scholarly journals Nautilia nitratireducens sp. nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent

2010 ◽  
Vol 60 (5) ◽  
pp. 1182-1186 ◽  
Author(s):  
Ileana Pérez-Rodríguez ◽  
Jessica Ricci ◽  
James W. Voordeckers ◽  
Valentin Starovoytov ◽  
Costantino Vetriani
Keyword(s):  
Gas Phase ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
East Pacific ◽  
Optimum Ph ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemosynthetic bacterium, designated strain MB-1T, was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at  ° 50′ N 10 ° 17′ W. The cells were Gram-negative-staining rods, approximately 1–1.5 μm long and 0.3–0.5 μm wide. Strain MB-1T grew at 25–65 °C (optimum 55 °C), with 10–35 g NaCl l−1 (optimum 20 g l−1) and at pH 4.5–8.5 (optimum pH 7.0). Generation time under optimal conditions was 45.6 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate was used as the electron acceptor, with resulting production of ammonium. Thiosulfate, sulfur and selenate were also used as electron acceptors. No growth was observed in the presence of lactate, peptone or tryptone. Chemo-organotrophic growth occurred in the presence of acetate, formate, Casamino acids, sucrose, galactose and yeast extract under a N2/CO2 gas phase. The G+C content of the genomic DNA was 36.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Nautilia profundicola AmHT, Nautilia abyssi PH1209T and Nautilia lithotrophica 525T (95, 94 and 93 % sequence identity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Nautilia, Nautilia nitratireducens sp. nov. The type strain is MB-1T (=DSM 22087T =JCM 15746T).

scholarly journals Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

2004 ◽  
Vol 54 (1) ◽  
pp. 175-181 ◽  
Author(s):  
Costantino Vetriani ◽  
Mark D. Speck ◽  
Susan V. Ellor ◽  
Richard A. Lutz ◽  
Valentin Starovoytov
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
East Pacific ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

scholarly journals Caminibacter mediatlanticus sp. nov., a thermophilic, chemolithoautotrophic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent on the Mid-Atlantic Ridge

2005 ◽  
Vol 55 (2) ◽  
pp. 773-779 ◽  
Author(s):  
James W. Voordeckers ◽  
Valentin Starovoytov ◽  
Costantino Vetriani
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Optimal Conditions ◽  
Rrna Gene Sequence ◽  
Optimum Ph ◽  
Mid Atlantic Ridge ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium, designated strain TB-2T, was isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge at 36° 14′ N 33° 54′ W. The cells were Gram-negative rods approximately 1·5 μm in length and 0·75 μm in width. Strain TB-2T grew between 45 and 70 °C (optimum 55 °C), 10 and 40 g NaCl l−1 (optimum 30 g l−1) and pH 4·5 and 7·5 (optimum pH 5·5). Generation time under optimal conditions was 50 min. Growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Nitrate or sulfur was used as the electron acceptor, with resulting production of ammonium and hydrogen sulfide, respectively. Oxygen, thiosulfate, sulfite, selenate and arsenate were not used as electron acceptors. Growth was inhibited by the presence of acetate, lactate, formate and peptone. The G+C content of the genomic DNA was 25·6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Caminibacter hydrogeniphilus and Caminibacter profundus (95·9 and 96·3 % similarity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Caminibacter, Caminibacter mediatlanticus sp. nov. The type strain is TB-2T (=DSM 16658T=JCM 12641T).

scholarly journals Exiguobacterium profundum sp. nov., a moderately thermophilic, lactic acid-producing bacterium isolated from a deep-sea hydrothermal vent

2007 ◽  
Vol 57 (2) ◽  
pp. 287-292 ◽  
Author(s):  
Sylvaine Crapart ◽  
Marie-Laure Fardeau ◽  
Jean-Luc Cayol ◽  
Pierre Thomas ◽  
Christian Sery ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Moderately Thermophilic ◽  
East Pacific ◽  
Carbohydrate Fermentation ◽  
Exiguobacterium Profundum

