scholarly journals Amphibacillus jilinensis sp. nov., a facultatively anaerobic, alkaliphilic bacillus from a soda lake

2010 ◽  
Vol 60 (11) ◽  
pp. 2540-2543 ◽  
Author(s):  
Xiao-Yue Wu ◽  
Gang Zheng ◽  
Wen-Wu Zhang ◽  
Xue-Wei Xu ◽  
Min Wu ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Soda Lake ◽  
Soluble Starch ◽  
Biochemical Properties ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Positive Staining ◽  
Strictly Anaerobic ◽  
Dna Relatedness ◽  
Facultatively Anaerobic

A facultatively anaerobic, alkaliphilic, spore-forming, Gram-positive-staining rod, designated Y1T, was isolated under strictly anaerobic conditions from sediment of a soda lake in Jilin province, China. The strain was not dependent on Na+ but was highly halotolerant and grew optimally in medium JY with 0.5 M Na+ (0.06 M NaHCO3 and 0.44 M NaCl). The optimum pH for growth was 9.0, with a range of pH 7.5–10.5. No growth occurred at pH 7.0 or 11.0. The strain was mesophilic, with a temperature range of 15–45 °C and optimum growth at 32 °C. Strain Y1T was able to use certain mono- and oligosaccharides. Soluble starch and casein were hydrolysed. The methyl red test, Voges–Proskauer test and tests for catalase and oxidase activities were negative. The predominant fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Comparative 16S rRNA gene sequence analysis revealed 93.4–96.8 % sequence similarity to members of the genus Amphibacillus. The DNA G+C content was 37.7 mol% (T m method). The DNA–DNA relatedness of strain Y1T with respect to Amphibacillus tropicus DSM 13870T and Amphibacillus sediminis DSM 21624T was 48 and 37 %, respectively. On the basis of its phylogenetic position and the DNA–DNA relatedness data as well as its physiological and biochemical properties, strain Y1T represents a novel species of the genus Amphibacillus, for which the name Amphibacillus jilinensis sp. nov. is proposed. The type strain is Y1T (=CGMCC 1.5123T =JCM 16149T).

scholarly journals Alkalibacterium subtropicum sp. nov., a slightly halophilic and alkaliphilic marine lactic acid bacterium isolated from decaying marine algae

2011 ◽  
Vol 61 (12) ◽  
pp. 2996-3002 ◽  
Author(s):  
Morio Ishikawa ◽  
Kazuyuki Nakajima ◽  
Shihomi Ishizaki ◽  
Kayo Kodama ◽  
Akiko Okamoto-Kainuma ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Marine Algae ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Molar Ratio ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Cultivation Conditions ◽  
Dna Relatedness

Two novel strains of marine lactic acid bacteria, isolated from decaying marine algae collected from a subtropical area of Japan, are described. The isolates, designated O24-2T and O25-2, were Gram-positive, non-sporulating and non-motile. They lacked catalase and quinones. Under anaerobic cultivation conditions, lactate was produced from glucose with the production of formate, acetate and ethanol in a molar ratio of approximately 2 : 1 : 1. Under aerobic cultivation conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. They were able to grow in 0–17.0 % (w/v) NaCl, with optimum growth of strains O24-2T and O25-2 at 1.0–3.0 and 1.0–2.0 % (w/v) NaCl, respectively. Growth of strain O24-2T was observed at pH 7.5–9.5, with optimum growth at pH 8.0–8.5. Comparative 16S rRNA gene sequence analysis revealed that the isolates occupied a phylogenetic position within the genus Alkalibacterium, showing highest similarity (99.6 %) to Alkalibacterium putridalgicola T129-2-1T. Although sequence similarity was high, the DNA–DNA relatedness value between strain O24-2T and A. putridalgicola T129-2-1T was 27 %, indicating that they are members of distinct species. The DNA G+C contents of O24-2T and O25-2 were 43.7 and 44.4 mol%, respectively, and DNA–DNA relatedness between the isolates was 89 %. The cell-wall peptidoglycan was type A4β, Orn-d-Asp. The major cellular fatty acid components were C14 : 0, C16 : 0 and C16 : 1ω9c. Based on phenotypic characteristics and genetic distinctiveness, the isolates were classified as representatives of a novel species within the genus Alkalibacterium, for which the name Alkalibacterium subtropicum sp. nov. is proposed; the type strain is O24-2T ( = DSM 23664T = NBRC 107172T).

scholarly journals Description of Mariniphaga anaerophila gen. nov., sp. nov., a facultatively aerobic marine bacterium isolated from tidal flat sediment, reclassification of the Draconibacteriaceae as a later heterotypic synonym of the Prolixibacteraceae and description of the family Marinifilaceae fam. nov.

