scholarly journals Methanobacterium movens sp. nov. and Methanobacterium flexile sp. nov., isolated from lake sediment

2011 ◽  
Vol 61 (12) ◽  
pp. 2974-2978 ◽  
Author(s):  
Jinxing Zhu ◽  
Xiaoli Liu ◽  
Xiuzhu Dong
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Qaidam Basin ◽  
Sequence Similarity ◽  
Single Cells ◽  
Rrna Gene ◽  
Qinghai Province ◽  
Gram Staining

Two mesophilic methanogenic strains, designated TS-2T and GHT, were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3–0.5×2–5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2T was motile with one or two polar flagella and used only H2/CO2 for growth and methanogenesis. Strain GHT was non-motile, used both H2/CO2 and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H2 and single cells under low pressure H2. Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2T was most closely related to Methanobacterium alcaliphilum NBRC 105226T (96 % 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA–DNA relatedness between the isolates and M. alcaliphilum DSM 3387T was 39–53 %. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2T = AS 1.5093T = JCM 15415T) and Methanobacterium flexile sp. nov. (type strain GHT = AS 1.5092T = JCM 15416T).

scholarly journals Haloactinobacterium album gen. nov., sp. nov., a halophilic actinobacterium, and proposal of Ruaniaceae fam. nov.

2010 ◽  
Vol 60 (9) ◽  
pp. 2113-2119 ◽  
Author(s):  
Shu-Kun Tang ◽  
Xiao-Yang Zhi ◽  
Yun Wang ◽  
Jin-Yuan Wu ◽  
Jae-Chan Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Gene Signature ◽  
Rrna Gene ◽  
North West ◽  
Gram Staining

A Gram-staining-positive, facultatively anaerobic, non-motile and moderately halophilic actinobacterium, designated YIM 93306T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic study. Strain YIM 93306T grew in the presence of 2–16 % (w/v) NaCl and did not grow without NaCl. The peptidoglycan type was A4α with an l-Lys–l-Glu interpeptide bridge. The whole-cell sugars were glucosamine, arabinose, mannose and two unknown sugars. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phosphoglycolipid and one unknown phospholipid. The DNA G+C content was 68.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 93306T fell within the radius of the suborder Micrococcineae. Its closest phylogenetic neighbour was the type strain of Ruania albidiflava (AS 4.3142T; 96.2 % 16S rRNA gene sequence similarity), the sole recognized species of the genus Ruania. Sequence similarities between strain YIM 93306T and members of other genera of the suborder Micrococcineae were <95.2 %. On the basis of phylogenetic analysis, phenotypic characteristics and chemotaxonomic differences, a novel genus and species, Haloactinobacterium album gen. nov., sp. nov., is proposed. The type strain of the species is YIM 93306T (=DSM 21368T =KCTC 19413T =CCTCC AB 208069T). Based on phylogenetic characteristics and 16S rRNA gene signature nucleotide patterns, the genera Ruania and Haloactinobacterium gen. nov. are proposed to belong to a novel family, Ruaniaceae fam. nov.

scholarly journals Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean

2010 ◽  
Vol 60 (9) ◽  
pp. 2187-2192 ◽  
Author(s):  
Munusamy Madhaiyan ◽  
Selvaraj Poonguzhali ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
Subbiah Sundaram
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Staining ◽  
Cultivated Soybean

An aerobic, yellow-pigmented, facultatively methylotrophic, Gram-staining-negative, non-spore-forming bacterium, designated strain Gm-149T, was isolated from the rhizosphere of cultivated soybean in India. Cells were motile by gliding. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C16 : 0 3-OH and anteiso-C15 : 0, and the major isoprenoid quinone was MK-6. The G+C content of the genomic DNA of strain Gm-149T was 35.6 mol%. Comparative 16S rRNA gene sequence analysis showed that strain Gm-149T formed a distinct phyletic line within the genus Flavobacterium. Based on levels of pairwise 16S rRNA gene sequence similarity, strain Gm-149T was related most closely to the type strain of Flavobacterium daejeonense (97.1 %), but the level of DNA–DNA relatedness between these two strains was about 11.2 %. On the basis of phenotypic and genotypic data, strain Gm-149T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium glycines sp. nov. is proposed. The type strain is Gm-149T (=ICMP 17618T=NBRC 105008T).

scholarly journals Devosia psychrophila sp. nov. and Devosia glacialis sp. nov., from alpine glacier cryoconite, and an emended description of the genus Devosia

