Paralcaligenes ureilyticus gen. nov., sp. nov. isolated from soil of a Korean ginseng field

A bacterial strain, designated GR24-5^T, was isolated from soil cultivated with Korean ginseng. Cells were Gram-negative, strictly aerobic, catalase- and oxidase-positive, non-spore-forming motile rods. Based on the 16S rRNA gene sequence, strain GR24-5^T could be assigned to the family Alcaligenaceae. Strain GR24-5^T showed the highest sequence similarities with Parapusillimonas granuli Ch07^T (97.1%), Pusillimonas noertemannii BN9^T (96.9%), Pigmentiphaga kullae DSM 13608^T (96.5%), and Castellaniella defragrans 54Pin^T (96.3%). Strain GR24-5^T demonstrated a low DNA-DNA relatedness (23%) with P. granuli Ch07^T. The major respiratory quinone is ubiquinone 8 (Q-8) and the major fatty acids are C_16:0, C_17:0 cyclo, and summed feature 1 (C_14:0 3-OH/iso-C_16:1 I/C_12:0 aide). Putrescine, spermidine, and 2-hydroxyputrescine are the major polyamines. The major polar lipids are phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, di-phosphatidylglycerol, and an unknown aminophospholipid. Polar lipid patterns of strain GR24-5^T were unique in having a large amount of phosphatidylmethylethanolamine. Based on phylogenetic analysis and physiological and biochemical characteristics, strain GR245^T represents a novel genus and species, for which the name Paralcaligenes ureilyticus gen. nov., sp. nov. is proposed. The type strain of P. aralcaligenes ureilyticus is GR24-5^T (=KACC 13888 =DSM 24591^T).     

Flavobacterium ginsengiterrae sp. nov., isolated from a ginseng field

A novel strain of Flavobacterium, DCY55(T), a Gram-negative, yellow-pigmented, rod-shaped, non-spore-forming and gliding-motile bacterium, was isolated from the soil of a ginseng field in South Korea. Phylogenetic analysis, based on the 16S rRNA sequence, demonstrated that strain DCY55(T) belongs to the genus Flavobacterium within the family Flavobacteriaceae. Strain DCY55(T) showed the highest similarity with F. johnsoniae UW101(T) (97.1%), F. ginsenosidimutans THG 01(T) (96.8%), F. defluvii EMB 117(T) (96.6%), F. banpakuense 15F3(T) (96.3%) and F. anhuiense D3(T) (95.8%). Chemotaxonomic results showed that strain DCY55(T) predominantly contains menaquinone MK-6, that its DNA G+C content is 36.1mol%, and that its major cellular fatty acids are iso-C(15:0), summed feature 3 (comprising iso-C(15:0) 2-OH and/or C(16:1) ω 7c) and C(16:0). The chemotaxonomic and genotypic characteristics support the taxonomic classification of strain DCY55(T) to the genus Flavobacterium. The results of physiological and biochemical tests confirmed that strain DCY55(T) is distinct from previously validated species. We conclude that strain DCY55(T) should be classified as a novel species of the genus Flavobacterium, for which the name Flavobacterium ginsengiterrae sp. nov. is proposed, with the type strain DCY55(T) (=KCTC 23319(T) = JCM 17337(T)).     

Sphingopyxis panaciterrae sp. nov., isolated from soil from ginseng field

A Gram-negative, strictly aerobic, motile bacterial strain, designated Gsoil 124T, was isolated from a soil sample taken from a ginseng field in Pocheon Province (South Korea). The isolate contained Q-10 as the predominant lipoquinone, plus C18:1 7c and summed feature 4 (C16:1 6c and/or iso- C15:0 2-OH) as the major fatty acids. The G+C content of the genomic DNA was 68.1 mol%, and the major polar lipids consisted of sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, and phosphatidylethanolamine. A comparative 16S rRNA gene sequence analysis showed that strain Gsoil 124T was most closely related to Sphingopyxis chilensis (98.7%), Sphingopyxis alaskensis (98.2%), Sphingopyxis witflariensis (98.2%), Sphingopyxis taejonensis (98.0%), and Sphingopyxis macrogoltabida (97.6%). However, the DNA-DNA relatedness between strain Gsoil 124T and its phylogenetically closest neighbors was less than 22%. Thus, on the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 124T should be classified as representing a novel species in the genus Sphingopyxis, for which the name Sphingopyxis panaciterrae sp. nov. is proposed. The type strain is Gsoil 124T (=KCTC 12580T=LMG 24003T).     

Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field

A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81^T, and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81^T belonged to the genus Arthrobacter. Major fatty acid was anteiso-C_15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H₂). The peptidoglycan type was A3α with an l-Lys–l-Ala–l-Thr–l-Ala interpeptide bridge. The DNA–DNA hybridization relatedness between strain DCY81^T and Arthrobacter siccitolerans LMG 27359^T (98.2 %), Arthrobacter sulfonivorans JCM 13520^T (97.81 %), Arthrobacter scleromae DSM 17756^T (97.59 %), Arthrobacter oxydans KCTC 3383^T (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81^T from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81^T represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225^T = JCM 19357^T).     

Flavobacterium kyungheensis sp. nov., isolated from soil of a ginseng field

A Gram-staining negative, strictly aerobic, motile by gliding, non-spore-forming, pale yellow pigmented and rod-shaped bacterium designated strain THG-107^T was isolated from soil of a ginseng field on Ganghwa Island in the Republic of Korea and its taxonomic position was investigated by using a polyphasic study. Growth of strain THG-107^T was found to occur at 4–37 °C (optimum, 20–30 °C), at pH 5.5–10 (optimum, pH 7.0) and in the presence of 0–1 % (w/v) NaCl (optimum, absence) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain THG-107^T was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium denitrificans ED5^T (99.1 % similarity). The G+C content of the genomic DNA was determined to be 34.2 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. The only isoprenoid quinone detected in strain THG-107^T was menaquinone-6 (MK-6) and the major polyamine was identified as homospermidine (82.9 %). The major polar lipid detected was phosphatidylethanolamine and the major cellular fatty acids were identified as iso-C_15:0 (26.3 %), iso-C_17:0 3OH (12.6 %) and summed feature 3 (comprising C_16:1 ω7c and/or C_16:1 ω6c; 11.6 %). Flexirubin-type pigments were found to be present. Strain THG-107^T has β-glucosidase activity to convert ginsenosides Rb₁ and Rd into Gyp17 and F₂. DNA-DNA hybridization with F. denitrificans ED5^T was 52 %. Strain THG-107^T could be distinguished from F. denitrificans ED5^T and the other species of the genus Flavobacterium by its phylogenetic and genetic distinctiveness and by several phenotypic properties. Therefore, strain THG-107^T is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium kyungheensis sp. nov. is proposed (type strain THG-107^T = KACC 16219^T = LMG 26575^T).     

Sphingomonas kyeonggiense sp. nov., isolated from soil of a ginseng field

A Gram-staining negative bacterium, THG-DT81^T, which was isolated from soil of a ginseng field, was investigated using a polyphasic taxonomic approach. Cells were oxidase- and catalase-positive, aerobic, rod-shaped and motile with one polar flagellum. Strain THG-DT81^T grew optimally at pH 7.0 and in the absence of NaCl on trypticase soy agar. Its optimum growth temperature was 25–28 °C. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain THG-DT81^T belongs to the family Sphingomonadaceae and was related to Sphingomonas pituitosa EDIV^T (98.0 % similarity), S. leidyi ATCC 15260^T (97.8 %), S. trueperi LMG 2142^T (97.1 %), S. azotifigens NBRC 15497^T (97.1 %), S. koreensis JSS26 ^T (97.1 %) and S. dokdonensis DS-4^T (97.0 %). Strain THG-DT81^T contained Q-10 as the predominant ubiquinone and C_18:1 ω7c and C_16:0 as the major fatty acids. The G+C content of the genomic DNA was determined to be 66.8 mol %. The major component in the polyamine pattern was identified as sym-homospermidine. The major polar lipids detected in strain THG-DT81^T were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The DNA–DNA relatedness values of the strain THG-DT81^T and its closest phylogenetically neighbors were below 21 %. The phenotypic characteristics and genotypic data demonstrated the affiliation of strain THG-DT81^T to the genus Sphingomonas. On the basis of the polyphasic taxonomic data presented, strain THG-DT81^T is described as a novel species of genus Sphingomonas, for which the name Sphingomonas kyeonggiense sp. nov. is proposed. The type strain is THG-DT81^T (= KACC 17173^T = JCM 18825^T).     

