Wan-Taek Im

Nocardioides ginsengisegetis sp. nov., isolated from soil of a ginseng field

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 485T) was isolated from the 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 the polyphasic approach. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 485T was shown to belong to the family Nocardioidaceae and related to Nocardioides koreensis (96.8% 16S rRNA gene sequence similarity), Nocardioides basaltis (96.7%), Nocardioides salarius (96.7%), and Nocardioides sediminis (96.5%). The sequence similarity with other species that had validly published names within the genus Nocardioides was less than 96.4%. Strain Gsoil 485T was characterized chemotaxonomically as having LL-2,6-diaminopimelic acid in a cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone, and iso-C16:0, C18:1ω9c as the major fatty acids. The G+C content of genomic DNA was 71.6 mol%. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 485T to the genus Nocardioides. The results of both physiological and biochemical tests allowed for genotypic differentiation of strain Gsoil 485T from the recognized Nocardioides species. Therefore, strain Gsoil 485T is considered to represent the novel species, for which the name Nocardioidesginsengisegetis sp. nov. is proposed, with the type strain Gsoil 485T (KACC 14269T =KCTC 19469T =DSM 21349T).

Flavobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside converting activity isolated from soil of a ginseng field.

A Gram-negative, aerobic, non-motile, non-spore-forming, yellow-pigmented, rod-shaped bacterium, designated strain THG 01(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 01(T) grew well at 25-37 °C and pH 6.0-7.5 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity data, strain THG 01(T) was shown to belong to the family Flavobacteriaceae and was related to Flavobacterium anhuiense D3(T) (97.5 % similarity), Flavobacterium johnsoniae UW101(T) (96.8 %) and Flavobacterium denitrificans ED5(T) (96.7 %). 16S rRNA gene sequence similarities between the novel strain and members of other recognized species within the family Flavobacteriaceae were less than 96.7 %. The G+C content of the genomic DNA of strain THG 01(T) was 32.1 mol%. Phenotypic and chemotaxonomic data (major menaquinone was MK-6 and major fatty acids were iso-C(15 : 0), iso-C(15 : 0) 3-OH and C(16 : 1)ω7c and/or C(16 : 1)ω6c ) supported the affiliation of strain THG 01(T) to the genus Flavobacterium. DNA-DNA hybridization experiments showed that DNA-DNA relatedness values between strain THG 01(T) and its closest phylogenetic neighbours were below 11 %. The results of physiological and biochemical tests enabled strain THG 01(T) to be differentiated genotypically and phenotypically from recognized species of the genus Flavobacterium. The isolate therefore represents a novel species, for which the name Flavobacterium ginsenosidimutans sp. nov. is proposed, with THG 01(T) (u200a=u200aKACC 14525(T)u200a=u200aJCM 16720(T)) as the type strain.

Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field.

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain, designated THG 15(T), was isolated from soil of a field cultivated with Rhus vernicifera in Okcheon province, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain THG 15(T) grew optimally at 25-30 °C and at pH 7 in the absence of NaCl on nutrient agar. Strain THG 15(T) displayed β-glucosidase (aesculinase) activity that was responsible for its ability to transform ginsenoside Rb(1) (one of the dominant active components of ginseng) into compound K via Rd and F(2). On the basis of 16S rRNA gene sequence similarities, strain THG 15(T) was shown to belong to the family Flavobacteriaceae and was most closely related to Chryseobacterium soldanellicola PSD1-4(T) (97.7 % sequence similarity), Chryseobacterium soli JS6-6(T) (97.5 %) and Chryseobacterium indoltheticum LMG 4025(T) (97.3 %). The G+C content of the genomic DNA was 35.7 mol%. The major menaquinone was MK-6 and the major fatty acids were iso-C(15 : 0) (50.3 %), iso-C(17u200a:u200a0) 3-OH (21.9 %), summed feature 4 (comprising C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH; 9.5 %) and iso-C(17 : 1)ω9c (9.3 %). DNA sequence analysis and chemotaxonomic data supported the affiliation of strain THG 15(T) to the genus Chryseobacterium. DNA-DNA relatedness values between strain THG 15(T) and its closest phylogenetic neighbours were <15 %. Strain THG 15(T) could be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. The isolate therefore represents a novel species, for which the name Chryseobacterium ginsenosidimutans sp. nov. is proposed. The type strain is THG 15(T) (u200a=u200aKACC 14527(T) u200a=u200aJCM 16719(T)).

Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of a ginseng field

A taxonomic study was carried out on Gsoil 142T, a bacterial strain isolated from the soil collected in a ginseng field in Pocheon province, South Korea. Comparative 16S rRNA gene sequence studies showed a clear affiliation of this bacterium to the Gammaproteobacteria, and it was most closely related to Hydrocarboniphaga effusa ATCC BAA 332T (94.4%, 16S rRNA gene sequence similarity), Nevskia ramosa DSM 11499T (94.1%) and Alkanibacter difficilis MN154.3T (92.0%). Strain Gsoil 142T was a Gram-negative, strictly aerobic, motile, and rod-shaped bacterium. The G+C content of the genomic DNA was 69.9% and predominant ubiquinone was Q-8. Major fatty acids were summed feature 8 (C18:1ω7c and/or ω6c, 36.3%), summed feature 3 (iso-C15:0 2-OH and/or C16:1ω7c, 20.6%) and C16:0 (17.4%). The major polar lipids detected in strain Gsoil 142T were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown glycolipid. On the basis of polyphasic evidence, it is proposed that strain Gsoil 142T should be placed in a novel genus and species, for which the name Panacagrimonas perspica gen. nov., sp. nov. is proposed. The type strain is Gsoil 142T (= KCTC 12982T = LMG 23239T).

Paenibacillus pocheonensis sp. nov., a facultative anaerobe isolated from soil of a ginseng field.

A Gram-positive, aerobic or facultatively anaerobic, rod-shaped, spore-forming bacterium, strain Gsoil 1138(T), was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 1138(T) was shown to belong to the family Paenibacillaceae and was most closely related to the type strains of Paenibacillus chondroitinus (98.2 % similarity) and Paenibacillus alginolyticus (96.5 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 1138(T) and the type strains of other recognized species of the genus Paenibacillus were below 96.5 %. The G+C content of the genomic DNA of strain Gsoil 1138(T) was 52.1+/-0.2 mol% (mean+/-sd of three determinations). Phenotypic and chemotaxonomic data (MK-7 as the major menaquinone and anteiso-C(15 : 0) and iso-C(16 : 0) as the predominant fatty acids) supported the affiliation of strain Gsoil 1138(T) to the genus Paenibacillus. The results of DNA-DNA hybridization experiments and physiological and biochemical tests allowed strain Gsoil 1138(T) to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus. Strain Gsoil 1138(T) is therefore considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 1138(T) (=KCTC 13941(T)=LMG 23404(T)).

Aeromicrobium ginsengisoli sp. nov., isolated from a ginseng field.

Strain Gsoil 098(T), a Gram-positive, non-spore-forming, non-motile coccus, was isolated from soil from a ginseng field in South Korea and characterized in order to determine its taxonomic position. 16S rRNA gene sequence analysis revealed that strain Gsoil 098(T) belongs to the family Nocardioidaceae, and the highest degrees of sequence similarity were found with Aeromicrobium marinum T2(T) (99.0%), A. panaciterrae Gsoil 161(T) (98.9%), A. alkaliterrae KSL-107(T) (98.4%), A. fastidiosum KCTC 9576(T) (98.1%) and A. erythreum NRRL B-3381(T) (97.5%). Chemotaxonomic analysis revealed that strain Gsoil 098(T) possesses menaquinone MK-9(H(4)) and predominant fatty acids C(16 : 0), 10-methyl C(18:0) and C(18:0). DNA-DNA hybridization results and physiological and biochemical tests clearly demonstrated that strain Gsoil 098(T) represents a distinct species. Based on these data, Gsoil 098(T) (=KCTC 19207(T) =JCM 14732(T) =GBS 39(T)) should be classified as the type strain of a novel Aeromicrobium species, for which the name Aeromicrobium ginsengisoli sp. nov. is proposed.

