scholarly journals Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer

2007 ◽  
Vol 57 (8) ◽  
pp. 1757-1761 ◽  
Author(s):  
Nihel Klouche ◽  
Marie-Laure Fardeau ◽  
Jean-François Lascourrèges ◽  
Jean-Luc Cayol ◽  
Hocine Hacene ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Deep Aquifer ◽  
Fermentation Products

A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68T, was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0–5.0×0.5 μm). Strain VNs68T grew at temperatures between 30 and 55 °C (optimum 42 °C) and at pH 5.6–8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l−1. Strain VNs68T was an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68T was affiliated to cluster XI, order Clostridiales, domain Bacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68T is considered to represent a novel species of a new genus, for which the name Geosporobacter subterraneus gen. nov., sp. nov. is proposed. The type strain of Geosporobacter subterraneus is VNs68T (=DSM 17957T =JCM 14037T).

scholarly journals Rarimicrobium hominis gen. nov., sp. nov., representing the fifth genus in the phylum Synergistetes that includes human clinical isolates

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 3965-3970 ◽  
Author(s):  
Estelle Jumas-Bilak ◽  
Philippe Bouvet ◽  
Emma Allen-Vercoe ◽  
Fabien Aujoulat ◽  
Paul A. Lawson ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Isolates ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence

Five human clinical isolates of an unknown, strictly anaerobic, slow-growing, Gram-stain-negative, rod-shaped micro-organism were subjected to a polyphasic taxonomic study. Comparative 16S rRNA gene sequence-based phylogeny showed that the isolates grouped in a clade that included members of the genera Pyramidobacter, Jonquetella, and Dethiosulfovibrio; the type strain of Pyramidobacter piscolens was the closest relative with 91.5–91.7 % 16S rRNA gene sequence similarity. The novel strains were mainly asaccharolytic and unreactive in most conventional biochemical tests. Major metabolic end products in trypticase/glucose/yeast extract broth were acetic acid and propionic acid and the major cellular fatty acids were C13 : 0 and C16 : 0, each of which could be used to differentiate the strains from P. piscolens. The DNA G+C content based on whole genome sequencing for the reference strain 22-5-S 12D6FAA was 57 mol%. Based on these data, a new genus, Rarimicrobium gen. nov., is proposed with one novel species, Rarimicrobium hominis sp. nov., named after the exclusive and rare finding of the taxon in human samples. Rarimicrobium is the fifth genus of the 14 currently characterized in the phylum Synergistetes and the third one in subdivision B that includes human isolates. The type strain of Rarimicrobium hominis is ADV70T ( = LMG 28163T = CCUG 65426T).

scholarly journals Brevundimonas denitrificans sp. nov., a denitrifying bacterium isolated from deep subseafloor sediment

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3709-3716 ◽  
Author(s):  
Taishi Tsubouchi ◽  
Sumihiro Koyama ◽  
Kozue Mori ◽  
Yasuhiro Shimane ◽  
Keiko Usui ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

A novel Gram-stain-negative, aerobic, heterotrophic, stalked and capsulated bacterium with potential denitrification ability, designated strain TAR-002T, was isolated from deep seafloor sediment in Japan. Colonies lacked lustre, and were viscous and translucent white. The ranges of temperature, pH and salt concentration for growth were 8–30 °C, pH 6.0–10.0 and 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain TAR-002T belongs to the genus Brevundimonas of the class Alphaproteobacteria . Levels of similarity between the 16S rRNA gene sequence of strain TAR-002T and those of the type strains of species of the genus Brevundimonas were 93.5–98.9 %; the most closely related species was Brevundimonas basaltis . In DNA–DNA hybridization assays between strain TAR-002T and its phylogenetic neighbours, Brevundimonas lenta DS-18T, B. basaltis J22T, Brevundimonas subvibrioides ATCC 15264T and Brevundimonas alba DSM 4736T, mean hybridization levels were 6.4–27.7 %. The G+C content of strain TAR-002T was 70.3 mol%. Q-10 was the major respiratory isoprenoid quinone. The major fatty acids were C18 : 1ω7c and C16 : 0, and the presence of 1,2-di-O-acyl-3-O-[d-glucopyranosyl-(1→4)-α-d-glucopyranuronosyl]glycerol (DGL) indicates the affiliation of strain TAR-002T with the genus Brevundimonas . On the basis of biological characteristics and 16S rRNA gene sequence comparisons, strain TAR-002T is considered to represent a novel species of the genus Brevundimonas , for which the name Brevundimonas denitrificans sp. nov. is proposed; the type strain is TAR-002T ( = NBRC 110107T = CECT 8537T).

scholarly journals Halomonas xinjiangensis sp. nov., a halotolerant bacterium isolated from a salt lake

2010 ◽  
Vol 60 (2) ◽  
pp. 349-352 ◽  
Author(s):  
Tong-Wei Guan ◽  
Jing Xiao ◽  
Ke Zhao ◽  
Xiao-Xia Luo ◽  
Xiao-Ping Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Salt Lake ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Terminal Electron Acceptor