Rhodanobacter fulvus sp. nov., a beta-galactosidase-producing gammaproteobacterium

A taxonomic study was carried out on a bacterial strain designated as Jip2T isolated from a soil sample mixed with rotten rice straw. It was a Gram-negative, aerobic, motile, and rod-shaped bacterium. It grew well on nutrient agar medium and utilized a fairly narrow spectrum of carbon source. The G+C content of the genomic DNA was 65.3 mol%. The major ubiquinone was Q-8. The major fatty acids were branched fatty acids, especially large amounts of iso C15:0 and iso C17:1 w9c were detected in the cells grown on TSA agar for 24 h. Comparative 16S rDNA study showed a clear affiliation of this bacterium to the genus Rhodanobacter. The 16S rDNA sequence of strain Jip2T showed 96.4% sequence similarity to that of Rhodanobacter lindaniclasticus RP5575T. On the basis of phenotypic characteristics and 16S rDNA sequence analysis, strain Jip2T is clearly distinct from Rhodanobacter lindaniclasticus. We propose the name Rhodanobacter fulvus sp. nov. for strain Jip2T (=IAM 15025T=KCTC 12098T).     

Chryseobacterium yeoncheonense sp. nov., with ginsenoside converting activity isolated from soil of a ginseng field

A Gram-staining negative, aerobic, non-motile, non-flagellate, yellow-pigmented, rod-shaped bacterial strain, designated strain DCY67^T, was isolated from ginseng field in Republic of Korea. Strain DCY67^T contained β-glucosidase activity which converts ginsenoside Rb1 to compound K. Optimum growth of DCY67^T occurred at 30 °C and pH 6.0–6.5. Analysis of the 16S rRNA gene sequences revealed that strain DCY67^T belonged to the family Flavobacteriaceae and was most closely related to Chryseobacterium ginsenosidimutans THG 15^T (97.5 %). The genomic DNA G+C content was 36.1 mol%. The predominant quinones were MK-6 (90.9 %) and MK-7 (9.15 %). The major fatty acids were iso-C_15:0, summed feature 3 (containing C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_17:0 3-OH. On the basis of these phenotypic, genotypic and chemotaxonomic studies, strain DCY67^T represents a novel species of the genus Chryseobacterium, for which, name Chryseobacterium yeoncheonense sp. nov. proposed the type strain is DCY67^T (=KCTC 32090^T = JCM 18516^T).     

Lysobacter telluris sp. nov., isolated from Korean rhizosphere soil

Archives of Microbiology - A Gram-stain-negative, aerobic, non-motile, non-spore-forming light-yellow-coloured rod-shaped bacterial strain, designated YJ15T, was isolated from soil at Bigeum island...     

Chitinophaga soli sp. nov. and Chitinophaga terrae sp. nov., isolated from soil of a ginseng field in Pocheon Province, Korea

Two novel strains of the Cytophaga-Flexibacter-Bacteroides (CFB) group, designated Gsoil 219" and Gsoil 2381, were isolated from soil of a ginseng field of Pocheon Province in Korea. Both strains were Gram-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Chitinophaga but were clearly separated from established species of this genus. The sequence similarities between strain Gsoil 219T and type strains of the established species and between strain Gsoil 238T and type strains of the established species ranged from 91.4 to 94.7% and 91.6 to 94.2%, respectively. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15:0 and C(16:1) omega5c; major hydroxy fatty acid, iso-C(17:0) 3-OH; major polyamine, homospermidine) supported the affiliation of both strains Gsoil 219T and Gsoil 238T to the genus Chitinophaga. Furthermore, the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of both strains from the other validated Chitinophaga species. Therefore, the two isolates represent two novel species, for which the name Chitinophaga soli sp. nov. (type strain, Gsoil 219T=KCTC 12650T=DSM 18093T) and Chitinophaga terrae sp. nov. (type strain, Gsoil 238T=KCTC 12651T=DSM 18078T) are proposed.     

Cohnella panacarvi sp. nov., a xylanolytic bacterium isolated from ginseng cultivating soil

A Gram-positive, aerobic, rod-shaped, nonmotile, endospore-forming bacterium, designated Gsoil 349T, was isolated from soil of a ginseng field and characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that the strain Gsoil 349T belongs to the family Paenibacillaceae, and the sequence showed closest similarity with Cohnella thermotolerans DSM 17683T (94.1%) and Cohnella hongkongensis DSM 17642T (93.6%). The strain showed less than 91.3% 16S rRNA gene sequence similarity with Paenibacillus species. In addition, the presence of MK-7 as the major menaquinone and anteiso-C(15:0), iso-C(16:0), and C(16:0) as major fatty acids suggested its affiliation to the genus Cohnella. The G+C content of the genomic DNA was 53.4 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 349T should be treated as a novel species within the genus Cohnella for which the name Cohnella panacarvi sp. nov. is proposed. The type strain is Gsoil 349T (=KCTC 13060T = DSM 18696T).