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PubMed | 2the third institute of oceanography, 5Universite Of Bretagne Occidentale, the Third Institute of Oceanography SOA, CNRS Lab for Microbiology of Extreme Environments and State Oceanic Administration
Type: | Journal: International journal of systematic and evolutionary microbiology | Year: 2016

A novel anaerobic, mesophilicheterotrophic bacterium, designated strain DY2726DT, was isolated from West Pacific Ocean sediments. Cells were long rods (0.5-0.8 m wide4-15 m long)Gram-positive and motile by means of flagella. The temperature and pH ranges for growth were 25-40 C and pH 6.5-9.0while optimal growth occurred at 37 C and pH 7.5, with a generation time 76 minutes. The strain required sea salts for growth from 10 to 30 g L-1 (optimum at 20 g L-1). Substrates used as carbon sources were yeast extract, tryptone, glucose, cellobiose, starch, gelatin, dextrin, fructose, fucose, galactose, galacturonic acid, gentiobiose, glucosaminic acid, mannose, melibiose, palatinose and rhamnose. Products of fermentation were carbon dioxide, acetic acid and butyric acid. Strain DY2726DT was able to reduce amorphous iron hydroxide, goethite, amorphous iron oxides, AQDS and crotonate, but did not reduce sulfur, sulfate, thiosulfate, sulfite and nitrate. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that strain DY2726DT was affiliated to the family Clostridiaceae and is most closely related to Alkaliphilus transvaalensis (90.0% similarity), Alkaliphilus oremlandii (89.6%). The genomic DNA G + C content, was 33.4 mol%. The major cellular fatty acids of strain DY2726DT were C16:1, C14:0 and C16:0. On the basis of its phenotypic and genotypic properties, strain DY2726DT is suggested to represent a novel species of a new genus in the family Clostridiaceae, for which the name Anaeromicrobium sediminis gen. nov., sp. nov. is proposed. The type strain of Anaeromicrobium sediminis is DY2726DT (=JCM 30224T =MCCC 1A00776T).


Xiao J.,The Third Institute of Oceanography SOA | Xiao J.,University of Tsukuba | Luo Y.,The Third Institute of Oceanography SOA | Xu J.,The Third Institute of Oceanography SOA | And 2 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

The taxonomic status of an actinobacterium that changed colour during growth, strain 42H12-1 T, isolated from deep-sea sediment collected from the Atlantic Ocean, was established using a combination of genotypic and phenotypic data. Strain 42H12-1 T formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Modestobacter. The highest sequence similarity by BLAST analysis was to Modestobacter versicolor CP153-2 T (98.5 %) and the second-highest sequence similarity was to Modestobacter multiseptatus AA-826 T (97.5 %). DNA-DNA relatedness of only 12% (SD 1.82 %) between strain 42H12-1 T and M. versicolor DSM 16678 T differentiated them as members of separate genomic species. Colonies of strain 42H12-1 T were black on oligotrophic medium, but orange to red, turning black, on copiotrophic medium. The peptidoglycan contained meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and an unknown aminophospholipid. The predominant menaquinone was MK-9(H 4). The major fatty acids were iso-C 16: 0 and C 17: 1ω8c. The DNA G+C content was 72.3±1 mol%. Strain 42H12-1 T (=DSM 45201 T =CGMCC 4.5581 T) is assigned as the type strain of a novel species of the genus Modestobacter, for which the name Modestobacter marinus sp. nov. is proposed. © 2011 IUMS.


Luo Y.,The Third Institute of Oceanography SOA | Xiao J.,The Third Institute of Oceanography SOA | Xiao J.,University of Tsukuba | Wang Y.,The Third Institute of Oceanography SOA | And 3 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C 15:0, anteiso-C 15:0, iso-C 16:0, iso-C 17:0 and anteiso-C 17:0 as the major cellular fatty acids, LL-diaminopimelic acid as the characteristic diamino acid, and MK-9(H 4, H 6 and H 8) as the major menaquinones supported the affiliation of strain IH32-1 T to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1 T exhibited highest similarities to the type strains of Streptomyces globosus (97.6%) and Streptomyces toxytricini (97.6%). However, DNA-DNA relatedness values between strain IH32-1 T and the type strains of S. globosus and S. toxytricini were determined as 55.2±4.7 and 38.3±2.5%, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1 T is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1 T (=DSM 42001 T =CGMCC 4.5727 T). © 2011 IUMS.