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 710-715 ◽  
Author(s):  
De-Chao Zhang ◽  
Mersiha Redzic ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Franz Schinner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Alpine Glacier ◽  
Emended Description

Two psychrophilic strains, Cr7-05T and Cr4-44T, isolated from alpine glacier cryoconite, were characterized by using a polyphasic approach. Both strains were psychrophilic, showing good growth over a temperature range of 1–20 °C. The chemotaxonomic characteristics of these isolates included the presence of C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major cellular fatty acids, Q-10 as the predominant ubiquinone and diphosphatidylglycerol, phosphatidylglycerol and unknown glycolipids as major polar lipids. The DNA G+C contents of strains Cr7-05T and Cr4-44T were 61.4 and 63.6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belong to the genus Devosia. The 16S rRNA gene sequence similarity between the two strains was 98.6 %, but DNA–DNA hybridization indicated 54 % relatedness. Strains Cr7-05T and Cr4-44T exhibited 16S rRNA gene sequence similarity of 94.7–97.2 and 94.9–96.9 %, respectively, to the type strains of recognized Devosia species. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strains Cr7-05T and Cr4-44T represent two novel species within the genus Devosia, for which the names Devosia psychrophila sp. nov. (type strain Cr7-05T  = DSM 22950T  = CGMCC 1.10210T  = CIP 110130T) and Devosia glacialis sp. nov. (type strain Cr4-44T  = CGMCC 1.10691T  = LMG 26051T) are proposed. An emended description of the genus Devosia is also provided.

scholarly journals Epilithonimonas lactis sp. nov., isolated from raw cow'smilk

2010 ◽  
Vol 60 (3) ◽  
pp. 675-679 ◽  
Author(s):  
Tamar Shakéd ◽  
Elionora Hantsis-Zacharov ◽  
Malka Halpern
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Gram Staining

A Gram-staining-negative, rod-shaped, oxidase-positive, aerobic, non-motile and yellow-pigmented bacterial strain containing flexirubin type pigments, designated H1T, was isolated from raw cow'smilk in Israel.16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Epilithonimonas (family Flavobacteriaceae, phylum Bacteroidetes). The level of 16S rRNA gene sequence similarity between strain H1T and the type strain of Epilithonimonas tenax was 97.6 %. Strain H1T grew at 5–33 °C and with 0–2.0 % NaCl. The dominant cellular fatty acids of strain H1T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), and the DNA G+C content was 38.0 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the milk isolate is classified as a new species in the genus Epilithonimonas, for which the name Epilithonimonas lactis sp. nov. (type strain H1T =LMG 24401T =DSM 19921T) is proposed.

scholarly journals Pseudomonas salina sp. nov., isolated from a salt lake

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2846-2851 ◽  
Author(s):  
Zhi-Ping Zhong ◽  
Ying Liu ◽  
Ting-Ting Hou ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Salt Lake ◽  
Qaidam Basin ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Respiratory Quinone ◽  
Qinghai Province ◽  
Gram Staining

A Gram-staining-negative, facultatively aerobic bacterium, strain XCD-X85T, was isolated from Xiaochaidan Lake, a salt lake (salinity 9.9  %, w/v) in Qaidam basin, Qinghai province, China. Its taxonomic position was determined by using a polyphasic approach. Cells of strain XCD-X85T were non-endospore-forming rods, 0.4–0.6 μm wide and 1.0–1.6 μm long, and motile by means of a single polar flagellum. Strain XCD-X85T was catalase- and oxidase-positive. Growth was observed in the presence of 0–12.0  % (w/v) NaCl (optimum, 1.0–2.0  %) and at 4–35 °C (optimum, 25–30 °C) and pH 6.5–10.5 (optimum, pH 8.0–8.5). Strain XCD-X85T contained (>10  %) summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C12 : 0, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major respiratory quinone was ubiquinone 9 (Q-9). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 57.4 mol%. Phylogenetic trees based on 16S rRNA gene sequences showed that strain XCD-X85T was associated with the genus Pseudomonas, and showed highest 16S rRNA gene sequence similarities to Pseudomonas pelagia CL-AP6T (99.0  %) and Pseudomonas bauzanensis BZ93T (96.8  %). DNA–DNA relatedness of strain XCD-X85T to P. pelagia JCM 15562T was 19 ± 1  %. On the basis of the data presented above, it is concluded that strain XCD-X85T represents a novel species of the genus Pseudomonas, for which the name Pseudomonas salina sp. nov. is proposed. The type strain is XCD-X85T ( = CGMCC 1.12482T = JCM 19469T).