A facultatively anaerobic, halotolerant, moderately thermophilic and non-sporulating bacterium, designated strain 10CT, was isolated from deep-sea hydrothermal vent samples collected on the 13° N East Pacific Rise at a depth of approximately 2600 m. Cells of strain 10CT were Gram-positive, motile rods, and grew optimally at 45 °C (range 12–49 °C), pH 7.0 (range pH 5.5–9.5) and 0–2 % NaCl (range 0–11 %). (+)-l-Lactate was the main organic acid detected from carbohydrate fermentation with traces of formate, acetate and ethanol. Strain 10CT was catalase-positive, oxidase-negative and reduced nitrate to nitrite under anaerobic conditions. The DNA G+C content was 50.4 mol%. Its closest phylogenetic relatives were Exiguobacterium aestuarii TF-16T and Exiguobacterium marinum TF-80T (16S rRNA gene sequence similarity >99 %). However, strain 10CT differed genotypically from these two Exiguobacterium species as indicated by DNA–DNA relatedness data. Therefore, on the basis of phenotypic, genotypic and phylogenetic characteristics, strain 10CT is considered to represent a novel species of the genus Exiguobacterium, for which the name Exiguobacterium profundum sp. nov. is proposed. The type strain is 10CT (=CCUG 50949T=DSM 17289T).

scholarly journals Mucilaginibacter ginsengisoli sp. nov., isolated from a ginseng-cultivated soil

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3933-3937 ◽  
Author(s):  
Jae-Hyung Ahn ◽  
Byoung-chan Kim ◽  
Jae-Ho Joa ◽  
Soo-Jin Kim ◽  
Jaekyeong Song ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Optimum Ph ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Dark Pink

A dark-pink-coloured bacterial strain, B4Y-8T, was isolated from a soil cultivated with ginseng. The 16S rRNA gene sequence of this strain showed highest similarity with Mucilaginibacter litoreus BR-18T (96.8 %), Mucilaginibacter lutimaris BR-3T (96.6 %) and Mucilaginibacter defluvii A5T (96.2 %) among the type strains of species of the genus Mucilaginibacter. Strain B4Y-8T was a strictly aerobic, Gram-stain-negative, non-motile, short-rod-shaped bacterium producing a large amount of extracellular polymeric substance. The strain grew at 10–35 °C (optimum, 25 °C), at pH 3.0–11.0 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, 0 %). The DNA G+C content of strain B4Y-8T was 49.0 mol%. It contained menaquinone 7 (MK-7) as the major isoprenoid quinone, and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C15 : 0 as the major fatty acids. On the basis of evidence from the present polyphasic taxonomic study, strain B4Y-8T should be classified as representing a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter ginsengisoli sp. nov. is proposed. The type strain is B4Y-8T ( = KACC 18152T = JCM 30759T).

Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Yurina Hashimoto ◽  
Akihiro Tame ◽  
Shigeki Sawayama ◽  
Junichi Miyazaki ◽  
Ken Takai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A novel mesophilic, strictly anaerobic, chemolithoautotrophic sulphate-reducing bacterium, designated strain KT2T, was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc. Strain KT2T grew at 25–40 °C (optimum 35 °C) and pH 5.5–7.0 (optimum 6.6) in the presence of 25–45 g l−1 NaCl (optimum 30 g l−1). Growth occurred with molecular hydrogen as the electron donor and sulphate, thiosulphate, and sulphite as the electron acceptors. The isolate utilized CO2 as the sole carbon source for chemolithoautotrophic growth on H2. Glycerol, succinate, fumarate, malate, glutamate, or casamino acids could serve as an alternative electron donor in the presence of CO2. Malate, citrate, glutamate, and casamino acids were used as fermentative substrates for weak growth. The G+C content of genomic DNA was 46.1 %. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KT2T is a member of the family Desulfobulbaceae , showing a sequence similarity of 94.3 % with Desulforhopalus singaporensis . Phylogenomic analysis based on concatenated 156 single-copy marker genes confirmed the same topology as the 16S rRNA gene phylogeny. The ANI and AAI values between strain KT2T and related genera of the family Desulfobulbaceae were 65.6–68.6 % and 53.1–62.9 %. Based on the genomic, molecular, and physiological characteristics, strain KT2T represents a novel genus and species within the family Desulfobulbaceae , for which the name Desulfomarina profundi gen. nov., sp. nov. is proposed, with KT2T (=JCM 34118T = DSM 111364T) as the type strain.