Zhang X.,The Third Institute of Oceanography SOA | Jiang L.,The Third Institute of Oceanography SOA | Alain K.,CNRS Lab for Microbiology of Extreme Environments | Jebbar M.,CNRS Lab for Microbiology of Extreme Environments | Shao Z.,The Third Institute of Oceanography SOA
International Journal of Systematic and Evolutionary Microbiology | Year: 2013

A hyperthermophilic, anaerobic, piezophilic archaeon (strain DY20341T) was isolated from a sediment sample collected from an East Pacific Ocean hydrothermal field (1° 37' S 102° 45' w) at a depth of 2737 m. The cells were irregular cocci, 0.8-1.5 mm in diameter. Growth was observed between 50 and 90 °C (optimum 80 ° C), pH 5.0 and 8.0 (optimum pH 7.0), 1% and 7% (w/v) sea salts (Sigma, optimum 3 %), 1% and 4% (w/v) NaCl (optimum 3%) and 0.1 and 80 MPa (optimum 30 MPa). The minimum doubling time was 66 min at 30 MPa and 80 ° C. The isolate was an obligate chemoorganoheterotroph, capable of utilizing complex organic compounds and organic acids including yeast extract, peptone, tryptone, casein, starch, Casamino acids, citrate, lactate, acetate, fumarate, propanoate and pyruvate for growth. It was strictly anaerobic and facultatively dependent on elemental sulfur or sulfate as electron acceptors, but did not reduce sulfite, thiosulfate, Fe(III) or nitrate. The presence of elemental sulfur enhanced growth. The G+C content of the genomic DNA was 43.6±1 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Palaeococcus ferrophilus DMJT (95.7% 16S rRNA gene similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Palaeococcus pacificus sp. nov. is proposed. The type strain is strain DY20341T (5JCM 17873T5DSM 24777T). © 2013 IUMS.


PubMed | The Third Institute of Oceanography SOA
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2013

A hyperthermophilic, anaerobic, piezophilic archaeon (strain DY20341(T)) was isolated from a sediment sample collected from an East Pacific Ocean hydrothermal field (1 37 S 102 45 W) at a depth of 2737 m. The cells were irregular cocci, 0.8-1.5 m in diameter. Growth was observed between 50 and 90 C (optimum 80 C), pH 5.0 and 8.0 (optimum pH 7.0), 1% and 7% (w/v) sea salts (Sigma, optimum 3%), 1% and 4% (w/v) NaCl (optimum 3%) and 0.1 and 80 MPa (optimum 30 MPa). The minimum doubling time was 66 min at 30 MPa and 80 C. The isolate was an obligate chemoorganoheterotroph, capable of utilizing complex organic compounds and organic acids including yeast extract, peptone, tryptone, casein, starch, Casamino acids, citrate, lactate, acetate, fumarate, propanoate and pyruvate for growth. It was strictly anaerobic and facultatively dependent on elemental sulfur or sulfate as electron acceptors, but did not reduce sulfite, thiosulfate, Fe(III) or nitrate. The presence of elemental sulfur enhanced growth. The G+C content of the genomic DNA was 43.6 1 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Palaeococcus ferrophilus DMJ(T) (95.7% 16S rRNA gene similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Palaeococcus pacificus sp. nov. is proposed. The type strain is strain DY20341(T) (=JCM 17873(T)=DSM 24777(T)).


