scholarly journals Sulfurovum aggregans sp. nov., a hydrogen-oxidizing, thiosulfate-reducing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent chimney, and an emended description of the genus Sulfurovum

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3195-3201 ◽  
Author(s):  
Sayaka Mino ◽  
Hideaki Kudo ◽  
Takayuki Arai ◽  
Tomoo Sawabe ◽  
Ken Takai ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
The Novel ◽  
Central Indian Ridge ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A novel mesophilic, strictly hydrogen-oxidizing, sulfur-, nitrate- and thiosulfate-reducing bacterium, designated strain Monchim33T, was isolated from a deep-sea hydrothermal vent chimney at the Central Indian Ridge. The non-motile, rod-shaped cells were Gram-stain-negative and non-sporulating. Growth was observed between 15 and 37 °C (optimum 33 °C; 3.2 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.0). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as the sole energy source and carbon dioxide as the sole carbon source. The G+C content of the genomic DNA was 42.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurovum and was closely related to Sulfurovum sp. NBC37-1 and Sulfurovum lithotrophicum 42BKT (95.6 and 95.4 % similarity, respectively). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurovum sp. NBC37-1 and Sulfurovum lithotrophicum . On the basis of the molecular and physiological traits of the new isolate, the name Sulfurovum aggregans sp. nov. is proposed, with the type strain Monchim33T ( = JCM 19824T = DSM 27205T).

Crassaminicella thermophila sp. nov., a moderately thermophilic bacterium isolated from a deep-sea hydrothermal vent chimney and emended description of the genus Crassaminicella

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Xue-Gong Li ◽  
Jin Lin ◽  
Shi-Jie Bai ◽  
Jie Dai ◽  
Ze-Xi Jiao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Hydrothermal Vent ◽  
Type Species ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Emended Description

A novel moderately thermophilic, anaerobic, heterotrophic bacterium (strain SY095T) was isolated from a hydrothermal vent chimney located on the Southwest Indian Ridge at a depth of 2730 m. Cells were Gram-stain-positive, motile, straight to slightly curved rods forming terminal endospores. SY095T was grown at 45–60 °C (optimum 50–55 °C), pH 6.0–7.5 (optimum 7.0), and in a salinity of 1–4.5 % (w/v) NaCl (optimum 2.5 %). Substrates utilized by SY095T included fructose, glucose, maltose, N-acetyl glucosamine and tryptone. Casamino acid and amino acids (glutamate, glutamine, lysine, methionine, serine and histidine) were also utilized. The main end products from glucose fermentation were acetate, H2 and CO2. Elemental sulphur, sulphate, thiosulphate, sulphite, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14 : 0 (60.5%) and C16 : 0 (7.6 %). The main polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, five unidentified phospholipids and two unidentified aminophospholipids. No respiratory quinones were detected. The chromosomal DNA G+C content was 30.8 mol%. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that SY095T was closely related to Crassaminicella profunda Ra1766HT (95.8 % 16S rRNA gene sequence identity). SY095T exhibited 78.1 % average nucleotide identity (ANI) to C. profunda Ra1766HT. The in silico DNA–DNA hybridization (DDH) value indicated that SY095T shared 22.7 % DNA relatedness with C. profunda Ra1766HT. On the basis of its phenotypic, genotypic and phylogenetic characteristics, SY095T is suggested to represent a novel species of the genus Crassaminicella , for which the name Crassaminicella thermophila sp. nov. is proposed. The type strain is SY095T (=JCM 34213=MCCC 1K04191). An emended description of the genus Crassaminicella is also proposed.

scholarly journals Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., thermoacidophilic members of the class Deltaproteobacteria isolated from deep-sea hydrothermal vent deposits

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1252-1258 ◽  
Author(s):  
Gilberto E. Flores ◽  
Ryan C. Hunter ◽  
Yitai Liu ◽  
Anchelique Mets ◽  
Stefan Schouten ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-rT, KM1, Mar08-272rT and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-rT, all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60–65 °C. Strain EP5-rT was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272rT could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-rT, Mar08-272rT and Mar08-368r could also use fumarate, while strains EP5-rT, KM1 and Mar08-272rT could also use propionate. All isolates were able to grow chemolithotrophically on H2, CO2, sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family Desulfurellaceae of the class Deltaproteobacteria , with the closest cultured relative being Hippea maritima MH2 T (~95–98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-rT, KM1, Mar08-272rT and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from H. maritima MH2 T in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272rT = DSM 24585T = OCM 985T) and Hippea alviniae sp. nov. (type strain EP5-rT = DSM 24586T = OCM 986T).

Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1235-1240 ◽  
Author(s):  
Tong Yu ◽  
Qi Yin ◽  
Xiangyu Song ◽  
Rui Zhao ◽  
Xiaochong Shi ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Gliding Motility ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated SW024T, was isolated from surface seawater of the South Pacific Gyre (26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina muelleri KMM 6020T, Aquimarina macrocephali JAMB N27T, Aquimarina addita JC2680T, Aquimarina mytili PSC33T, Aquimarina intermedia KMM 6258T, Aquimarina latercula ATCC 23177T, Aquimarina spongiae A6T, Aquimarina agarilytica ZC1T and Aquimarina brevivitae SMK-19T (96.1, 95.5, 95.0, 94.4, 94.3, 94.0, 93.4, 93.3 and 93.2 % similarities, respectively), demonstrating that the novel strain belonged to the genus Aquimarina . The DNA G+C content of strain SW024T was 30.8 mol%. The major respiratory quinone of strain SW024T was MK-6. The dominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 G, C16 : 0 10-methyl and/or iso-C17 : 1ω9c, and iso-C15 : 0 3-OH. The polar lipids of strain SW024T were phosphatidylethanolamine, three unknown aminolipids and five unknown polar lipids. On the basis of combined phenotypic and phylogenetic analyses, strain SW024T represents a novel species of the genus Aquimarina , for which the name Aquimarina longa sp. nov. is proposed. The type strain is SW024T ( = CGMCC 1.11007T = JCM 17859T). An emended description of A. muelleri is also proposed.

Ruminococcoides bili gen. nov., sp. nov., a bile-resistant bacterium from human bile with autolytic behavior

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Natalia Molinero ◽  
Elena Conti ◽  
Borja Sánchez ◽  
Alan W. Walker ◽  
Abelardo Margolles ◽  
...  
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
The Novel ◽  
Bile Sample ◽  
Human Bile ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Genome Analyses

A strictly anaerobic, resistant starch-degrading, bile-tolerant, autolytic strain, IPLA60002T, belonging to the family Ruminococcaceae , was isolated from a human bile sample of a liver donor without hepatobiliary disease. Cells were Gram-stain-positive cocci, and 16S rRNA gene and whole genome analyses showed that Ruminococcus bromii was the phylogenetically closest related species to the novel strain IPLA60002T, though with average nucleotide identity values below 90 %. Biochemically, the new isolate has metabolic features similar to those described previously for gut R. bromii strains, including the ability to degrade a range of different starches. The new isolate, however, produces lactate and shows distinct resistance to the presence of bile salts. Additionally, the novel bile isolate displays an autolytic phenotype after growing in different media. Strain IPLA60002T is phylogenetically distinct from other species within the genus Ruminococcus . Therefore, we propose on the basis of phylogenetic, genomic and metabolic data that the novel IPLA60002T strain isolated from human bile be given the name Ruminococcoides bili gen. nov., sp. nov., within the new proposed genus Ruminococcoides and the family Ruminococcaceae . Strain IPLA60002T (=DSM 110008T=LMG 31505T) is proposed as the type strain of Ruminococcoides bili.

scholarly journals Reclassification of Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov., description of Leuconostoc gelidum subsp. aenigmaticum subsp. nov., designation of Leuconostoc gelidum subsp. gelidum subsp. nov. and emended description of Leuconostoc gelidum

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1290-1295 ◽  
Author(s):  
Riitta Rahkila ◽  
Katrien De Bruyne ◽  
Per Johansson ◽  
Peter Vandamme ◽  
Johanna Björkroth
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
The Novel ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type ◽  
Emended Description ◽  
Leuconostoc Gelidum ◽  
Reference Strains

In the present study we investigated the taxonomic status of 20 lactic acid bacteria (LAB) originating from packaged meat. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Leuconostoc with Leuconostoc gelidum , Leuconostoc inhae and Leuconostoc gasicomitatum as the closest phylogenetic relatives. The novel strains shared more than 70 % DNA–DNA relatedness with type and reference strains of both L. gelidum and L. gasicomitatum . The DNA–DNA relatedness values between L. gelidum type and reference strains and L. gasicomitatum type and reference strains were also above 70 %, showing that all these strains belonged to the same species. Sequence analyses of concatenated atpA, pheS, and rpoA genes demonstrated that the novel strains as well as type and reference strains of L. gelidum and L. gasicomitatum are phylogenetically closely related, but form three clearly separated subgroups. Numerical analysis of HindIII ribopatterns and phenotypic tests supported this subdivision. Based on the data presented in this study, we propose to reclassify Leuconostoc gasicomitatum as Leuconostoc gelidum subsp. gasicomitatum comb. nov. (type strain, LMG 18811T = DSM 15947T). The novel strains isolated in the present study represent a novel subspecies, for which the name Leuconostoc gelidum subsp. aenigmaticum subsp. nov. is proposed, with POUF4dT ( = LMG 27840T = DSM 19375T) as the type strain. The proposal of these two novel subspecies automatically creates the subspecies Leuconostoc gelidum subsp. gelidum subsp. nov. (type strain, NCFB 2775T = DSM 5578T). An emended description of Leuconostoc gelidum is also provided.

