scholarly journals Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring

2011 ◽  
Vol 61 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Galina Dubinina ◽  
Margarita Grabovich ◽  
Natalia Leshcheva ◽  
Frederick A. Rainey ◽  
Ekaterina Gavrish
Keyword(s):  
Gene Sequence ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Saline Spring

A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated PT was isolated from a sulfur ‘Thiodendron’ mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain PT exhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H2O2 with sulfide and deposit it in the periplasmic space. Growth occurred at 4–32 °C (optimum at 28–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5), and in 0.1–1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO2 and H2. The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain PT fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is proposed. The type strain is PT (=DSM 19205T =VKM B-2514T).

scholarly journals Paenibacillus ripae sp. nov., isolated from bank side soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4757-4762 ◽  
Author(s):  
Ying Sun ◽  
Zhaohui Guo ◽  
Qi Zhao ◽  
Qiyu Gao ◽  
QinJian Xie ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China ◽  
Diamino Acid

A Gram-stain-variable, rod-shaped, non-motile and endospore-forming bacterium, designated strain HZ1T, was isolated from a sample of bank side soil from Hangzhou city, Zhejiang province, PR China. On the basis of 16S rRNA gene sequence analysis, strain HZ1T was closely related to members of the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus agarexedens DSM 1327T (94.4 %), Paenibacillus sputi KIT00200-70066-1T (94.4 %). Growth occurred at 15–42 °C (optimum 30–37 °C), pH 5.0–9.5 (optimum pH 7.0–8.0) and NaCl concentrations of up to 6.0 % (w/v) were tolerated (optimum 0.5 %). The dominant respiratory quinone was MK-7 and the DNA G+C content was 40.1 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids of strain HZ1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain HZ1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus ripae sp. nov. (type strain HZ1T = CCTCC AB 2014276T = LMG 28639T) is proposed.

scholarly journals Sphingobacterium daejeonense sp. nov., isolated from a compost sample

2006 ◽  
Vol 56 (9) ◽  
pp. 2031-2036 ◽  
Author(s):  
Kyoung-Ho Kim ◽  
Leonid N. Ten ◽  
Qing-Mei Liu ◽  
Wan-Taek Im ◽  
Sung-Taik Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
The Family

A Gram-negative, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated TR6-04T, was isolated from compost and characterized taxonomically by using a polyphasic approach. The organism grew optimally at 30 °C and at pH 6.5–7.0. The isolate was positive for catalase and oxidase tests but negative for gelatinase, indole and H2S production. Comparative 16S rRNA gene sequence analysis showed that strain TR6-04T fell within the radiation of the cluster comprising Sphingobacterium species and clustered with Sphingobacterium mizutaii ATCC 33299T (96.7 % sequence similarity); the similarity to sequences of other species within the family Sphingobacteriaceae was less than 92.0 %. The G+C content of the genomic DNA was 38.7 mol%. The predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c). These chemotaxonomic data supported the affiliation of strain TR6-04T to the genus Sphingobacterium. However, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain TR6-04T (=KCTC 12579T=LMG 23402T=CCUG 52468T) should be classified as the type strain of a novel species, for which the name Sphingobacterium daejeonense sp. nov. is proposed.

scholarly journals Bacillus panaciterrae sp. nov., isolated from soil of a ginseng field

2006 ◽  
Vol 56 (12) ◽  
pp. 2861-2866 ◽  
Author(s):  
Leonid N. Ten ◽  
Sang-Hoon Baek ◽  
Wan-Taek Im ◽  
Qing-Mei Liu ◽  
Zubair Aslam ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Distinct Phylogenetic Lineage

A Gram-positive, non-motile, endospore-forming bacterium, designated Gsoil 1517T, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized in order to determine its taxonomic position, using a polyphasic approach. It was found to rod-shaped and aerobic or facultatively anaerobic. It grew optimally at 30 °C and at pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 1517T forms a distinct phylogenetic lineage within the genus Bacillus, being related to Bacillus funiculus JCM 11201T (96.8 %). The strain showed less than 94.3 % sequence similarity with other Bacillus species. The G+C content of the genomic DNA was found to be 47.8 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were iso-C15 : 0 (42.4 %), anteiso-C15 : 0 (17.4 %), iso-C14 : 0 (9.7 %) and C16 : 0 (6.0 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1517T represents a novel species of the genus Bacillus, for which the name Bacillus panaciterrae sp. nov. is proposed. The type strain is Gsoil 1517T (=KCTC 13929T=CCUG 52470T=LMG 23408T).

scholarly journals Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin

2011 ◽  
Vol 61 (6) ◽  
pp. 1436-1441 ◽  
Author(s):  
Patrick Grégoire ◽  
Malek Bohli ◽  
Jean-Luc Cayol ◽  
Manon Joseph ◽  
Sophie Guasco ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Optimum Ph ◽  
Aquitaine Basin ◽  
Negative Growth

An anaerobic, thermophilic, filamentous (0.45 × >100 µm) bacterium, designated D1-25-10-4T, was isolated from a deep hot aquifer in France. Cells were non-motile and Gram-negative. Growth was observed at 43–65 °C (optimum 55 °C), at pH 6.8–7.8 (optimum pH 7.0) and with 0–5 g NaCl l−1 (optimum 0 g NaCl l−1). Strain D1-25-10-4T was a chemo-organotroph and fermented ribose, maltose, glucose, galactose, arabinose, fructose, mannose, sucrose, raffinose, xylose, glycerol, fumarate, peptone, starch and xylan. Yeast extract was required for growth. Sulfate, thiosulfate, sulfite, elemental sulfur, nitrate, nitrite and fumarate were not used as terminal electron acceptors. The G+C content of the DNA was 61.9 mol%. The major cellular fatty acids of strain D1-25-10-4T were C17 : 0, C18 : 0, C16 : 0 and iso-C17 : 0. The closest phylogenetic relative of strain D1-25-10-4T was Caldilinea aerophila STL-6-O1T (97.9 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain D1-25-10-4T and Caldilinea aerophila DSM 14535T was 8.7±1 %. On the basis of phylogenetic, genotypic and phenotypic characteristics, strain D1-25-10-4T represents a novel species within the genus Caldilinea, class Caldilineae, phylum Chloroflexi, for which the name Caldilinea tarbellica sp. nov. is proposed. The type strain is D1-25-10-4T ( = DSM 22659T  = JCM 16120T).