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3660-3667 ◽  
Author(s):  
Takao Iino ◽  
Koji Mori ◽  
Takashi Itoh ◽  
Takuji Kudo ◽  
Ken-ichiro Suzuki ◽  
...  
Keyword(s):  
Tidal Flat ◽  
Sequence Similarity ◽  
Soluble Starch ◽  
Tokyo Bay ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Tidal Flat Sediment ◽  
The Family

A mesophilic, chemoheterotrophic bacterium, strain Fu11-5T, was isolated from tidal-flat sediment from Tokyo Bay, Chiba, Japan. Cells of strain Fu11-5T were facultatively aerobic, Gram-negative, non-sporulating, non-motile and rod-shaped (1.9–6.9 µm long). Strain Fu11-5T grew optimally at 35–37 °C and pH 6.5–7.0 and with 1–2 % (w/v) NaCl. Oxygen and l-cysteine were used as an alternative electron acceptor and donor, respectively. Strain Fu11-5T also grew fermentatively on some pentoses, hexoses and disaccharides and soluble starch. Succinic acid was the major end product from d-glucose. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain Fu11-5T was affiliated with the order Bacteroidales , and its nearest neighbours were members of the genera Meniscus , Prolixibacter , Sunxiuqinia , Mangrovibacterium and Draconibacterium, with 87–91 % sequence similarity. Cell morphology, optimum growth temperature and utilization of sugars of strain Fu11-5T distinguished the strain from phylogenetically related bacteria. On the basis of its phenotypic features and phylogenetic position, a novel genus and species are proposed to accommodate strain Fu11-5T, with the name Mariniphaga anaerophila gen. nov., sp. nov. The type strain of Mariniphaga anaerophila is strain Fu11-5T ( = JCM 18693T = NBRC 109408T = DSM 26910T). We also propose to combine the family Draconibacteriaceae into the family Prolixibacteraceae as a later heterotypic synonym and to place the distinct sublineage of the genus Marinifilum in the family Marinifilaceae fam. nov.

scholarly journals Gluconacetobacter kakiaceti sp. nov., an acetic acid bacterium isolated from a traditional Japanese fruit vinegar

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1465-1469 ◽  
Author(s):  
Takao Iino ◽  
Rei Suzuki ◽  
Naoto Tanaka ◽  
Yoshimasa Kosako ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Acetic Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Diospyros Kaki ◽  
Rrna Gene ◽  
Content Type ◽  
Dna Relatedness ◽  
Link Type

Two novel acetic acid bacteria, strains G5-1T and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1T and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01T (99.3 % 16S rRNA gene sequence similarity). The isolates showed 96–100 % DNA–DNA relatedness with each other, but <53 % DNA–DNA relatedness with closely related members of the genus Gluconacetobacter . The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30 % (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1T and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1T and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1T ( = JCM 25156T = NRIC 0798T = LMG 26206T).

Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 180-186 ◽  
Author(s):  
Sofiya N. Parshina ◽  
Anna V. Ermakova ◽  
Malin Bomberg ◽  
Ekaterina N. Detkova
Keyword(s):  
Low Temperature ◽  
Type Species ◽  
Sequence Similarity ◽  
Granular Sludge ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Methanospirillum Hungatei ◽  
Link Type

A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2 and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genus Methanospirillum and showed 97.5 % sequence similarity to Methanospirillum hungatei JF1T and 94 % sequence similarity to Methanospirillum lacunae Ki8-1T. DNA–DNA hybridization of strain Pt1 with Methanospirillum hungatei JF1T revealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genus Methanospirillum , for which the name Methanospirillum stamsii sp. nov. is proposed. The type strain is Pt1T ( = DSM 26304T = VKM B-2808T).

scholarly journals Halorubrum alkaliphilum sp. nov., a novel haloalkaliphile isolated from a soda lake in Xinjiang, China

2005 ◽  
Vol 55 (1) ◽  
pp. 149-152 ◽  
Author(s):  
Jie Feng ◽  
Peijin Zhou ◽  
Yu-Guang Zhou ◽  
Shuang-Jiang Liu ◽  
Kimberly Warren-Rhodes
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Soda Lake ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Dna Relatedness