scholarly journals Nonomuraea monospora sp. nov., an actinomycete isolated from cave soil in Thailand, and emended description of the genus Nonomuraea

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 3007-3012 ◽  
Author(s):  
Nareeluk Nakaew ◽  
Rungroch Sungthong ◽  
Akira Yokota ◽  
Saisamorn Lumyong
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Anticancer Activities ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Forest Park ◽  
Link Type ◽  
Emended Description

A novel actinomycete, designated strain PT708T, was isolated from cave soil collected in Pha Tup Cave Forest Park, Nan province, Thailand. It produced compounds with antimicrobial and anticancer activities. Its chemotaxonomic properties were consistent with those of members of the genus Nonomuraea . The major menaquinone was MK-9(H4), with minor amounts of MK-9(H6), MK-9(H2), MK-10(H2) and MK-8(H4). The polar lipid profile contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, hydroxy-phosphatidylmonomethylethanolamine, hydroxy-phosphatidylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannoside and phosphatidylinositol. The major fatty acids were iso-C16 : 0, 10-methyl C17 : 0, C16 : 0 and C17 : 1ω6c. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PT708T belonged to the genus Nonomuraea and was most closely related to Nonomuraea rhizophila YIM 67092T (98.50 % sequence similarity) and Nonomuraea rosea GW 12687T (98.30 %). The genomic DNA G+C content of strain PT708T was 73.3 mol%. Unlike the recognized members of the genus Nonomuraea , the novel strain formed single spores at the tips of aerial hyphae. Based on the phenotypic, phylogenetic and genotypic evidence, strain PT708T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea monospora sp. nov. is proposed. The type strain is PT708T ( = TISTR 1910T = JCM 16114T).

Gibbsiella papilionis sp. nov., isolated from the intestinal tract of the butterfly Mycalesis gotama, and emended description of the genus Gibbsiella

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2607-2611 ◽  
Author(s):  
Pil Soo Kim ◽  
Na-Ri Shin ◽  
Joon Yong Kim ◽  
Ji-Hyun Yun ◽  
Dong-Wook Hyun ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Intestinal Tract ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Genotypic Analysis ◽  
Emended Description

A novel Gram-negative, non-motile, facultative anaerobic and rod-shaped bacterium, designated strain LEN33T, was isolated from the intestinal tract of a butterfly (Mycalesis gotama). Strain LEN33T grew optimally at 37 °C in the presence of 1 % (w/v) NaCl and at pH 9. The novel strain was oxidase-negative and catalase-positive. The major cellular fatty acids were C14 : 0, C16 : 0 and cyclo-C17 : 0. Strain LEN33T contained two unidentified lipids, three unidentified amino-phospholipids, phosphatidylethanolamine (PE) and phosphatidylglycerol (PG). The major isoprenoid quinone was ubiquinone-8 (Q-8). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain LEN33T was most closely related to Gibbsiella quercinecans FRB 97T and Gibbsiella dentisursi NUM 1720T, with 98.7 % similarities. DNA–DNA hybridization experiments indicated less than 40.7±2 % relatedness to the closest phylogenetic species, G. quercinecans FRB 97T. The G+C content of genomic DNA was 58.7 mol%. Phenotypic, phylogenetic and genotypic analysis indicated that strain LEN33T represents a novel species within the genus Gibbsiella , for which the name Gibbsiella papilionis is proposed. The type strain is referred to as LEN33T ( = KACC 16707T = JCM 18389T). An emended description of the genus Gibbsiella is also proposed.

scholarly journals Defluviimonas indica sp. nov., a marine bacterium isolated from a deep-sea hydrothermal vent environment

