Hae-Min Jung

Deinococcus aquaticus sp. nov., isolated from fresh water, and Deinococcus caeni sp. nov., isolated from activated sludge.

The taxonomic positions of two environmental isolates from South Korea were established using a combination of genotypic and phenotypic data. The organisms, designated PB314(T) and Ho-08(T), were Gram-negative, rod-shaped and non-spore-forming and had chemotaxonomic properties consistent with their classification in the genus Deinococcus 16S rRNA gene tree, the highest sequence similarities being shown to the type strains of Deinococcus grandis (96.3-96.7 %) and Deinococcus indicus (96.3-96.4 %). The isolates shared relatively high 16S rRNA gene sequence similarity (98.1 %) but had a DNA-DNA relatedness value of only 22 %. Chemotaxonomic data revealed that both strains possess quinone system MK-8 as the predominant compound, C(16 : 1)omega7c and C(16 : 0) as major fatty acids and ornithine as a diamino acid in the peptidoglycan structure, corroborating our assignment of the strains to the genus Deinococcus. The results of phylogenetic analyses based on 16S rRNA gene sequences, DNA-DNA relatedness values and physiological and biochemical tests clearly demonstrated that the two strains represent distinct species. On the basis of these data, two novel species, Deinococcus aquaticus sp. nov. (type strain PB314(T) =KCTC 12552(T) =NBRC 101311(T)) and Deinococcus caeni sp. nov. (type strain Ho-08(T) =KCTC 12553(T) =NBRC 101312(T)), are proposed.

Lysobacter daecheongensis sp. nov., isolated from sediment of stream near the Daechung dam in South Korea

A Gram-negative, aerobic, rod shaped, non-spore-forming bacterial strain, designated Dae08T, was isolated from sediment of the stream near Daechung dam in South Korea, and was characterized in order to determine its taxonomic position, using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Dae08T belongs to the family Xanthomonadaceae of the Gammaproteobacteria, and is related to Lysobacter brunescens ATCC 29482T (97.3%). The phylogenetic distances from any other species with validly published names within the genus Lysobacter were greater than 3.7%. The G+C contents of the genomic DNA of strain Dae08T was 69.3 mol%. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with iso-C15:0, iso-C17:1, ω9c, iso-C17:0, iso-C16:0, and iso-C11:0 3-OH as the major acids supported the affiliation of strain Dae08T to the genus Lysobacter. DNA-DNA relatedness between strain Dae08T and its phylogenetically closest neighbour was 28%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Dae08T (= KCTC 12600T) should be classified in the genus Lysobacter as the novel species, for which the name Lysobacter daecheongensis sp. nov. is proposed.

Lysobacter panaciterrae sp. nov., isolated from soil of a ginseng field

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, designated Gsoil 068(T), was isolated from soil of a ginseng field in Pocheon Province (South Korea), and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 068(T) belonged to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Lysobacter brunescens ATCC 29482(T) and Lysobacter gummosus ATCC 29489(T) (96.1 % sequence similarity). The G+C content of the genomic DNA of strain Gsoil 068(T) was 67.0 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C(15 : 0), iso-C(17 : 1)omega9c, iso-C(17 : 0) and iso-C(11 : 0) 3-OH as the major components supported the affiliation of strain Gsoil 068(T) to the genus Lysobacter. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 068(T) is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panaciterrae sp. nov. is proposed. The type strain is Gsoil 068(T) (=KCTC 12601(T) =DSM 17927(T)).

Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.

A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).

Stenotrophomonas daejeonensis sp. nov., isolated from sewage.

A Gram-stain-negative, motile, aerobic bacterial strain, designated MJ03(T), was isolated from sewage and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ03(T) belongs to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Stenotrophomonas acidaminiphila AMX 19(T) (97.9  % sequence similarity), Stenotrophomonas humi R-32729(T) (97.1  %), Stenotrophomonas nitritireducens L2(T) (96.9  %), Stenotrophomonas maltophila ATCC 13637(T) (96.8  %) and Stenotrophomonas terrae R-32768(T) (96.7  %). The G+C content of the genomic DNA of strain MJ03(T) was 64.7 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C₁₅:₀, iso-C₁₁:₀, iso-C₁₄:₀, iso-C₁₇:₁ω9c, iso-C₁₁:₀ 3-OH and iso-C₁₃:₀ 3-OH as major components supported the affiliation of strain MJ03(T) to the genus Stenotrophomonas. However, levels of DNA-DNA relatedness between strain MJ03(T) and the type strains of five closely related species of the genus Stenotrophomonas ranged from 11 to 34  %, showing clearly that the isolate represents a novel genospecies. Strain MJ03(T) could be differentiated clearly from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ03(T) is considered to represent a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas daejeonensis sp. nov. is proposed. The type strain is MJ03(T) (=KCTC 22451(T) =JCM 16244(T)).

Dokdonella ginsengisoli sp. nov., isolated from soil from a ginseng field, and emended description of the genus Dokdonella

A Gram-negative, aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated Gsoil 191T, was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 191T belongs to the family Xanthomonadaceae and is related to Dokdonella fugitiva LMG 23001T (97.8% sequence similarity) and Dokdonella koreensis KCTC 12396T (96.9%). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-8 and the major fatty acids were iso-C17:1omega9c (30.6%), iso-C17:0 (21.6%) and iso-C15:0 (13.0%), supporting the affiliation of strain Gsoil 191T to the genus Dokdonella. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil 191T and its closest phylogenetic neighbours were below 40%. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Gsoil 191T from recognized species of the genus Dokdonella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 191T represents a novel species of the genus Dokdonella, for which the name Dokdonella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 191T (=KCTC 12564T=DSM 17954T=CCUG 52462T).

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 (98.9 % similarity to both). Strain Gsoil 080(T) shared ≤91.3 % 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(18 : 1)ω9c/ω12t/ω7c) and C(19 : 0) 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 12 %. 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)).

Castellaniella daejeonensis sp. nov., isolated from soil

A Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06(T), was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06(T) contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06(T) was 66.2 mol%. The major fatty acids were summed feature 4 (C(16 : 1)ω 7c and/or iso-C(15 : 0) 2-OH; 32.5 %), C(16 : 0) (22.8 %) and summed feature 7 (one or more of C(18 : 1)ω 7c, C(18 : 1)ω 9t and C(18 : 1)ω 12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06(T) belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06(T) and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAU(T), Castellaniella defragrans 54Pin(T), Castellaniella ginsengisoli DCY36(T) and Castellaniella caeni Ho-11(T), were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06(T) and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06(T) exhibited relatively low levels of DNA-DNA relatedness with respect to C. defragrans DSM 12141(T) (52 %), C. denitrificans DSM 11046(T) (31 %), C. ginsengisoli KCTC 22398(T) (18 %) and C. caeni KCTC 12197(T) (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06(T) is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06(T) (=KCTC 22454(T) =JCM 16240(T)).