scholarly journals Phenylobacterium koreense sp. nov., isolated from South Korea

2005 ◽  
Vol 55 (5) ◽  
pp. 2001-2005 ◽  
Author(s):  
Zubair Aslam ◽  
Wan-Taek Im ◽  
Leonid N. Ten ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Treatment Plant ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterium, Slu-01T, was isolated from activated sludge from a wastewater treatment plant in Daejeon, South Korea. After 3 days on R2A medium, strain Slu-01T developed colourless colonies (0·7–1·2 mm). The non-motile rods (0·7–1·0×1·0–2·0 μm) were slightly curved and occurred singly and in pairs. No filamentous cells were found. On the basis of 16S rRNA gene sequence similarity, strain Slu-01T was shown to belong to the family Caulobacteraceae and was most closely related to Phenylobacterium immobile (96·6 %) and Phenylobacterium lituiforme (96·5 %). The genomic DNA G+C content of strain Slu-01T was 68·1 mol%, within the range of 67·3–68·4 mol% for the genus Phenylobacterium. Chemotaxonomic data (major ubiquinone, Q-10; major fatty acids C18 : 1 ω7c, C16 : 0, C15 : 0 and C17 : 0) and 16S rRNA gene sequence analysis supported the affiliation of strain Slu-01T to the genus Phenylobacterium. However, DNA–DNA hybridization data and phenotypic properties showed that strain Slu-01T could be distinguished from the two other Phenylobacterium species with validly published names. Thus, it is suggested that strain Slu-01T represents a novel species of the genus Phenylobacterium, for which the name Phenylobacterium koreense is proposed. The type strain is Slu-01T (=KCTC 12206T=IAM 15119T).

scholarly journals Pedobacter panaciterrae sp. nov., isolated from soil in South Korea

2007 ◽  
Vol 57 (2) ◽  
pp. 381-386 ◽  
Author(s):  
Min-Ho Yoon ◽  
Leonid N. Ten ◽  
Wan-Taek Im ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
South Korea ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis

A Gram-negative, facultatively anaerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 042T, was isolated from a soil sample of a ginseng field in Pocheon province (South Korea) and was characterized taxonomically by using a polyphasic approach. The isolate was positive for catalase and oxidase, but negative for gelatinase and production of indole and H2S. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major cellular fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 35.7 %), iso-C15 : 0 (24.3 %) and iso-C17 : 0 3-OH (11.6 %). Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 042T fell within the radiation of the cluster comprising Pedobacter species. On the basis of 16S rRNA gene sequence similarities, the phylogenetically closest recognized species of the genus Pedobacter to strain Gsoil 042T included Pedobacter heparinus DSM 2366T (98.1 %), Pedobacter africanus DSM 12126T (97.8 %) and Pedobacter caeni LMG 22862T (97.2 %). The 16S rRNA gene sequence similarity with other recognized species of the genus Pedobacter was less than 96.1 %. DNA–DNA hybridization experiments showed that the DNA–DNA relatedness between strain Gsoil 042T and its phylogenetically closest neighbours was less than 43 %. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 042T should be classified as representing a novel species in the genus Pedobacter, for which the name Pedobacter panaciterrae sp. nov. is proposed. The type strain is Gsoil 042T (=KCTC 12594T=LMG 23400T).

scholarly journals Sphingobacterium shayense sp. nov., isolated from forest soil

2010 ◽  
Vol 60 (10) ◽  
pp. 2377-2381 ◽  
Author(s):  
Xiang He ◽  
Ting Xiao ◽  
Haiju Kuang ◽  
Xiaojun Lan ◽  
Maripat Tudahong ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Populus Euphratica ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-staining-negative, yellow-coloured, strictly aerobic, non-spore-forming, rod-shaped bacterium, designated HS39T, isolated from a soil sample collected from a natural Populus euphratica forest in Xinjiang, China, was characterized using a polyphasic approach. The isolate grew optimally at 30–37 °C, at pH 6.5–8.0 and with 0–3 % NaCl. Analysis of the 16S rRNA gene sequence of strain HS39T revealed that it is a member of the genus Sphingobacterium. Sphingobacterium mizutaii ATCC 33299T was the nearest relative (94.0 % 16S rRNA gene sequence similarity). The G+C content of the genomic DNA was 40.2 mol%. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω6c and/or C16 : 1 ω7c). The predominant isoprenoid quinone was MK-7. On the basis of phenotypic properties and phylogenetic inference, strain HS39T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium shayense sp. nov. is proposed. The type strain is HS39T (=CCTCC AB 209006T =NRRL B-59203T).

scholarly journals Rhodanobacter spathiphylli sp. nov., a gammaproteobacterium isolated from the roots of Spathiphyllum plants grown in a compost-amended potting mix