scholarly journals Methylibium fulvum sp. nov., a member of the Betaproteobacteria isolated from ginseng field soil, and emended description of the genus Methylibium

2007 ◽  
Vol 57 (9) ◽  
pp. 2062-2066 ◽  
Author(s):  
Min-Ho Yoon ◽  
Leonid N. Ten ◽  
Wan-Taek Im ◽  
Sung-Taik Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Physiological Profiles

Two bacterial strains, designated Gsoil 322T and Gsoil 328, were isolated from soil of a ginseng field in Pocheon province (Republic of Korea). The strains were Gram-negative, motile, aerobic rods that showed nearly identical physiological profiles and similar chemotaxonomic profiles. The two strains were oxidase-positive but catalase-negative, reduced nitrate to nitrite and had fatty acid profiles in which C16 : 0, C17 : 0 cyclo and C16 : 1 ω7c/iso-C15 : 0 2-OH were predominant. The DNA G+C contents of Gsoil 322T and Gsoil 328 were 66.6 and 66.7 mol%, respectively. Q-8 was observed as the major quinone. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 322T belongs to the class Betaproteobacteria and was most closely related to Methylibium petroleiphilum ATCC BAA-1232T (97.5 % sequence similarity). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 322T (=KCTC 12591T =LMG 23394T) was classified in the genus Methylibium as the type strain of a novel species, for which the name Methylibium fulvum sp. nov. is proposed.

scholarly journals Actinocorallia cavernae sp. nov., isolated from a natural cave in Jeju, Korea

2006 ◽  
Vol 56 (5) ◽  
pp. 1085-1088 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Dilution Method ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Phylogenetic Cluster ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain

A novel actinomycete, strain N3-7T, was isolated from a natural cave in Jeju, Republic of Korea, using a dilution method and was subjected to characterization using polyphasic taxonomy. A 16S rRNA gene sequence analysis revealed that the organism belonged to the phylogenetic cluster of the genus Actinocorallia and was most closely related to Actinocorallia glomerata and Actinocorallia longicatena (97.6 and 97.5 % similarity, respectively). The main chemotaxonomic properties of strain N3-7T, such as the principal amino acid of the peptidoglycan, the predominant menaquinone and the polar lipid profile, supported classification in the genus Actinocorallia. The organism was readily differentiated from Actinocorallia species with validly published names on the basis of a broad range of phenotypic properties. Thus the isolate represents a novel species of the genus Actinocorallia, for which the name Actinocorallia cavernae sp. nov. is proposed. The type strain is strain N3-7T (=JCM 13278T=NRRL B-24429T).

scholarly journals Pedobacter boryungensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Yong-Taek Jung ◽  
Soo-Young Lee ◽  
Won-Chan Choi ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-sporulating, non-flagellated rod, designated BR-9T, was isolated from soil collected on the Korean peninsula. Strain BR-9T grew optimally at pH 6.0–7.0, at 30 °C and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BR-9T belonged to the genus Pedobacter and clustered with Pedobacter insulae DS-139T and Pedobacter koreensis WPCB189T. Strain BR-9T exhibited 98.2 and 97.5 % 16S rRNA gene sequence similarity with P. insulae DS-139T and P. koreensis WPCB189T, respectively, and <96.7 % sequence similarity with the type strains of other species in the genus Pedobacter. Strain BR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content of strain BR-9T was 38.5 mol%. DNA–DNA relatedness between strain BR-9T and P. insulae DS-139T and P. koreensis KCTC 12536T was 3.4–4.2 %, which indicated that the isolate was genetically distinct from these type strains. Strain BR-9T was also distinguishable by differences in phenotypic properties. On the basis of the data presented, strain BR-9T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter boryungensis sp. nov. is proposed. The type strain is BR-9T ( = KCTC 23344T  = CCUG 60024T).

scholarly journals Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4003-4007 ◽  
Author(s):  
Dong-Uk Kim ◽  
Hyosun Lee ◽  
Song-Gun Kim ◽  
Jae-Hyung Ahn ◽  
So Yoon Park ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Air Conditioning System ◽  
Optimum Ph ◽  
Sequence Similarities

A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR1012KT, was isolated from a motor car evaporator core collected in Korea. Cells of the strain were facultatively anaerobic, non-spore-forming and rod-shaped. The strain grew at 10–40 °C (optimum, 25 °C), at pH 6.5–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–1 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Spirosoma (97.50–90.74 % 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (97.50 %). Its predominant fatty acids included summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso B) and it had MK-7 as the major menaquinone. The polar lipids present included phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and five unknown polar lipids. The DNA G+C content of this strain was 54 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain PR1012KT represents a novel species in the genus Spirosoma, for which the name Spirosoma aerolatum sp. nov. is proposed. The type strain is PR1012KT ( = KACC 17939T = NBRC 110794T).

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Sphingobacterium paludis sp. nov., isolated from wetland soil

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3453-3458 ◽  
Author(s):  
Hao Feng ◽  
Yanhua Zeng ◽  
Yili Huang
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Xixi Wetland

A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus Sphingobacterium and shared highest similarity with Sphingobacterium composti 4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.

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