scholarly journals Sphingomonas soli sp. nov., a β-glucosidase-producing bacterium in the family Sphingomonadaceae in the α-4 subgroup of the Proteobacteria

2006 ◽  
Vol 56 (4) ◽  
pp. 703-707 ◽  
Author(s):  
Deok-Chun Yang ◽  
Wan-Taek Im ◽  
Myung Kyum Kim ◽  
Hiroyuki Ohta ◽  
Sung-Taik Lee
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Physiological And Biochemical

Strain T5-04T, a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil of a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain T5-04T belongs to the α-4 subgroup of the Proteobacteria, and the highest degrees of sequence similarity determined were to Sphingomonas asaccharolytica IFO 10564T (97·5 %), Sphingomonas koreensis JSS26T (97·1 %), Sphingomonas mali IFO 15500T (96·7 %) and Sphingomonas pruni IFO 15498T (96·6 %). Chemotaxonomic data revealed that strain T5-04T possesses ubiquinone Q-10 predominantly, C18 : 1 as the predominant fatty acid and sphingoglycolipids, all of which corroborate its assignment to the genus Sphingomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain T5-04T represents a distinct species. Based on polyphasic evidence, T5-04T (=KCTC 12210T=NBRC 100801T=IAM 15213T) should be classified as the type strain of a novel Sphingomonas species, for which the name Sphingomonas soli sp. nov. is proposed.

scholarly journals Parapedobacter koreensis gen. nov., sp. nov.

2007 ◽  
Vol 57 (6) ◽  
pp. 1336-1341 ◽  
Author(s):  
Myung Kyum Kim ◽  
Ju-Ryun Na ◽  
Dong Ha Cho ◽  
Nak-Kyun Soung ◽  
Deok-Chun Yang
Keyword(s):  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Novel Genus And Species ◽  
Physiological And Biochemical

Strain Jip14T, a Gram-negative, non-spore-forming, rod-shaped, non-motile bacterium, was isolated from dried rice straw and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Jip14T belongs to the family Sphingobacteriaceae, and the highest degree of sequence similarity was determined to be to Pedobacter saltans DSM 12145T (88.5 %), Pedobacter africanus DSM 12126T (87.6 %), Pedobacter heparinus DSM 2366T (87.1 %) and Pedobacter caeni LMG 22862T (86.9 %). Chemotaxonomic data revealed that strain Jip14T possesses menaquinone MK-7 and the predominant fatty acids C15 : 0 iso, C16 : 0, C16 : 0 10-methyl, C17 : 0 iso 3-OH and summed feature 3 (C15 : 0 iso 2-OH/C16 : 1 ω7c). The results of physiological and biochemical tests clearly demonstrated that strain Jip14T represents a distinct species. Based on these data, Jip14T should be classified within a novel genus and species, for which the name Parapedobacter koreensis gen. nov., sp. nov. is proposed. The type strain of Parapedobacter koreensis is Jip14T (=KCTC 12643T=LMG 23493T).

scholarly journals Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field

2010 ◽  
Vol 60 (10) ◽  
pp. 2358-2363 ◽  
Author(s):  
Sathiyaraj Srinivasan ◽  
Myung Kyum Kim ◽  
Gayathri Sathiyaraj ◽  
Vaidyanathan Veena ◽  
Muthusamy Mahalakshmi ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, motile bacterium was isolated from the soil of a ginseng field in Daejeon, South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence analysis revealed that strain DCY34T belonged to the family Sphingomonadaceae, and the highest degree of sequence similarity was found with Sphingopyxis witflariensis W-50T (97.1 %), Sphingopyxis ginsengisoli Gsoil 250T (97.0 %), Sphingopyxis chilensis S37T (96.9 %), Sphingopyxis macrogoltabida IFO 15033T (96.8 %), Sphingopyxis alaskensis RB2256T (96.7 %) and Sphingopyxis taejonensis JSS54T (96.7 %). Chemotaxonomic data revealed that strain DCY34T possessed ubiquinone Q-10 as the predominant respiratory lipoquinone, which is common to members of the genus Sphingopyxis. The predominant fatty acids were C18 : 1 ω7c (27.5 %), summed feature 4 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH; 18.6 %), C16 : 0 (15.6 %) and summed feature 8 (C19 : 1 ω6c and/or unknown 18.864; 15.4 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and an unknown polar lipid. The results of physiological and biochemical tests clearly demonstrated that strain DCY34T represented a separate species and supported its affiliation to the genus Sphingopyxis. Based on these data, the new isolate represents a novel species, for which the name Sphingopyxis panaciterrulae sp. nov. is proposed. The type strain is DCY34T (=KCTC 22112T=JCM 14844T).