Mesoaciditoga lauensis gen. nov., sp. nov., a moderately thermoacidophilic member of the order Thermotogales from a deep-sea hydrothermal vent

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4724-4729 ◽  
Author(s):  
Anna-Louise Reysenbach ◽  
Yitai Liu ◽  
Annie R. Lindgren ◽  
Isaac D. Wagner ◽  
Christine D. Sislak ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
New Genus ◽  
Heterotrophic Bacterium ◽  
Spreading Center ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Optimum Ph ◽  
The 16S Rrna Gene

A novel moderately thermophilic, heterotrophic bacterium was isolated from a deep-sea hydrothermal vent deposit from the Mariner field along the Eastern Lau Spreading Center of the south-western Pacific Ocean. Cells were short motile rods (about 0.4×0.8 µm) that occurred singly or in pairs and were surrounded by a sheath-like membrane or ‘toga’. The cells grew between 45 and 65 °C (optimum 57–60 °C) and at pH 4.1–6.0 (optimum pH 5.5–5.7) and grew optimally at 3 % (w/v) NaCl. The isolate grew on a range of carbon and proteinaceous substrates and reduced sulfur. The G+C content of the DNA was about 45 mol%. Phylogenetic analysis of the 16S rRNA gene sequence placed the new isolate as a deeply diverging lineage within the order Thermotogales . Based on the physiological, morphological and phylogenetic data, the isolate represents a novel species of a new genus with the proposed name Mesoaciditoga lauensis gen. nov., sp. nov. The type strain of Mesoaciditoga lauensis is cd-1655RT ( = DSM 25116T = OCM 1212T).

scholarly journals Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1167-1171 ◽  
Author(s):  
Satoru Shimizu ◽  
Akio Ueno ◽  
Takeshi Naganuma ◽  
Katsuhiko Kaneko
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
Shale Formation ◽  
The 16S Rrna Gene

A methanogenic archaeon, strain HC-2T, was isolated from a deep diatomaceous shale formation. The strain grew on methanol, monomethylamine, dimethylamine, trimethylamine and dimethylsulphide, but not on acetate, H2/CO2, formate, 2-propanol, 2-butanol or cyclopentanol. Cells were Gram-stain-negative, non-motile, and coccus-like, 0.9–1.4 µm in diameter, and occurred singly, in pairs, or as aggregates. The strain grew at 10–40 °C (optimum 35 °C), pH 5.9–7.4 (optimum pH 6.6–6.8) and in 0–0.6 M NaCl (optimum 0.1–0.2 M). The genomic DNA G+C content was 41.5 mol% and the 16S rRNA gene sequence was closely related to those of Methanosarcina lacustris DSM 13486T (99.1 %) and Methanosarcina siciliae DSM 3028T (98.3 %). Values for DNA–DNA hybridization with these strains were less than 30 %. The phenotypic and phylogenetic features of HC-2T indicate that it represents a novel species of the genus Methanosarcina , for which the name Methanosarcina subterranea sp. nov. is proposed. The type strain is HC-2T ( = DSM 22503T = JCM 15540T = NBRC 102578T).