PubMed | The Third Institute of Oceanography SOA
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2011

The taxonomic status of an actinobacterium that changed colour during growth, strain 42H12-1(T), isolated from deep-sea sediment collected from the Atlantic Ocean, was established using a combination of genotypic and phenotypic data. Strain 42H12-1(T) formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Modestobacter. The highest sequence similarity by blast analysis was to Modestobacter versicolor CP153-2(T) (98.5%) and the second-highest sequence similarity was to Modestobacter multiseptatus AA-826(T) (97.5%). DNA-DNA relatedness of only 12% (sd 1.82%) between strain 42H12-1(T) and M. versicolor DSM 16678(T) differentiated them as members of separate genomic species. Colonies of strain 42H12-1(T) were black on oligotrophic medium, but orange to red, turning black, on copiotrophic medium. The peptidoglycan contained meso-diaminopimelic acid. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and an unknown aminophospholipid. The predominant menaquinone was MK-9(H(4)). The major fatty acids were iso-C(16:0) and C(17:1)8c. The DNA G+C content was 72.31 mol%. Strain 42H12-1(T) (=DSM 45201(T) =CGMCC 4.5581(T)) is assigned as the type strain of a novel species of the genus Modestobacter, for which the name Modestobacter marinus sp. nov. is proposed.


PubMed | The Third Institute of Oceanography SOA
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2011

A Gram-reaction-positive bacterial strain of the genus Serinicoccus, designated MCCC 1A05965(T), was isolated from a deep-sea (5368 m) sediment of the Indian Ocean. Comparison of 16S rRNA gene sequences revealed that the isolate shared 97.6% sequence similarity with Serinicoccus marinus JC1078(T), the type strain of the only described species of the genus Serinicoccus. The DNA-DNA relatedness between these two strains was 46.2% (standard deviation 1.86%). The cell wall contained alanine, glycine, serine, l-ornithine and glutamic acid, which corresponds to the description of the genus Serinicoccus. The acyl type of the glycan chain of the peptidoglycan was glycolyl. Other characteristics of strain MCCC 1A05965(T) were consistent with those of the genus Serinicoccus. Cells were coccoid, moderately halophilic, oxidase-negative, catalase-positive and non-spore-forming. The major menaquinone was MK-8(H(4)). The predominant cellular fatty acids were iso-C(15:0) (34.7%) and iso-C(16:0) (17.0%). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glycolipid. The DNA G+C content was 72 mol%. Strain MCCC 1A05965(T) (=0714S6-1(T) =DSM 21363(T) =CGMCC 4.5582(T)) is assigned as the type strain of a novel species, for which the name Serinicoccus profundi sp. nov. is proposed.


PubMed | the Third Institute of Oceanography SOA and CNRS Lab for Microbiology of Extreme Environments
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2015

A thermophilic, anaerobic, iron-reducing bacterium (strain DY22619T) was isolated from a sulfide sample collected from an East Pacific Ocean hydrothermal field at a depth of 2901 m. Cells were Gram-stain-negative, motile rods (2-10 m in length, 0.5 m in width) with multiple peritrichous flagella. The strain grew at 40-70 C inclusive (optimum 60 C), at pH 4.5-8.5 inclusive (optimum pH 7.0) and with sea salts concentrations of 1-10 % (w/v) (optimum 3 % sea salts) and NaCl concentrations of 1.5-5.0 % (w/v) (optimum 2.5 % NaCl). Under optimal growth conditions, the generation time was around 55 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, amino acids, carbohydrates and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamate, methionine, threonine, fructose, mannose, galactose, glucose, palatinose, rhamnose, turanose, gentiobiose, xylose, sorbose, pyruvate, tartaric acid, -ketobutyric acid, -ketovaleric acid, galacturonic acid and glucosaminic acid. Strain DY22619T was strictly anaerobic and facultatively dependent on various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulfate, thiosulfate or nitrate. The genomic DNA G+C content was 29.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that the closest relative of strain DY22619T was Caloranaerobacter azorensis MV1087T, sharing 97.41 % 16S rRNA gene sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus Caloranaerobacter, for which the name Caloranaerobacterhttp://dx.doi.org/10.1601/nm.4081ferrireducens sp. nov. is proposed. The type strain is DY22619T (=JCM 19467T = DSM 27799T = MCCC1A06455T).