scholarly journals Thermomonas koreensis sp. nov., a mesophilic bacterium isolated from a ginseng field

2006 ◽  
Vol 56 (7) ◽  
pp. 1615-1619 ◽  
Author(s):  
Myung Kyum Kim ◽  
Wan-Taek Im ◽  
Jun-Gyo In ◽  
Sung-Hoon Kim ◽  
Deok-Chun Yang
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Distinct Species ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Mesophilic Bacterium ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped, motile bacterium, strain Ko06T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Ko06T belongs to the Gammaproteobacteria, and the highest levels of sequence similarity were with Thermomonas brevis LMG 21746T (98.4 %), Thermomonas fusca LMG 21737T (97.7 %), Thermomonas haemolytica A50-7-3T (96.5 %) and Thermomonas hydrothermalis SGM-6T (95.8 %). Chemotaxonomic data revealed that strain Ko06T possesses ubiquinone Q-8 and that the predominant fatty acids are C15 : 0 iso, C11 : 0 iso and C11 : 0 iso 3-OH, all of which corroborated assignment of the strain to the genus Thermomonas. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain Ko06T represents a distinct species. On the basis of these data, strain Ko06T (=KCTC 12540T=NBRC 101155T) should be classified as the type strain of a novel Thermomonas species, for which the name Thermomonas koreensis sp. nov. is proposed.

scholarly journals Brevibacillus ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field

2006 ◽  
Vol 56 (11) ◽  
pp. 2665-2669 ◽  
Author(s):  
Sang-Hoon Baek ◽  
Wan-Taek Im ◽  
Hyun Woo Oh ◽  
Jung-Sook Lee ◽  
Hee-Mock Oh ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Brevibacillus Laterosporus ◽  
The Family ◽  
Brevibacillus Brevis ◽  
Physiological And Biochemical

A Gram-positive, rod-shaped, spore-forming bacterium, Gsoil 3088T, was isolated from soil from a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 3088T was shown to belong to the family Paenibacillaceae, being related to Brevibacillus centrosporus (96.6 %), Brevibacillus borstelensis (96.3 %), Brevibacillus parabrevis (96.1 %), Brevibacillus formosus (96.1 %), Brevibacillus brevis (96.1 %) and Brevibacillus laterosporus (96.0 %). The phylogenetic distances from other validly described species within the genus Brevibacillus were greater than 4.0 % (i.e. there was less than 96.0 % similarity). The G+C content of the genomic DNA was 52.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; fatty acid profile, iso-C15 : 0, iso-C14 : 0 and anteiso-C15 : 0) supported the affiliation of strain Gsoil 3088T to the genus Brevibacillus. The results of physiological and biochemical tests allowed strain Gsoil 3088T to be distinguished genotypically and phenotypically from Brevibacillus species with validly published names. Strain Gsoil 3088T, therefore, represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3088T (=KCTC 13938T=LMG 23403T).

scholarly journals Stenotrophomonas ginsengisoli sp. nov., isolated from a ginseng field

2010 ◽  
Vol 60 (7) ◽  
pp. 1522-1526 ◽  
Author(s):  
Ho-Bin Kim ◽  
Sathiyaraj Srinivasan ◽  
Gayathri Sathiyaraj ◽  
Lin-Hu Quan ◽  
Se-Hwa Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gene Sequence Analysis ◽  
Stenotrophomonas Nitritireducens ◽  
Physiological And Biochemical