A novel haloalkaliphilic archaeon, strain DZ-1T, was isolated from a soda lake in Xinjiang, China. The taxonomy of strain DZ-1T was studied by polyphasic methods. According to 16S rRNA gene sequence similarity, strain DZ-1T was phylogenetically related to Halorubrum tibetense (97·5 %), Halorubrum vacuolatum (95·7 %) and Halorubrum saccharovorum (95·9 %). Strain DZ-1T was able to grow at 20–44 °C and was also physiologically different from the above-mentioned species with respect to assimilation of sugars and utilization of organic acids. The DNA G+C content of strain DZ-1T was 62·1 mol% (T m). The DNA–DNA relatedness of strain DZ-1T to H. tibetense and H. vacuolatum was 22 and 13 %, respectively. It was concluded that strain DZ-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum alkaliphilum (type strain, DZ-1T=AS 1.3528T=JCM 12358T) is proposed.

scholarly journals Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii (Séguin 1928) Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov.

2010 ◽  
Vol 60 (3) ◽  
pp. 585-590 ◽  
Author(s):  
Jean-Philippe Carlier ◽  
Marie Bedora-Faure ◽  
Guylène K'ouas ◽  
Corentine Alauzet ◽  
Francine Mory
Keyword(s):  
Type Strain ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Clinical Samples ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Distinct Cluster ◽  
Nearest Neighbours ◽  
Clostridial Cluster ◽  
Sequence Similarities

We isolated several strains from various clinical samples (five samples of blood, four of intra-abdominal pus and one of infected soft tissue) that were anaerobic, motile or non-motile and Gram-positive rods. Some of the strains formed spores. Phylogenetic analysis of the 16S rRNA gene sequence showed that these organisms could be placed within clostridial cluster IV as defined by Collins et al. [(1994). Int J Syst Bacteriol 44, 812–826] and shared more than 99 % sequence similarity with Clostridium orbiscindens DSM 6740T and Eubacterium plautii DSM 4000T. Together, they formed a distinct cluster, with Bacteroides capillosus ATCC 29799T branching off from this line of descent with sequence similarities of 97.1–97.4 %. The next nearest neighbours of these organisms were Clostridium viride, Oscillibacter valericigenes, Papillibacter cinnamivorans and Sporobacter termitidis, with sequence similarities to the respective type strains of 93.1–93.4, 91.2–91.4, 89.8–90 and 88.7–89.3 %. On the basis of biochemical properties, phylogenetic position, DNA G+C content and DNA–DNA hybridization, it is proposed to unify Clostridium orbiscindens and Eubacterium plautii in a new genus as Flavonifractor plautii gen. nov., comb. nov., with the type strain Prévot S1T (=ATCC 29863T =VPI 0310T =DSM 4000T), and to reassign Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov., with the type strain CCUG 15402AT (=ATCC 29799T =VPI R2-29-1T).

scholarly journals Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei

2010 ◽  
Vol 60 (11) ◽  
pp. 2563-2566 ◽  
Author(s):  
Takao Iino ◽  
Koji Mori ◽  
Ken-ichiro Suzuki
Keyword(s):  
Novel Species ◽  
Sequence Similarity ◽  
Basal Medium ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Methanospirillum Hungatei ◽  
Single Flagellum

A mesophilic, hydrogenotrophic methanogen, designated strain Ki8-1T, was isolated from soil. Cells were strictly anaerobic, Gram-stain-negative, non-sporulating, motile by means of a single flagellum or tufted flagella, and curved or wavy rod-shaped (11–25 μm long). The temperature and pH for optimum growth were 30 °C and 7.5. The strain grew best in basal medium without the addition of NaCl. Methane was produced from H2 and formate. Acetate or yeast extract was required for growth. The G+C content of the genomic DNA of strain Ki8-1T was 45.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Ki8-1T was a member of the genus Methanospirillum and showed 95.1 % sequence similarity to Methanospirillum hungatei NBRC 100397T. On the basis of its phenotypic characteristics and phylogenetic position, strain Ki8-1T is considered to represent a novel species of the genus Methanospirillum, for which the name Methanospirillum lacunae sp. nov. is proposed. The type strain is Ki8-1T (NBRC 104920T =JCM 16384T =DSM 22751T). Emended descriptions of the genus Methanospirillum and of Methanospirillum hungatei are also provided.

scholarly journals Cellulomonas bogoriensis sp. nov., an alkaliphilic cellulomonad

2005 ◽  
Vol 55 (4) ◽  
pp. 1711-1714 ◽  
Author(s):  
Brian E. Jones ◽  
William D. Grant ◽  
A. W. Duckworth ◽  
Peter Schumann ◽  
Norbert Weiss ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Optimal Growth ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Diamino Acid ◽  
Bacterium Strain ◽  
Metabolic Properties ◽  
Type Strains ◽  
The 16S Rrna Gene