scholarly journals Halobacillus dabanensis sp. nov. and Halobacillus aidingensis sp. nov., isolated from salt lakes in Xinjiang, China

2005 ◽  
Vol 55 (5) ◽  
pp. 1991-1996 ◽  
Author(s):  
W. Y. Liu ◽  
J. Zeng ◽  
L. Wang ◽  
Y. T. Dou ◽  
S. S. Yang
Keyword(s):  
Fatty Acids ◽  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Salt Lakes ◽  
Rrna Gene ◽  
Dna Relatedness ◽  
Type Strains

Two moderately halophilic spore-forming bacteria were isolated from salt lakes in the Xinjiang region of China. The two strains, designated AD-6T and D-8T, were aerobic, Gram-positive, rod-shaped and motile by means of peritrichous flagella. Strains AD-6T and D-8T grew in the presence of 0·5–20 % and 0·5–25 % (w/v) NaCl in complex medium, respectively. Their cell-wall peptidoglycan was of the l-orn–d-Asp type. The major menaquinone found in both strains was menaquinone-7 (MK-7). The fatty acid profile contained a large amount of branched fatty acids; the main fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The DNA G+C content of strains D-8T and AD-6T was 41·4 and 42·2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains D-8T and AD-6T were located in the genus Halobacillus. Levels of 16S rRNA gene sequence similarity between the isolated strains and the type strains of Halobacillus species were in the range 96·2–99·5 %. DNA–DNA relatedness values of 17·0–52·2 % were found between the two strains and other Halobacillus species. The DNA–DNA relatedness value between D-8T and AD-6T was 50·6 %. On the basis of phenotypic and chemotaxonomic properties, phylogenetic analysis and genomic distinctiveness, strains D-8T and AD-6T should be placed in the genus Halobacillus as two novel species, for which the names Halobacillus dabanensis sp. nov. (type strain=JCM 12772T=CGMCC 1.3704T) and Halobacillus aidingensis sp. nov. (type strain=JCM 12771T=CGMCC 1.3703T) are proposed, respectively.

scholarly journals Pseudoseohaeicola caenipelagi gen. nov., sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1819-1824 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Chul-Hyung Kang ◽  
Song-Gun Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

A Gram-stain-negative, non-motile, aerobic and pleomorphic bacterium, designated BS-W13T, was isolated from a tidal flat on the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain BS-W13T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 1.0–2.0 % (w/v) NaCl. Neighbour-joining and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain BS-W13T clustered with the type strain of Seohaeicola saemankumensis , showing the highest sequence similarity (95.96 %) to this strain. Strain BS-W13T exhibited 16S rRNA gene sequence similarity values of 95.95, 95.91, 95.72 and 95.68 % to the type strains of Sulfitobacter donghicola , Sulfitobacter porphyrae , Sulfitobacter mediterraneus and Roseobacter litoralis , respectively. Strain BS-W13T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain BS-W13T, containing phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid as major components, was distinguishable from those of some phylogenetically related taxa. The DNA G+C content of strain BS-W13T was 58.1 mol%. The phylogenetic data and differential chemotaxonomic and other phenotypic properties revealed that strain BS-W13T constitutes a novel genus and species within family Rhodobacteraceae of the class Alphaproteobacteria , for which the name Pseudoseohaeicola caenipelagi gen. nov., sp. nov. is proposed. The type strain is BS-W13T ( = KCTC 42349T = CECT 8724T).

scholarly journals Exiguobacterium aestuarii sp. nov. and Exiguobacterium marinum sp. nov., isolated from a tidal flat of the Yellow Sea in Korea