A novel bacterium, TRM 0175T, belonging to the genus Halomonas, was isolated from a soil sample taken from a salt lake in Xinjiang Province, north-west China. The isolate was Gram-negative, aerobic, rod-shaped and motile by means of peritrichous flagella. It was catalase-positive and oxidase-negative. Growth occurred at NaCl concentrations of 0–20 % (optimum at 10–13 %), at 15–50 °C (optimum at 37 °C) and at pH 6.0–9.0 (optimum at pH 7.0). Metabolism was respiratory with oxygen as terminal electron acceptor. Acid was produced from d-ribose, d- and l-arabinose, d-xylose, d-galactose, d-mannose, l-rhamnose, cellobiose, maltose, trehalose and d- and l-fucose and was produced weakly from aesculin. The predominant ubiquinone was Q-9. The major fatty acids were C18 : 1 ω7c and C19 : 0 cyclo ω8c. The G+C content of the genomic DNA was 60.0 mol%. The affiliation of strain TRM 0175T with the genus Halomonas was confirmed by 16S rRNA gene sequence comparisons. The most closely related species was Halomonas anticariensis; 16S rRNA gene sequence similarity between H. anticariensis FP35T and strain TRM 0175T was 95.3 %. Phenotypically, some characteristics of TRM 0175T differed from those of H. anticariensis. On the basis of data from this polyphasic study, strain TRM 0175T represents a novel species of the genus Halomonas, for which the name Halomonas xinjiangensis sp. nov. is proposed; the type strain is TRM 0175T (=CCTCC AB 208329T =KCTC 22608T).

scholarly journals Agromyces salentinus sp. nov. and Agromyces neolithicus sp. nov.

2005 ◽  
Vol 55 (1) ◽  
pp. 153-157 ◽  
Author(s):  
Valme Jurado ◽  
Ingrid Groth ◽  
Juan M. Gonzalez ◽  
Leonila Laiz ◽  
Cesareo Saiz-Jimenez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA–DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces neolithicus sp. nov. (type strain, 23-23T=HKI 0321T=DSM 16197T=NCIMB 13989T).

scholarly journals Actinophytocola timorensis sp. nov. and Actinophytocola corallina sp. nov., isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 834-838 ◽  
Author(s):  
Misa Otoguro ◽  
Hideki Yamamura ◽  
Tomohiko Tamura ◽  
Rohmatussolihat Irzaldi ◽  
Shanti Ratnakomala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons

Two actinomycete strains, ID05-A0653T and ID06-A0464T, were isolated from soils of West Timor and Lombok island, respectively, in Indonesia. 16S rRNA gene sequence analysis clearly demonstrated that the isolates belonged to the family Pseudonocardiaceae and were closely related to the genus Actinophytocola. Strains ID05-A0653T and ID06-A0464T exhibited 98.1 and 98.2 % 16S rRNA gene sequence similarity, respectively, with Actinophytocola oryzae GMKU 367T. The isolates grew well on ISP media and produced white aerial mycelium. Short spore chains were formed directly on the substrate mycelium. The isolates contained meso-diaminopimelic acid, arabinose and galactose as cell-wall components, MK-9(H4) as the sole isoprenoid quinone, iso-C16 : 0 as the major cellular fatty acid and phosphatidylethanolamine as the diagnostic polar lipid. The DNA G+C contents of strains ID05-A0653T and ID06-A0464T were 69.7 and 71.2 mol%, respectively. On the basis of phenotypic characteristics, DNA–DNA relatedness and 16S rRNA gene sequence comparisons, strains ID05-A0653T and ID06-A0464T each represent a novel species of the genus Actinophytocola, for which the names Actinophytocola timorensis sp. nov. (type strain ID05-A0653T  = BTCC B-673T  = NBRC 105524T) and Actinophytocola corallina sp. nov. (type strain ID06-A0464T  = BTCC B-674T  = NBRC 105525T) are proposed.

scholarly journals Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent

2004 ◽  
Vol 54 (6) ◽  
pp. 1953-1957 ◽  
Author(s):  
Laurent Urios ◽  
Valérie Cueff-Gauchard ◽  
Patricia Pignet ◽  
Anne Postec ◽  
Marie-Laure Fardeau ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Fermentation Products ◽  
Mid Atlantic Ridge

A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1·8 μm long and 0·4 μm wide, surrounded by an outer sheath-like structure (toga). They grew at 45–80 °C (optimum 65 °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 DV1140T 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 DV1140T (=CIP 108053T=DSM 15807T).

scholarly journals Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral

2010 ◽  
Vol 60 (10) ◽  
pp. 2293-2297 ◽  
Author(s):  
Maya Shnit-Orland ◽  
Alex Sivan ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
The Family

