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).     

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).     

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).     

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)).     

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).     

Rhodanobacter umsongensis sp. nov., isolated from a Korean ginseng field

A bacterial isolate designated GR24-2^T was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28–30°C, pH 7.0, and in a range of 0–1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47^T (98.4%), R. soli DCY45^T (98.2%), and R. ginsengisoli GR17-7^T (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C_17:1 ω9c (24.5%), iso-C_16:0 (22.8%), anteiso-C_15:0 (10.5%), and iso-C_15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2^T was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA-DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2^T =KACC 12917^T =DSM 21300^T).     

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).     

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).     

Nocardioides panaciterrulae sp. nov., isolated from soil of a ginseng field, with ginsenoside converting activity

A Gram-positive, coccoid to rod-shaped, non-spore-forming bacterium, designated Gsoil 958^T, was isolated from soil of a ginseng field located in Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using a polyphasic approach. Strain Gsoil 958^T was observed to grow well at 25–30 °C and at pH 7.0 on R2A and nutrient agar without NaCl supplementation. Strain Gsoil 958^T was determined to have β-glucosidase activity and the ability to transform ginsenoside Rb₁ (one of the dominant active components of ginseng) to F₂ via gypenoside XVII and Rd. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 958^T was shown to belong to the family Nocardioidaceae and related most closely to Nocardioides koreensis MSL-09^T (97.6 % 16S rRNA gene sequence similarity), Nocardioides aquiterrae GW-9^T (97.0 %), and Nocardioides sediminis MSL-01^T (97.0 %). The sequence similarities with other validly named species within the genus Nocardioides were less than 96.8 %. Strain Gsoil 958^T was characterized chemotaxonomically as having LL-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H₄) as the predominant menaquinone, and iso-C_16:0, iso-C_16:1 H, iso-C_14:0, iso-C_15:0 were identified as the major fatty acids. The G + C content of genomic DNA was determined to be 70.8 mol %. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 958^T to the genus Nocardioides. The results of both physiological and biochemical tests allowed for differentiation of strain Gsoil 958^T from the recognized Nocardioides species. Therefore, strain Gsoil 958^T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides panaciterrulae sp. nov. is proposed, with the type strain Gsoil 958^T (KACC 14271^T = KCTC 19471^T = DSM 21350^T).     

Bacillus huizhouensis sp. nov., isolated from a paddy field soil

A Gram-stain positive, facultative aerobic bacterium, designated as strain GSS03^T, was isolated from a paddy field soil. The cells were observed to be endospore forming, rod-shaped and motile with flagella. The organism was found to grow optimally at 35 °C at pH 7.0 and in the presence of 1 % NaCl. The strain was classified as a novel taxon within the genus Bacillus on the basis of phenotypic and phylogenetic analyses. The closest phylogenetic relatives were identified as Bacillus psychrosaccharolyticus DSM 6^T (97.61 %), Bacillus muralis DSM 16288^T (97.55 %), Bacillus asahii JCM 12112^T (97.48 %), Bacillus simplex DSM 1321^T (97.48 %) and “Bacillus frigoritolerans” DSM 8801^T (97.38 %). The menaquinone was identified as MK-7, the major cellular fatty acid was identified as anteiso-C_15:0 and the major cellular polar lipids as phosphatidylethanolamine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and three unknown polar lipids. The DNA G+C content was determined to be 40.2 mol%. The DNA–DNA relatedness with the closest relatives was below 48 %. Therefore, on the basis of all the results, strain GSS03^T is considered to represent a novel species within the genus Bacillus, for which the name Bacillus huizhouensis sp. nov. is proposed. The type strain is GSS03^T (=KCTC 33172^T =CCTCC AB 2013237^T).     

Lysobacter ginsengisoli sp. nov., a novel species isolated from soil in Pocheon Province, South Korea

A Gram-negative, aerobic, rod-shaped, nonspore-forming bacterial strain, designated Gsoil 357T, was isolated from soil sample of a ginseng field in Pocheon Province (South Korea). The isolate contained Q-8 as the predominant ubiquinone and iso-C16:0, iso-C17:1 9c, and iso-C15:0 as the major fatty acids. The G+C content of the genomic DNA was 69.3mol%. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Gsoil 357T was most closely related to Lysobacter gummosus (97.6%) and Lysobacter antibioticus (97.6%). However, the DNA-DNA relatedness value between strain Gsoil 357T and its phylogenetically closest neighbors was less than 17%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 357T should be classified as representing a novel species in the genus Lysobacter, for which the name Lysobacter ginsengisoli sp. nov. is proposed. The type strain is Gsoil 357T (=KCTC 12602T=DSM 18420T).     

Arthrobacter enclensis sp. nov., isolated from sediment sample

A novel bacterial strain designated as NIO-1008^T was isolated from marine sediments sample in Chorao Island India. Cells of the strains were gram positive and non-motile, displayed a rod–coccus life cycle and formed cream to light grey colonies on nutrient agar. Strain NIO-1008^T had the chemotaxonomic markers that were consistent for classification in the genus Arthrobacter, i.e. MK-9(H₂) (50.3 %), as the major menaquinone, and the minor amount of MK-7 (H₂-27.5 %), MK-8 (H₄-11.6 %) and MK-8 (H₂-10.4 %). anteiso-C_15:0, iso-C_15:0, iso-C_16:0 and C_15:0 were the predominant fatty acids. Galactose, glucose and rhamnose are the cell-wall sugars, and DNA G+C content was 61.3 mol%. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were most similar to Arthrobacter equi IMMIB L-1606^T, Arthrobacter chlorophenolicus DSM 12829^T, Arthrobacter defluvii KCTC 19209^T and Arthrobacter niigatensis CCTCC AB 206012^T with 98.5, 98.4, 98.0 and 97.8 %, respectively, and formed a separate lineage. Combined phenotypic data and DNA–DNA hybridization data supported the conclusion that strains NIO-1008^T represent a novel species within the genus Arthrobacter, for which the name Arthrobacter enclensis sp. nov., is proposed. The type strain is NIO-1008^T = (NCIM 5488^T = DSM 25279^T).     

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.