An alkaliphilic, slightly halotolerant, chemo-organotrophic, Gram-positive, rod-shaped bacterium, strain 69B4T, was isolated from the sediment of the littoral zone of Lake Bogoria, Kenya. Phylogenetically, it is a member of the genus Cellulomonas, showing less than 97·5 % sequence similarity to the type strains of other Cellulomonas species. The highest level of similarity, albeit moderate, was found with respect to Cellulomonas cellasea DSM 20118T. Chemotaxonomic properties confirm the 16S rRNA gene-based generic affiliation, i.e. a DNA G+C content of 71·5 mol%, anteiso-C15 : 0 and C16 : 0 as the major fatty acids, MK-9(H4) as the major isoprenoid quinone, a peptidoglycan containing l-ornithine as the diamino acid and d-aspartic acid in the interpeptide bridge and phosphatidylglycerol as the only identified main polar lipid. The strain is aerobic to facultatively anaerobic, being capable of growth under strictly anaerobic conditions. Optimal growth occurs between pH values 9·0 and 10·0. On the basis of its distinct phylogenetic position and metabolic properties, strain 69B4T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas bogoriensis sp. nov. is proposed. The type strain is 69B4T (=DSM 16987T=CIP 108683T).

scholarly journals Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria

2010 ◽  
Vol 60 (6) ◽  
pp. 1376-1382 ◽  
Author(s):  
Takao Iino ◽  
Koji Mori ◽  
Yoshihito Uchino ◽  
Tatsunori Nakagawa ◽  
Shigeaki Harayama ◽  
...  
Keyword(s):  
Microbial Mats ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Green Sulfur Bacteria ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Moderately Thermophilic ◽  
Sulfur Bacteria ◽  
Green Sulfur

A moderately thermophilic chemoheterotrophic bacterium, strain Mat9-16T, was isolated from microbial mats developed in hot spring water streams from Yumata, Nagano, Japan. Cells of strain Mat9-16T were strictly anaerobic, Gram-stain-negative, non-sporulating, non-motile and short to long rods (2.0–15.5 μm in length). Strain Mat9-16T grew fermentatively with optimum growth at 45 °C, pH 7.0–7.5 and 1 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene revealed that strain Mat9-16T was affiliated with an uncultivated lineage, and the nearest cultivated neighbours were green sulfur bacteria belonging to the class Chlorobea with 77–83 % sequence similarity. However, strain Mat9-16T could not grow phototrophically and did not possess light-harvesting structures, morphologically and genetically, such as the chlorosomes of green sulfur bacteria. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed for strain Mat9-16T, to be named Ignavibacterium album gen. nov., sp. nov. (=NBRC 101810T =DSM 19864T). We also propose to place the cultivated bacterial lineage accommodating the sole representative Mat9-16T in a novel class, Ignavibacteria classis nov. In addition, we present a formal description of the phylum-level taxon ‘Chlorobi’ as Chlorobi phyl. nov.

scholarly journals Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment

2010 ◽  
Vol 60 (12) ◽  
pp. 2996-3001 ◽  
Author(s):  
Shi-Ping Tian ◽  
Yong-Xia Wang ◽  
Bin Hu ◽  
Xiao-Xia Zhang ◽  
Wei Xiao ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Soda Lake ◽  
Optimal Growth ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Sequence Comparisons ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone ◽  
Respective Type

A novel alkaliphilic, halotolerant, rod-shaped bacterium, designated strain YIM CH208T, was isolated from a soda lake in Yunnan, south-west China. The taxonomy of strain YIM CH208T was investigated by a polyphasic approach. Strain YIM CH208T was Gram-negative, strictly aerobic and non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.5 and 0.5–2.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the isolate formed a distinct line within a clade containing the genus Echinicola in the phylum Bacteroidetes and was related to the species Echinicola pacifica and Rhodonellum psychrophilum, with sequence similarity of 91.7 and 91.6 % to the respective type strains. The DNA G+C content was 45.1 mol%. The major respiratory quinone was menaquinone-7 (MK-7). The predominant cellular fatty acids were iso-C17 : 1 ω9c (19.9 %), C15 : 0 3-OH (12.1 %), iso-C17 : 0 3-OH (11.3 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 10.7 %) and C17 : 1 ω6c (8.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain YIM CH208T represents a novel species of a new genus, for which the name Litoribacter ruber gen. nov., sp. nov. is proposed. The type strain of Litoribacter ruber is YIM CH208T (=ACCC 05414T =KCTC 22899T).

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