A marine bacterial strain, designated fav-2-10-05T, was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05T was affiliated with the family Shewanellaceae. The closest relatives of strain fav-2-10-05T were Shewanella marisflavi SW-117T (96.0 % 16S rRNA gene sequence similarity) and Shewanella haliotis DW-1T (95.9 %). Strain fav-2-10-05T was Gram-negative, rod-shaped and motile by means of a single polar flagellum and formed yellow–brownish colonies within 2 days of incubation at 26 °C. Strain fav-2-10-05T demonstrated antibacterial activity against indicator strains and grew in the presence of 0.5–8.0 % (w/v) NaCl and at 10–37 °C. The major fatty acids were C17 : 1 ω8c (21.6 %), iso-C15 : 0 (18.6 %), C15 : 0 (9.1 %) and iso-C13 : 0 (8.9 %). The DNA G+C content was 49.1 mol%. The phylogenetic and phenotypic analyses of strain fav-2-10-05T suggested that it belongs to a novel species of the genus Shewanella, for which the name Shewanella corallii sp. nov. is proposed. The type strain is fav-2-10-05T (=LMG 24563T =DSM 21332T).

scholarly journals Terrisporobacter petrolearius sp. nov., isolated from an oilfield petroleum reservoir

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3522-3526 ◽  
Author(s):  
Yu Deng ◽  
Xiang Guo ◽  
Yanwei Wang ◽  
Mingxiong He ◽  
Kedong Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Petroleum Reservoir ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

A Gram-staining-positive, spore-forming, strictly anaerobic bacterium, designated strain LAM0A37T, was isolated from enrichment samples collected from a petroleum reservoir in Shengli oilfield. Cells of strain LAM0A37T were rod-shaped and motile by peritrichous flagella. The optimal temperature and pH for growth were 40 °C and 7.0–7.5, respectively. The strain did not require NaCl for growth but tolerated up to 3 % (w/v) NaCl. Strain LAM0A37T was able to utilize glucose, fructose, maltose, xylose, sorbitol, cellobiose, melibiose and melezitose as sole carbon sources. Sulfite was used as an electron acceptor. The main products of glucose fermentation were acetate and CO2. The predominant fatty acid was C16 : 0 (23.6 %). The main polar lipid profile comprised of five glycolipids, six phospholipids and two lipids. No menaquinone was detected. The genomic DNA G+C content was 27.1 ± 0.2 mol% as determined by the T m method. Analysis of the 16S rRNA gene sequence indicated that the isolate was a member of the genus Terrisporobacter, and was most closely related to Terrisporobacter glycolicus JCM 1401T and Terrisporobacter mayombei DSM 6539T with 98.3 % 16S rRNA gene sequence similarity to both. DNA–DNA hybridization values between strain LAM0A37T and type strains of Terrisporobacter glycolicus and Terrisporobacter mayombei were 45.6 ± 0.3 % and 38.3 ± 0.4 %, respectively. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, strain LAM0A37T is suggested to represent a novel species of the genus Terrisporobacter, for which the name Terrisporobacter petrolearius sp. nov. is proposed. The type strain is LAM0A37T ( = ACCC 00740T = JCM 19845T).

scholarly journals Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1714-1718 ◽  
Author(s):  
Xiang Zeng ◽  
Zhao Zhang ◽  
Xi Li ◽  
Mohamed Jebbar ◽  
Karine Alain ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sea Salts ◽  
Content Type ◽  
Link Type

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 µm in length, 0.5 µm 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, α-ketobutyric acid, α-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 Caloranaerobacter http://dx.doi.org/10.1601/nm.4081 ferrireducens sp. nov. is proposed. The type strain is DY22619T ( = JCM 19467T = DSM 27799T = MCCC1A06455T).

scholarly journals Terrimicrobium sacchariphilum gen. nov., sp. nov., an anaerobic bacterium of the class ‘Spartobacteria’ in the phylum Verrucomicrobia, isolated from a rice paddy field

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1718-1723 ◽  
Author(s):  
Yan-Ling Qiu ◽  
Xiao-zhu Kuang ◽  
Xiao-shuang Shi ◽  
Xian-zheng Yuan ◽  
Rong-bo Guo
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Paddy Field ◽  
Gene Sequence ◽  
Rice Paddy ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Rice Paddy Field

A strictly anaerobic, mesophilic, carbohydrate-fermenting bacterium, designated NM-5T, was isolated from a rice paddy field. Cells of strain NM-5T were Gram-stain-negative, non-motile, non-spore-forming, short rods (0.5–0.7 µm×0.6–1.2 µm). The strain grew optimally at 37 °C (growth range 20–40 °C) and pH 7.0 (pH 5.5–8.0). The strain could grow fermentatively on arabinose, xylose, fructose, galactose, glucose, ribose, mannose, cellobiose, lactose, maltose and sucrose. The main end-products of glucose fermentation were acetate and propionate. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required but stimulated the growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite, and Fe (III) nitrilotriacetate were not used as terminal electron acceptors. The DNA G+C content was 46.3 mol%. The major cellular fatty acids were iso-C14 : 0, C18 : 0 and C16 : 0. 16S rRNA gene sequence analysis revealed that strain NM-5T belongs to the class ‘S partobacteria’, subdivision 2 of the bacterial phylum Verrucomicrobia . Phylogenetically, the closest species was ‘Chthoniobacter flavus’ (89.6 % similarity in 16S rRNA gene sequence). A novel genus and species, Terrimicrobium sacchariphilum gen. nov., sp. nov., is proposed. The type strain of the type species is NM-5T ( = JCM 17479T = CGMCC 1.5168T).

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