Vagococcus acidifermentans sp. nov., isolated from an acidogenic fermentation bioreactor.

A Gram-staining-positive, coccus-shaped, non-spore-forming, facultatively anaerobic bacterium, designated AC-1(T), was isolated from an acidogenic fermentation bioreactor treating food wastewater. On the basis of 16S rRNA gene sequence analysis, strain AC-1(T) was shown to belong to the genus Vagococcus. The closest phylogenetic relatives were Vagococcus elongatus PPC9(T) (97.4 % 16S rRNA gene sequence similarity), Vagococcus penaei CD276(T) (96.7 %) and Vagococcus carniphilus ATCC BAA-640(T) (96.6 %). The major fatty acids were C(18u200a:u200a1)ω9c (24.8 %) and C(16 : 0) (19.5 %) and the G+C content of genomic DNA was 44.2 mol%, which supported the affiliation of strain AC-1(T) to the genus Vagococcus. Strain AC-1(T) and V. elongatus DSM 21480(T) exhibited 11 % DNA-DNA relatedness. Physiological and biochemical tests differentiated strain AC-1(T) from the type strains of recognized species of the genus Vagococcus. Therefore, strain AC-1(T) is considered to represent a novel species, for which the name Vagococcus acidifermentans sp. nov. is proposed. The type strain is AC-1(T) (u200a=u200aKCTC 13418(T) u200a=u200aLMG 24798(T)).

Variovorax ginsengisoli sp. nov., a denitrifying bacterium isolated from soil of a ginseng field

A Gram-negative, aerobic or facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium (strain Gsoil 3165(T)) was isolated from soil of a ginseng field in Pocheon, South Korea. Its taxonomic position was determined by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 3165(T) was shown to belong to the family Comamonadaceae, class Betaproteobacteria, and was related most closely to the type strains of Variovorax boronicumulans (98.9 % similarity), Variovorax paradoxus (98.3 %), Variovorax soli (98.2 %) and Variovorax dokdonensis (96.6 %). Levels of 16S rRNA gene sequence similarity between strain Gsoil 3165(T) and the type strains of other species in the family Comamonadaceae were less than 97.0 %. The G+C content of the genomic DNA of strain Gsoil 3165(T) was 66 mol%. Phenotypic and chemotaxonomic data (Q-8 as the major ubiquinone; C(16 : 0) and C(17 : 0) cyclo as major fatty acids) supported the affiliation of strain Gsoil 3165(T) to the genus Variovorax. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 3165(T) from recognized Variovorax species. Gsoil 3165(T) is therefore considered to represent a novel species of the genus Variovorax, for which the name Variovorax ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3165(T) (=KCTC 12583(T) =LMG 23392(T)).

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

A Gram-reaction-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (strain Gsoil 080(T)) was isolated from soil collected in a ginseng field in Pocheon Province, South Korea, and was investigated by using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 080(T) was related most closely to Inquilinus limosus strains AU0476(T) and AU1979 (98.9u200a% similarity to both). Strain Gsoil 080(T) shared ≤91.3u200a% 16S rRNA gene sequence similarity with the type strains of other recognized species examined. The genus Inquilinus belongs to the family Rhodospirillaceae in the order Rhodospirillales, class Alphaproteobacteria. The predominant ubiquinone was Q-10 and the major fatty acids were summed feature 7 (C(18u200a:u200a1)ω9c/ω12t/ω7c) and C(19u200a:u200a0) cyclo ω8c. The G+C content of the genomic DNA of strain Gsoil 080(T) was 69.9 mol%. The level of DNA-DNA relatedness between strain Gsoil 080(T) and I. limosus LMG 20952(T) was 12u200a%. The results of genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Gsoil 080(T) represents a novel species of the genus Inquilinus, for which the name Inquilinus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 080(T) (=KCTC 12574(T) =LMG 23638(T)).