2006 ◽  
Vol 56 (8) ◽  
pp. 1755-1759 ◽  
Author(s):  
Deborah De Clercq ◽  
Stefanie Van Trappen ◽  
Ilse Cleenwerck ◽  
An Ceustermans ◽  
Jean Swings ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Growth Temperature ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Control Activity

Three Gram-negative, yellow-pigmented strains were isolated from the rhizospheres of Spathiphyllum plants grown in a compost-amended potting mix. The strains showed biological control activity towards the root-rot plant pathogen Cylindrocladium spathiphylli, and were characterized to determine their taxonomic position. Cells of the strains were non-motile rods, and the strains were oxidase- and catalase-positive and unable to ferment most sugars tested. The three strains showed differences in growth temperature range, optimal growth temperature and some biochemical reactions. The majority of the fatty acids were branched, and large amounts of 15 : 0 iso and 17 : 1 iso ω9c were present. The 16S rRNA gene sequence (1497 bp) of strain B39T showed the highest level of similarity (98.5 %) to that of Rhodanobacter fulvus IAM 15025T, followed by Rhodanobacter lindaniclasticus LMG 18385T (96.0 %; strain no longer extant), Dyella koreensis CCUG 50883T (96.4 %), Dyella japonica DSM 16301T (96.3 %), Frateuria aurantia LMG 1558T (96.2 %) and Fulvimonas soli LMG 19981T (95.9 %). Less than 90 % 16S rRNA gene sequence similarity was observed for other members of the Gammaproteobacteria. The mean DNA–DNA reassociation value for the three strains was 100 % and was 25 % when the strains were compared with DNA from R. fulvus LMG 23003T. The strains had a mean DNA G+C content of 67.6 mol%. On the basis of their phylogenetic, genomic and phenotypic properties, the three strains represent a novel species within the genus Rhodanobacter, for which the name Rhodanobacter spathiphylli sp. nov. is proposed. The type strain is strain B39T (=LMG 23181T=DSM 17631T).

scholarly journals Saccharopolyspora phatthalungensis sp. nov., isolated from rhizosphere soil of Hevea brasiliensis

2010 ◽  
Vol 60 (8) ◽  
pp. 1904-1908 ◽  
Author(s):  
Kannika Duangmal ◽  
Ratchanee Mingma ◽  
Arinthip Thamchaipenet ◽  
Atsuko Matsumoto ◽  
Yoko Takahashi
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Rhizosphere Soil ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

The taxonomic position of a rhizosphere soil isolate, designated strain SR8.15T, was determined by using a polyphasic approach. Phylogenetic analysis based on an almost-complete 16S rRNA gene sequence of the strain showed that it formed a well-separated sub-branch within the radiation encompassing the genus Saccharopolyspora. Highest levels of 16S rRNA gene sequence similarity were found between strain SR8.15T and Saccharopolyspora shandongensis CGMCC 4.3530T (98.9 %) and Saccharopolyspora spinosa DSM 44228T (98.5 %). However, these strains shared low levels of DNA–DNA relatedness (<26 %). Strain SR8.15T had chemical characteristics consistent with its classification in the genus Saccharopolyspora. It contained meso-diaminopimelic acid as the diagnostic diamino acid. Whole-cell hydrolysates contained arabinose and galactose. The diagnostic phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The main menaquinone was MK-9(H4). No mycolic acid was detected. The predominant cellular fatty acid was iso-C16 : 0. The G+C content of the genomic DNA of strain SR8.15T was 70.3 mol%. Strain SR8.15T had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from its combined genotypic and phenotypic properties that strain SR8.15T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora phatthalungensis sp. nov. is proposed. The type strain is SR8.15T (=TISTR 1921T=BCC 35844T=NRRL B-24798T).

scholarly journals Thalassomonas agariperforans sp. nov., an agarolytic bacterium isolated from marine sand

2011 ◽  
Vol 61 (11) ◽  
pp. 2573-2576 ◽  
Author(s):  
Sooyeon Park ◽  
Won-Chan Choi ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Gram Staining ◽  
Marine Sand

A Gram-staining-negative, motile, agarolytic bacterium, designated M-M1T, was isolated from marine sand obtained from Geoje Island, South Sea, Korea, and its taxonomic position was investigated using a polyphasic taxonomic approach. Strain M-M1T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. It did not grow in the presence of >7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M-M1T fell within the clade comprising members of the genus Thalassomonas, clustering with Thalassomonas agarivorans TMA1T, Thalassomonas loyana CBMAI 722T and Thalassomonas ganghwensis JC2041T, with which it exhibited 16S rRNA gene sequence similarity values of 96.4, 96.0 and 94.9 % respectively. Strain M-M1T exhibited 94.7–95.2 % 16S rRNA gene sequence similarity to the other species of the genus Thalassomonas. Strain M-M1T contained Q-8 as the predominant ubiquinone and C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c as the major fatty acids. The DNA G+C content was 44.2 mol%. Strain M-M1T could be differentiated from phylogenetically related species of the genus Thalassomonas by differences in some phenotypic properties. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain M-M1T is considered to represent a novel species of the genus Thalassomonas, for which the name Thalassomonas agariperforans sp. nov. is proposed. The type strain is M-M1T ( = KCTC 23343T  = CCUG 60020T).