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2084-2088 ◽  
Author(s):  
Lijing Jiang ◽  
Hongxiu Xu ◽  
Zongze Shao ◽  
Minnan Long
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Species ◽  
Marine Bacterium ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, strictly aerobic, chemoheterotrophic marine bacterium, designated 20V17T, was isolated from a deep-sea hydrothermal vent chimney collected from the South-west Indian Ridge. Cells of strain 20V17T were motile, short rods, 1.2–1.8 µm in length and 0.5–0.7 µm in width. Growth was observed at between 20 and 37 °C (optimum 25 °C–28 °C), pH 5.0 and 8.0 (optimum pH 7.0) and 0.5 and 8 % (w/v) NaCl (optimum 1.5–2.0 % NaCl). The major fatty acids were C18 : 1ω7c (74.4 %), C19 : 0 cyclo ω8c (11 %), C18 : 0 (5.1 %) and C18 : 0 3-OH (2.8 %), and the polar lipid profile comprised diphosphatidylglycerol, phosphatidylethanolamine, an unidentified glycolipid and four unidentified phospholipids. Ubiquinone 10 was the major quinone. The G+C content of genomic DNA was 66.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain 20V17T belonged to the genus Defluviimonas and shared 96.5 and 96.1 % sequence similarity with Defluviimonas denitrificans D9-3T and Defluviimonas aestuarii BS14T, respectively. On the basis of the taxonomic data obtained in this study, strain 20V17T represents a novel species of the genus Defluviimonas , for which the name Defluviimonas indica sp. nov. is proposed. The type strain is 20V17T (CGMCC 1.10859T = JCM 17871T = MCCC 1A01802T).

scholarly journals Streptomyces nanhaiensis sp. nov., a marine streptomycete isolated from a deep-sea sediment

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 864-868 ◽  
Author(s):  
Xin-Peng Tian ◽  
Li-Juan Long ◽  
Fa-Zuo Wang ◽  
Ying Xu ◽  
Jie Li ◽  
...  
Keyword(s):  
Deep Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Northern South China Sea ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

A novel aerobic streptomycete, strain SCSIO 01248T, was isolated from a sample of deep-sea sediment collected from the northern South China Sea, at a depth of 1632 m. This isolate formed yellow–white substrate mycelium and grey–white aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCSIO 01248T was most closely related to Streptomyces radiopugnans R97T (98.8 % sequence similarity), S. macrosporus NBRC 14748T (97.5 %) and S. megasporus NBRC 14749T (97.3 %). The novel strain could, however, be readily differentiated from S. radiopugnans DSM 41901T on the basis of some physiological and cellular chemical characteristics; the level of DNA–DNA relatedness between these two strains was only 40 %. Based on phylogenetic and phenotypic evidence, strain SCSIO 01248T represents a novel species, for which the name Streptomyces nanhaiensis sp. nov. is proposed. The type strain is SCSIO 01248T ( = DSM 41926T  = KCTC 19401T  = CCTCC AA 208007T).

scholarly journals Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1978-1983 ◽  
Author(s):  
Stéphane L’Haridon ◽  
Morgane Chalopin ◽  
Delphine Colombo ◽  
Laurent Toffin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Mud Volcano ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A novel, strictly anaerobic, methylotrophic marine methanogen, strain SLH33T, was isolated from deep sediment samples covered by an orange microbial mat collected from the Napoli Mud Volcano. Cells of strain SLH33T were Gram-stain-negative, motile, irregular cocci that occurred singly. Cells utilized trimethylamine, dimethylamine, monomethylamine, methanol, betaine, N,N-dimethylethanolamine and choline (N,N,N-trimethylethanolamine) as substrates for growth and methanogenesis. The optimal growth temperature was 30 °C; maximum growth rate was obtained at pH 7.0 in the presence of 0.5 M Na+. The DNA G+C content of strain SLH33T was 43.4 mol%. Phylogenetic analyses based on 16S rRNA gene sequences placed strain SLH33T within the genus Methanococcoides . The novel isolate was related most closely to Methanococcoides methylutens TMA-10T (98.8 % 16S rRNA gene sequence similarity) but distantly related to Methanococcoides burtonii DSM 6242T (97.6 %) and Methanococcoides alaskense AK-5T (97.6 %). DNA–DNA hybridization studies indicated that strain SLH33T represents a novel species, given that it shared less than 16 % DNA–DNA relatedness with Methanococcoides methylutens TMA-10T. The name Methanococcoides vulcani sp. nov. is proposed for this novel species, with strain SLH33T ( = DSM 26966T = JCM 19278T) as the type strain. An emended description of the genus Methanococcoides is also proposed.

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