2005 ◽  
Vol 55 (2) ◽  
pp. 885-889 ◽  
Author(s):  
In-Gi Kim ◽  
Mi-Hwa Lee ◽  
Seo-Youn Jung ◽  
Jae Jun Song ◽  
Tae-Kwang Oh ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Yellow Sea ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Three Gram-variable, rod-shaped bacterial strains, TF-16T, TF-19 and TF-80T, were isolated from a tidal flat of Daepo Beach (Yellow Sea) near Mokpo City, Korea, and their taxonomic positions were investigated by a polyphasic approach. These isolates grew optimally in the presence of 2 % NaCl and at 30 °C. Their peptidoglycan types were based on l-Lys–Gly. The predominant menaquinone detected in the three strains was MK-7. The three strains contained large amounts of the branched fatty acids iso-C17 : 0, anteiso-C13 : 0, iso-C13 : 0 and iso-C15 : 0. The DNA G+C contents of strains TF-16T, TF-19 and TF-80T were 48·6, 48·4 and 48·0 mol%, respectively. The three strains formed a coherent cluster with Exiguobacterium species in a phylogenetic tree based on 16S rRNA gene sequences. They showed closest phylogenetic affiliation to Exiguobacterium aurantiacum, with 16S rRNA gene sequence similarity values of 98·1–98·3 %. The three strains exhibited 16S rRNA gene sequence similarity values of 94·0–94·6 % to the type strains of other Exiguobacterium species. Levels of DNA–DNA relatedness indicated that strains TF-16T and TF-19 and strain TF-80T are members of two species that are separate from E. aurantiacum. On the basis of phenotypic, phylogenetic and genetic data, strains TF-16T and TF-19 and strain TF-80T represent two novel species in the genus Exiguobacterium; the names Exiguobacterium aestuarii sp. nov. (type strain TF-16T=KCTC 19035T=DSM 16306T; reference strain TF-19) and Exiguobacterium marinum sp. nov. (type strain TF-80T=KCTC 19036T=DSM 16307T) are proposed.

scholarly journals Bacillus thermolactis sp. nov., isolated from dairy farms, and emended description of Bacillus thermoamylovorans

2011 ◽  
Vol 61 (8) ◽  
pp. 1954-1961 ◽  
Author(s):  
An Coorevits ◽  
Niall A. Logan ◽  
Anna E. Dinsdale ◽  
Gillian Halket ◽  
Patsy Scheldeman ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Emended Description

A polyphasic taxonomic study was performed on 22 thermotolerant, aerobic, endospore-forming bacteria from dairy environments. Seventeen isolates were retrieved from raw milk, one from a filter cloth and four from grass, straw or milking equipment. These latter four isolates (R-6546, R-7499, R-7764 and R-7440) were identified as Bacillus thermoamylovorans based on DNA–DNA hybridizations (values above 70 % with Bacillus thermoamylovorans LMG 18084T) but showed discrepancies in characteristics with the original species description, so an emended description of this species is given. According to 16S rRNA gene sequence analysis and DNA–DNA hybridization experiments, the remaining 18 isolates (R-6488T, R-28193, R-6491, R-6492, R-7336, R-33367, R-6486, R-6770, R-31288, R-28160, R-26358, R-7632, R-26955, R-26950, R-33520, R-6484, R-26954 and R-7165) represented one single species, most closely related to Bacillus thermoamylovorans (93.9 % 16S rRNA gene sequence similarity), for which the name Bacillus thermolactis is proposed. Cells were Gram-stain-positive, facultatively anaerobic, endospore-forming rods that grew optimally at 40–50 °C. The cell wall peptidoglycan type of strain R-6488T, the proposed type strain, was A1γ based on meso-diaminopimelic acid. Major fatty acids of the strains were C16 : 0 (28.0 %), iso-C16 : 0 (12.1 %) and iso-C15 : 0 (12.0 %). MK-7 was the predominant menaquinone, and major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and some unidentified phospholipids. DNA G+C content was 35.0 mol%. Phenotypic properties allowed discrimination from other thermotolerant species of the genus Bacillus and supported the description of the novel species Bacillus thermolactis, with strain R-6488T ( = LMG 25569T  = DSM 23332T) as the proposed type strain.

Chryseobacterium yonginense sp. nov., isolated from a mesotrophic artificial lake

2011 ◽  
Vol 61 (6) ◽  
pp. 1413-1417 ◽  
Author(s):  
Yochan Joung ◽  
Kiseong Joh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Gram Staining

A Gram-staining-negative, non-motile, yellow-pigmented bacterial strain, designated HMD1043T, was isolated from a mesotrophic artificial lake in Korea. The major fatty acids were anteiso-C15 : 0 (28.3 %), iso-C15 : 0 (22.9 %), summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0; 8.8 %) and iso-C13 : 0 (5.3 %). The DNA G+C content was 31.3 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1043T formed a lineage within the genus Chryseobacterium and was most closely related to Chryseobacterium antarcticum AT1013T (96.8 % 16S rRNA gene sequence similarity) and Chryseobacterium jeonii AT1047T (96.4 %). On the basis of the evidence presented in this study, strain HMD1043T is described as belonging to a novel species of the genus Chryseobacterium, for which the name Chryseobacterium yonginense sp. nov. is proposed. The type strain is HMD1043T ( = KCTC 22744T  = CECT 7547T).

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