Desulfothermus okinawensis sp. nov., a thermophilic and heterotrophic sulfate-reducing bacterium isolated from a deep-sea hydrothermal field

2007 ◽  
Vol 57 (10) ◽  
pp. 2360-2364 ◽  
Author(s):  
Takuro Nunoura ◽  
Hanako Oida ◽  
Masayuki Miyazaki ◽  
Yohey Suzuki ◽  
Ken Takai ◽  
...  
Keyword(s):  
Deep Sea ◽  
Gene Sequence ◽  
Okinawa Trough ◽  
Hydrothermal Field ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel thermophilic and heterotrophic sulfate-reducing bacterium, strain TFISO9T, was isolated from a deep-sea hydrothermal field at the Yonaguni Knoll IV in the Southern Okinawa Trough. The cells were motile rods 2.5–5.0 μm in length and 0.6–0.9 μm in width. Strain TFISO9T was an obligate heterotroph and reduced sulfate. It grew between 35 and 60 °C (optimum 50 °C), at pH 5.4–7.9 (optimum pH 5.9–6.4) and with 1.5–4.5 % NaCl (optimum 2.5 %). The fatty acid composition was C16 : 0 (61.5 %) and 12Me16 : 0 (38.5 %). The DNA G+C content was 34.9 mol%. The 16S rRNA gene sequence analysis indicated that strain TFISO9T belonged to the genus Desulfothermus. Based on physiological and phylogenetic characteristics, strain TFISO9T represents a novel species for which the name Desulfothermus okinawensis sp. nov. is proposed. The type strain is TFISO9T (=JCM 13304T=DSM 17375T).

scholarly journals Fusibacter fontis sp. nov., a sulfur-reducing, anaerobic bacterium isolated from a mesothermic Tunisian spring

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3501-3506 ◽  
Author(s):  
Khaled Fadhlaoui ◽  
Wajdi Ben Hania ◽  
Anne Postec ◽  
Guy Fauque ◽  
Moktar Hamdi ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Rrna Gene ◽  
Gram Staining ◽  
Lateral Flagellum ◽  
Wide Range ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Strain KhalAKB1T, a mesophilic, anaerobic, rod-shaped bacterium, was isolated from water collected from a mesothermic Tunisian spring. Cells were Gram-staining-positive rods, occurring singly or in pairs and motile by one lateral flagellum. Strain KhalAKB1T grew at 15–45 °C (optimum 30 °C), at pH 5.5–8.5 (optimum pH 7.0) and in the presence of 0–35 g NaCl l− 1 (optimum 1 g NaCl l− 1). It fermented yeast extract and a wide range of carbohydrates including cellobiose, d-glucose, d-ribose, sucrose, d-xylose, maltose, d-galactose and starch as electron donors. Acetate, ethanol, CO2 and H2 were end products of glucose metabolism. It reduced elemental sulfur, but not sulfate, thiosulfate or sulfite, into sulfide. The DNA G+C content was 37.6 mol%. The predominant cellular fatty acids were C14 : 0 and C16 : 0. Phylogenetic analysis of the 16S rRNA gene sequence suggested Fusibacter bizertensis as the closest relative of this isolate (identity of 97.2 % to the type strain). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain KhalAKB1T is proposed to be assigned to a novel species within the genus Fusibacter, order Clostridiales, Fusibacter fontis sp. nov. The type strain is KhalAKB1T ( = DSM 28450T = JCM 19912T).

scholarly journals Planotetraspora silvatica sp. nov. and emended description of the genus Planotetraspora

2004 ◽  
Vol 54 (6) ◽  
pp. 2053-2056 ◽  
Author(s):  
Tomohiko Tamura ◽  
Takeshi Sakane
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Subtropical Forest ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Monophyletic Cluster ◽  
Aerial Hyphae ◽  
Emended Description ◽  
The 16S Rrna Gene

An actinomycete that developed sporangia containing four spores in a single row at the ends of short sporangiophores on branched aerial hyphae was isolated from subtropical forest soil. The isolate contained menaquinone MK-9(H4), glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and madurose in the whole-cell hydrolysate. The 16S rRNA gene sequence indicated that the isolate formed a monophyletic cluster with Planotetraspora mira. On the basis of morphological and chemotaxonomic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species of the genus Planotetraspora is proposed, Planotetraspora silvatica sp. nov. (type strain, TT 00-51T=NBRC 100141T=DSM 44746T).

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