scholarly journals Nocardioides daedukensis sp. nov., a halotolerant bacterium isolated from soil

2010 ◽  
Vol 60 (6) ◽  
pp. 1334-1338 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
So-Jung Kang ◽  
Jung-Sook Lee ◽  
Keun Chul Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A Gram-positive, non-motile and rod- or coccoid-shaped bacterial strain, MDN22T, was isolated from a soil sample from Korea. Strain MDN22T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 0–0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain MDN22T was phylogenetically most closely related to the genera Nocardioides and Marmoricola. In the neighbour-joining phylogenetic tree, strain MDN22T was most closely related to Nocardioides jensenii KCTC 9134T, with which it exhibited 98.3 % 16S rRNA gene sequence similarity. The strain exhibited 93.1–96.9 % and 95.3–95.9 % 16S rRNA gene sequence similarities to the type strains of other species of the genera Nocardioides and Marmoricola, respectively. The chemotaxonomic properties of strain MDN22T were consistent with those of the genus Nocardioides; the cell-wall peptidoglycan type was based on ll-2,6-diaminopimelic acid, the predominant menaquinone was MK-8(H4) and the major fatty acids were iso-C16 : 0 and C17 : 1. The DNA G+C content was 68.7 mol%. DNA–DNA relatedness data and differential phenotypic properties suggested that strain MDN22T could be differentiated from N. jensenii and Nocardioides dubius. On the basis of the data obtained, strain MDN22T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides daedukensis sp. nov., is proposed. The type strain is MDN22T (=KCTC 19601T=CCUG 57505T).

scholarly journals Crassaminicella profunda gen. nov., sp. nov., an anaerobic marine bacterium isolated from deep-sea sediments

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3097-3102 ◽  
Author(s):  
Raja Lakhal ◽  
Nathalie Pradel ◽  
Anne Postec ◽  
Bernard Ollivier ◽  
Jean-Luc Cayol ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gulf Of California ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Heterotrophic Bacterium ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A novel, anaerobic, chemo-organotrophic bacterium, designated strain Ra1766HT, was isolated from sediments of the Guaymas basin (Gulf of California, Mexico) taken from a depth of 2002 m. Cells were thin, motile, Gram-stain-positive, flexible rods forming terminal endospores. Strain Ra1766HT grew at temperatures of 25–45 °C (optimum 30 °C), pH 6.7–8.1 (optimum 7.5) and in a salinity of 5–60 g l− 1 NaCl (optimum 30 g l− 1). It was an obligate heterotrophic bacterium fermenting carbohydrates (glucose and mannose) and organic acids (pyruvate and succinate). Casamino acids and amino acids (glutamate, aspartate and glycine) were also fermented. The main end products from glucose fermentation were acetate, butyrate, ethanol, H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, fumarate, nitrate, nitrite and Fe(III) were not used as terminal electron acceptors. The predominant cellular fatty acids were C14  : 0, C16 : 1ω7, C16 : 1ω7 DMA and C16 : 0. The main polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phospholipids. The G+C content of the genomic DNA was 33.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Ra1766HT was affiliated to cluster XI of the order Clostridiales, phylum Firmicutes. The closest phylogenetic relative of Ra1766HT was Geosporobacter subterraneus (94.2 % 16S rRNA gene sequence similarity). On the basis of phylogenetic inference and phenotypic properties, strain Ra1766HT ( = DSM 27501T = JCM 19377T) is proposed to be the type strain of a novel species of a novel genus, named Crassaminicella profunda.

scholarly journals Sphingobacterium wenxiniae sp. nov., a cypermethrin-degrading species from activated sludge

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 683-687 ◽  
Author(s):  
Jun Zhang ◽  
Jin-Wei Zheng ◽  
Byung Cheol Cho ◽  
Chung Yeon Hwang ◽  
Chengxiang Fang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Activated Sludge ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Treatment Plant ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Optimum Ph

