich proteinaceous substrates. BHI-S medium supports rapid growth, with a final concentration of more than 1.2쎽 cells ml-1, but strain MA898 exhibits poor growth on 2216S medium (yeast/peptone) and poor growth on starch. Growth is inhibited by rifampicin and chloramphenicol at a concentration of 100 g/ml. The DNA G+C content is 50 mol%. Sequencing of the 16S rRNA gene indicates that strain MA898 belongs to the Thermococcus genus, and from DNA/DNA hybridization data it is proposed as a new species: Thermococcus atlanticus. The deposition numbers are CIP-107420T and DSM15226.
Extremophiles 03/2003; 7(2):101-109. · 2.94 Impact Factor
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Karine Alain, Patricia Pignet,
Magali Zbinden,
Morgane Quillevere,
Francis Duchiron,
Jean-Pierre Donval,
Françoise Lesongeur,
Gérard Raguenes,
Philippe Crassous,
Joël Querellou,
Marie-Anne Cambon-Bonavita
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ABSTRACT: A novel thermophilic, anaerobic, strictly chemoorganoheterotrophic bacterium, designated as AM1114T, was isolated from a deep-sea hydrothermal vent sample from the East-Pacific Rise (EPR 13 degrees N). The cells were long (3-10 microm) 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 degrees C inclusive (optimum 55-60 degrees C; 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 AM1114T was an obligately heterotrophic bacterium able to ferment a mixture of 20 amino acids, complex proteinaceous substrates (such as yeast extract, brain-heart infusion or peptone), and carbohydrates such as glucose, galactose or maltose. The main fermentation products on glucose/yeast extract/peptone/sulfur medium were hydrogen, carbon dioxide, butyrate, ethanol, acetate, formate and L-alanine. The G+C content of the genomic DNA (determined by thermal denaturation) was 24.2+/-1 mol%. Phylogenetic analyses of the 16S rRNA gene located the strain within cluster XI of the lineage encompassing the genus Clostridium and related genera (sensu Collins et al., 1994), in the bacterial domain. On the basis of 16S rDNA sequence comparisons and physiological and biochemical characteristics, it is proposed that the isolate should be described as a novel genus, namely Caminicella gen. nov., of which Caminicella sporogenes sp. nov. is the type species. The type strain is AM1114T (= DSM 14501T = CIP 107141T).
International journal of systematic and evolutionary microbiology 10/2002; 52(Pt 5):1621-8. · 2.27 Impact Factor
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ABSTRACT: A novel thermophilic, anaerobic, hydrogen-oxidizing bacterium, designated strain AM1116T, was isolated from an East Pacific Rise hydrothermal vent sample. The cells were rod-shaped (1.01-5 x 0.5 microm), motile with polar flagella. They grew at temperatures between 50 and 70 degrees C (optimum 60 degrees C; doubling time approximately 1.5 h), at between pH 5.0 and 7.5 (optimum around pH 5.5-6.0) and in between 10 and 40 g NaCl l(-1) (optimum 20-25 g l(-1)). Cells grew chemolithoautotrophically in a H2/CO2 atmosphere (80:20; 200 kPa). Poor heterotrophic growth was observed on complex organic substrates. Elemental sulphur and nitrate served as electron acceptors, respectively yielding hydrogen sulphide and ammonia (doubling times were equal with the two electron acceptors). In contrast, when cystine was used as electron acceptor, growth was poor. The G+C content of the genomic DNA was 29 +/- 1 mol %. Phylogenetic analyses of the 16S rRNA gene located the strain within the epsilon-Proteobacteria, in the bacterial domain. On the basis of 16S rDNA sequence comparisons, physiological and biochemical characteristics, it is proposed that the isolate should be described as the type species of a new genus, Caminibacter gen. nov., as Caminibacter hydrogeniphilus sp. nov. The type strain is strain AM1116T (= DSM 14510T = CIP 107140T).
International journal of systematic and evolutionary microbiology 08/2002; 52(Pt 4):1317-23. · 2.27 Impact Factor
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ABSTRACT: A thermophilic, anaerobic, chemo-organotrophic bacterium, designated MV1087T, was isolated from a deep-sea hydrothermal chimney sample collected from the Mid-Atlantic Ridge. The cells were straight, motile and stained gram-negative. Growth was observed from 45 to 65 degrees C, with an optimum around 65 degrees C. No growth was observed at 40 or 70 degrees C. Growth was observed from pH 5.5 to 9.0 and the optimum pH was around 7. The salinity range for growth was 10-100 g sea salt l(-1) (corresponding to 6.5-65 g NaCl l(-1)) with an optimum at 30 g sea salt l(-1) (20 g NaCl l(-1)). Strain MV1087T was heterotrophic, able to ferment proteinaceous substrates, such as brain/heart infusion and gluten, and carbohydrates, such as glucose, xylan and starch. The DNA G+C content was 27 mol%. Phylogenetic analyses using 16S rDNA sequences indicated that strain MV1087T belonged to cluster XII of the Clostridium subphylum. Due to its phenotypic and genotypic characteristics, isolate MV1087T is proposed as a novel species of a new genus, Caloranaerobacter azorensis gen. nov., sp. nov. The type strain is MV1087T (= CNCM I-2543T = DSM 13643T).
International Journal of Systematic and Evolutionary Microbiology. 51(Pt 5):1789-96.
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ABSTRACT: 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 80 °C, 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 nutriments were replaced and a defined medium containing maltose, 19 amino acids and the two nitrogenous bases adenine and thymine, was determined. Secondly, selective feedings and withdrawal of amino acids showed requirements for 14 amino acids.
Research in Microbiology · 2.76 Impact Factor