A Gram-negative, non-spore-forming, rod-shaped bacterium, designated strain DCY01T, was isolated from soil from a ginseng field in South Korea and was characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain DCY01T belonged to the Gammaproteobacteria and was most closely related to Stenotrophomonas koreensis KCTC 12211T (98.4 % similarity), Stenotrophomonas humi R-32729T (97.2 %), Stenotrophomonas terrae R-32768 (97.1 %), Stenotrophomonas maltophilia DSM 50170T (96.9 %) and Stenotrophomonas nitritireducens DSM 12575T (96.8 %). Chemotaxonomic analyses revealed that strain DCY01T possessed a quinone system with Q-8 as the predominant compound, and iso-C15 : 0 (28.2 %), C16 : 0 10-methyl (13.2 %), iso-C15 : 1 F (10.8 %) and C15 : 0 (7.5 %) as major fatty acids, corroborating assignment of strain DCY01T to the genus Stenotrophomonas. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The results of DNA–DNA hybridization and physiological and biochemical tests clearly demonstrated that strain DCY01T represents a species distinct from recognized Stenotrophomonas species. Based on these data, DCY01T (=KCTC 12539T=NBRC 101154T) should be classified as the type strain of a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas ginsengisoli sp. nov. is proposed.

scholarly journals Devosia soli sp. nov., isolated from greenhouse soil in Korea

2006 ◽  
Vol 56 (11) ◽  
pp. 2689-2692 ◽  
Author(s):  
Seung-Hee Yoo ◽  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Beom Hong ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Greenhouse Soil ◽  
Gene Sequence Analysis ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5 %) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0 %. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA–DNA hybridization experiments (47 % relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3807-3811 ◽  
Author(s):  
Heung-Min Son ◽  
Jung-Eun Yang ◽  
Eun-Ji Yi ◽  
YongJin Park ◽  
Kyung-Hwa Won ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Physiological And Biochemical

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53T (98.7 % similarity), Dyella terrae JS14-6T (98.0 %), Dyella koreensis BB4T (96.9 %), Dyella soli JS12-10T (96.9 %) and Dyella thiooxydans ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus Dyella . The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus Dyella , and represents a novel species of this genus. The name Dyella kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).

scholarly journals Actinomycetospora rishiriensis sp. nov., isolated from a lichen

2011 ◽  
Vol 61 (11) ◽  
pp. 2621-2625 ◽  
Author(s):  
Hideki Yamamura ◽  
Haruna Ashizawa ◽  
Youji Nakagawa ◽  
Moriyuki Hamada ◽  
Yuumi Ishida ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain ◽  
Biochemical Analyses ◽  
Physiological And Biochemical

An actinomycete, strain RI109-Li102T, was isolated from a lichen sample obtained from Rishiri Island in Japan. Cells of strain RI109-Li102T were Gram-positive, aerobic and non-motile and formed bud-like spore chains. The isolate grew with 0–3 % (w/v) NaCl, at pH 5–9 and at 10–30 °C (optimum 30 °C). The whole-cell hydrolysate contained meso-diaminopimelic acid, arabinose and galactose. The predominant menaquinone was MK-8(H4) and the diagnostic phospholipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were iso-C16 : 0 and iso-C16 : 1 H. Comparative 16S rRNA gene sequence analysis revealed that strain RI109-Li102T was most closely related to Actinomycetospora corticicola 014-5T (99.0 % rRNA gene sequence similarity) and Actinomycetospora chiangmaiensis YIM 0006T (98.4 %). However, DNA–DNA hybridization assays, as well as physiological and biochemical analyses, showed that strain RI109-Li102T could be differentiated from its closest phylogenetic relatives. It is proposed that strain RI109-Li102T ( = NBRC 106356T  = KCTC 19782T) be classified as the type strain of a novel species, with the name Actinomycetospora rishiriensis sp. nov.

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

2010 ◽  
Vol 60 (11) ◽  
pp. 2577-2582 ◽  
Author(s):  
Myungjin Lee ◽  
Sung-Geun Woo ◽  
Joonhong Park ◽  
Soon-Ae Yoo
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Degrading Bacterium ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Low Levels

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20T, was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20T belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053T (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200T (98.0 %) and Dyadobacter ginsengisoli KCTC 12589T (96.4 %). The G+C content of the genomic DNA of strain MJ20T was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0, C16 : 0 and C16 : 1 ω5c as major components supported the affiliation of strain MJ20T to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA–DNA relatedness with respect to D. fermentans DSM 18053T (mean±sd of three determinations, 47±7 %) and D. beijingensis JCM 14200T (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20T (=KCTC 22481T =JCM 16232T) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

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