PubMed | The Third Institute of Oceanography SOA
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2011

The taxonomic position of an actinomycete isolated from deep-sea sediment from the Indian Ocean was determined by using a polyphasic approach. The presence of iso-C(15 : 0), anteiso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0) as the major cellular fatty acids, ll-diaminopimelic acid as the characteristic diamino acid, and MK-9(H(4), H(6) and H(8)) as the major menaquinones supported the affiliation of strain IH32-1(T) to the genus Streptomyces. Comparison of 16S rRNA gene sequences showed that strain IH32-1(T) exhibited highest similarities to the type strains of Streptomyces globosus (97.6 %) and Streptomyces toxytricini (97.6 %). However, DNA-DNA relatedness values between strain IH32-1(T) and the type strains of S. globosus and S. toxytricini were determined as 55.2 4.7 and 38.3 2.5 %, respectively. Based on its chemotaxonomic, phenotypic and genotypic characteristics, strain IH32-1(T) is considered to represent a novel species in the genus Streptomyces, for which the name Streptomyces indicus sp. nov. is proposed. The type strain is IH32-1(T) ( = DSM 42001(T) = CGMCC 4.5727(T)).


PubMed | the Third Institute of Oceanography SOA and CNRS Lab for Microbiology of Extreme Environments
Type: Journal Article | Journal: International journal of systematic and evolutionary microbiology | Year: 2015

A novel piezophilic, thermophilic, anaerobic, fermentative bacterial strain, designated strain DY22613(T), was isolated from a deep-sea hydrothermal sulfide deposit at the East Pacific Rise (GPS position: 102.6 W 3.1 S). Cells of strain DY22613(T) were long, motile rods (10 to 20 m in length and 0.5 m in width) with peritrichous flagella and were Gram-stain-negative. Growth was recorded at 44-72 C (optimum 60-62 C) and at hydrostatic pressures of 0.1-55 MPa (optimum 20 MPa). The pH range for growth was from pH 5.0 to 9.0 with an optimum at pH 7.0. Growth was observed in the presence of 1 to 8 % (w/v) sea salts and 0.65 to 5.2 % (w/v) NaCl, with optimum salt concentrations at 3.5 % for sea salts and at 2.3 % for NaCl. Under optimal growth conditions, the shortest generation time observed was 27 min (60 C, 20 MPa). Strain DY22613(T) was heterotrophic, able to utilize complex organic compounds, amino acids, sugars and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamine, methionine, phenylalanine, serine, threonine, fructose, fucose, galactose, gentiobiose, glucose, mannose, melibiose, palatinose, rhamnose, turanose, pyruvate, lactic acid, methyl ester, erythritol, galacturonic acid and glucosaminic acid. Strain DY22613(T) was able to reduce Fe(III) compounds, including Fe(III) oxyhydroxide (pH 7.0), amorphous iron(III) oxide (pH 9.0), goethite (-FeOOH, pH 12.0), Fe(III) citrate and elementary sulfur. Products of fermentation were butyrate, acetate and hydrogen. Main cellular fatty acids were iso-C15 : 0, iso-C14 : 0 3-OH and C14 : 0. The genomic DNA G+C content of strain DY22613(T) was 36.7 mol%. Based on 16S rRNA gene sequence analysis, the strain forms a novel lineage within the class Clostridia and clusters with the order Haloanaerobiales (86.92 % 16S rRNA gene sequence similarity). The phylogenetic data suggest that the lineage represents at least a novel genus and species, for which the name Anoxybacter fermentans gen. nov., sp. nov. is proposed. The type strain is DY22613(T) (= JCM 19466(T)= DSM 28033(T)= MCCC 1A06456(T)).

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