A Gram-negative, non-motile, non-spore-forming, non-flagellated rod capable of degrading cypermethrin, designated LQY-18T, was isolated from activated sludge of a wastewater treatment plant in China. Strain LQY-18T grew at 8–40 °C (optimum 30 °C), at pH 5.0–10.0 (optimum pH 7.0) and with 0–5 % (w/v) NaCl (optimum 1 %). The predominant menaquinone was MK-7 (97 %) and the major fatty acids were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 40.3 mol%. Phylogenetic analysis revealed that the isolate belonged to the genus Sphingobacterium of the phylum Bacteroidetes and showed low 16S rRNA gene sequence similarity with recognized members of the genus Sphingobacterium. The closest neighbour was Sphingobacterium mizutaii ATCC 33299T (92.9 % 16S rRNA gene sequence similarity). On the basis of phenotypic, genetic and phylogenetic data, strain LQY-18T ( = ACCC 05410T = CCTCC AB 2010005T = KCTC 23009T) should be classified as a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium wenxiniae sp. nov. is proposed.

scholarly journals Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants

2006 ◽  
Vol 56 (2) ◽  
pp. 433-438 ◽  
Author(s):  
Myung Soo Park ◽  
Se Ra Jung ◽  
Kang Hyun Lee ◽  
Myung-Sook Lee ◽  
Jin Ok Do ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sand Dune ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

Two Gram-negative, yellow-pigmented bacteria designated PSD1-4T and PHA3-4T, isolated from two sand-dune plant species inhabiting coastal areas in Tae-an, Korea, were subjected to taxonomic investigation. 16S rRNA gene sequence analysis indicated that both isolates should be placed in the genus Chryseobacterium of the family Flavobacteriaceae. The phenotypic properties of the strains were also consistent with their classification into this genus. The levels of 16S rRNA gene sequence similarity between strain PSD1-4T and other Chryseobacterium species were 95·2–97·2 %; those between PHA3-4T and others were 93·7–97·8 %. The DNA–DNA relatedness data indicated that strains PSD1-4T and PHA3-4T were clearly different from the nearest species, Chryseobacterium indoltheticum and Chryseobacterium taichungense. The major fatty acids were 13-methyltetradecanoic acid (iso-C15 : 0), 3-hydroxy-15-methylhexadecanoic acid (iso-C17 : 0 3-OH) and omega-9-cis-15-methylhexadecenoic acid (iso-C17 : 1ω9c) for both strains. On the basis of polyphasic taxonomic analysis results, it is evident that each of these strains represents a novel species of Chryseobacterium, for which the names Chryseobacterium soldanellicola sp. nov. (type strain PSD1-4T=KCTC 12382T=NBRC 100864T) and Chryseobacterium taeanense sp. nov. (type strain PHA3-4T=KCTC 12381T=NBRC 100863T) are proposed.

scholarly journals Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge

2011 ◽  
Vol 61 (1) ◽  
pp. 53-59 ◽  
Author(s):  
Yuto Yashiro ◽  
Sanae Sakai ◽  
Masayuki Ehara ◽  
Masayuki Miyazaki ◽  
Takashi Yamaguchi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Amino Acid Sequence Similarity ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties

A novel methane-producing archaeon, strain SMSPT, was isolated from an anaerobic, propionate-degrading enrichment culture that was originally obtained from granular sludge in a mesophilic upflow anaerobic sludge blanket (UASB) reactor used to treat a beer brewery effluent. Cells were non-motile, blunt-ended, straight rods, 1.0–2.6 μm long by 0.5 μm wide; cells were sometimes up to 7 μm long. Asymmetrical cell division was observed in rod-shaped cells. Coccoid cells (0.5–1.0 μm in diameter) were also observed in mid- to late-exponential phase cultures. Growth was observed between 10 and 40 °C (optimum, 30–33 °C) and pH 7.0 and 7.6 (optimum, pH 7.4). The G+C content of the genomic DNA was 56.2 mol%. The strain utilized formate and hydrogen for growth and methane production. Based on comparative sequence analyses of the 16S rRNA and mcrA (encoding the alpha subunit of methyl-coenzyme M reductase, a key enzyme in the methane-producing pathway) genes, strain SMSPT was affiliated with group E1/E2 within the order Methanomicrobiales. The closest relative based on both 16S rRNA and mcrA gene sequences was Methanoregula boonei 6A8T (96.3 % 16S rRNA gene sequence similarity, 85.4 % deduced McrA amino acid sequence similarity). The percentage of 16S rRNA gene sequence similarity indicates that strain SMSPT and Methanoregula boonei 6A8T represent different species within the same genus. This is supported by our findings of shared phenotypic properties, including cell morphology and growth temperature range, and phenotypic differences in substrate usage and pH range. Based on these genetic and phenotypic properties, we propose that strain SMSPT represents a novel species of the genus Methanoregula, for which we propose the name Methanoregula formicica sp. nov., with the type strain SMSPT (=NBRC 105244T =DSM 22288T).

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