Heung-Min Son

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

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117(T), 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-B117(T) 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-B117(T) was shown to belong to the family Xanthomonadaceae and be related to Dyella japonica XD53(T) (98.7 % similarity), Dyella terrae JS14-6(T) (98.0 %), Dyella koreensis BB4(T) (96.9 %), Dyella soli JS12-10(T) (96.9 %) and Dyella thiooxydans ATSB10(T) (96.7 %). DNA-DNA hybridization experiments showed that DNA relatedness between strain THG-B117(T) and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117(T) 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-B117(T) with the genus Dyella. The results of physiological and biochemical tests suggested that strain THG-B117(T) 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-B117(T) ( = KACC 16981(T) = JCM 18747(T)).

Lysobacter terrae sp. nov. isolated from Aglaia odorata rhizosphere soil.

A Gram-stain negative, facultatively anaerobic, non-motile, rod-shaped bacterium, designated strain THG-A13(T), was isolated from Aglaia odorata rhizosphere soil in Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-A13(T) had close similarity with Lysobacter niabensis GH34-4(T) (98.5 %), Lysobacter oryzae YC6269(T) (97.9 %) and Lysobacter yangpyeongensis GH19-3(T) (97.3 %). Chemotaxonomic data revealed that strain THG-A13(T) possesses ubiquinone-8 (Q8) as the predominant isoprenoid quinone and iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1ω9c as the major fatty acids. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol) and diphosphatidylglycerol. The G+C content was 66.3 mol%. The DNA-DNA relatedness values between strain THG-A13(T) and its closest phylogenetic neighbours were below 18.0 %. These data corroborated the affiliation of strain THG-A13(T) to the genus Lysobacter. These data suggest that the isolate represents a novel species for which the name Lysobacter terrae sp. nov. is proposed, with THG-A13(T) as the type strain ( = KACC 17646(T) = JCM 19613(T)).

Chryseobacterium camelliae sp. nov., isolated from green tea.

A Gram-staining-negative, strictly aerobic, non-motile, rod-shaped and flexirubin-type-pigmented strain, THG C4-1(T), was isolated from green tea leaves in Jangheung-gun, Republic of Korea. Strain THG C4-1(T) grew well at 20-30 °C, at pH 7.0-7.5 and in the absence of NaCl on nutrient agar. Based on 16S rRNA gene sequence comparisons, strain THG C4-1(T) was most closely related to Chryseobacterium taiwanense Soil-3-27(T) (97.7 %), C. hagamense RHA2-9(T) (97.2 %), C. gregarium P 461/12(T) (97.2 %), C. ginsenosidimutans THG 15(T) (97.1 %), C. taeanense PHA3-4(T) (97.0 %) and C. daeguense K105(T) (97.0 %), but DNA-DNA relatedness between strain THG C4-1(T) and its closest phylogenetic neighbours was below 21 %. The DNA G+C content was 41.7 mol%. The only isoprenoid quinone detected in strain THG C4-1(T) was menaquinone 6 (MK-6). The major component of the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminolipids. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1ω9c. These data supported the affiliation of strain THG C4-1(T) to the genus Chryseobacterium. The results of physiological and biochemical tests enabled strain THG C4-1(T) to be differentiated genotypically and phenotypically from recognized species of the genus Chryseobacterium. Therefore, the novel isolate represents a novel species, for which the name Chryseobacterium camelliae sp. nov. is proposed, with THG C4-1(T) ( = KACC 16985(T) = JCM 18745(T)) as the type strain.

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

A bacterial strain THG-B283(T), which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283(T) grew optimally at around pH 7.0, at 25-28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283(T) belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224(T) (98.2 %), S. aquatilis JSS7(T) (98.1 %), S. insulae DS-28(T) (97.6 %), S. mali IFO 15500(T) (97.1 %) and S. pruni IFO 15498(T) (97.0 %). Strain THG-B283(T) contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283(T) to the genus Sphingomonas. DNA-DNA relatedness between strain THG-B283(T) and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283(T) represents a novel species of genus Sphingomonas, for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283(T) ( = KACC 16224(T) = LMG 26582(T)).

Pedobacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated THG-45(T), was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 4-30 °C, at pH 5.5-9.0 and with 0-2 % (w/v) NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-45(T) was shown to belong to the genus Pedobacter and was related to Pedobacter borealis G-1(T) (98.8 %), P. alluvionis NWER-II11(T) (97.9 %), P. agri PB92(T) (97.9 %), P. terrae DS-57(T) (97.5 %), P. suwonensis 15-52(T) (97.4 %), P. sandarakinus DS-27(T) (97.0 %) and P. soli 15-51(T) (97.0 %), but DNA relatedness between strain THG-45(T) and these strains was below 36 %. The G+C content of the genomic DNA was 39 mol%. The only isoprenoid quinone detected in strain THG-45(T) was menaquinone-7 (MK-7). The predominant fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH, and the major polar lipids were phosphatidylethanolamine and an unidentified aminophosphoglycolipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-45(T) to the genus Pedobacter, and a number of biochemical tests differentiated strain THG-45(T) from the recognized species of the genus Pedobacter. Therefore, the novel isolate represents a novel species, for which the name Pedobacter ginsenosidimutans sp. nov. is proposed, with THG-45(T) as the type strain ( = KACC 14530(T) = JCM 16721(T)).

Chryseobacterium gwangjuense sp. nov., isolated from soil.

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped bacterial strain, THG-A18(T), was isolated from soil of Gwangju province in South Korea. Strain THG-A18(T) grew optimally at 25-30 °C, at pH 7.0-8.0 and in the absence of NaCl. Strain THG-A18(T) displayed β-glucosidase activity, which enabled it to convert ginsenoside Rb1 to Rd. According to 16S rRNA gene sequence analysis, strain THG-A18(T) was shown to belong to the genus Chryseobacterium. The closest phylogenetic neighbours were Chryseobacterium ginsenosidimutans THG 15(T) (97.9 % 16S rRNA gene sequence similariity), C. defluvii B2(T) (97.7 %), C. daeguense K105(T) (97.6 %), C. taiwanense BCRC 17412(T) (97.5 %), C. indoltheticum LMG 4025(T) (97.4 %), C. gregarium P 461/12(T) (97.4 %) and C. lathyri RBA2-6(T) (97.3 %), but DNA-DNA relatedness values between these strains and strain THG-A18(T) were below 41.9 %. The G+C content of the genomic DNA was 36.4 mol%. The major respiratory quinone (MK-6) and fatty acids [iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0)] supported the affiliation of strain THG-A18(T) with the genus Chryseobacterium. The polar lipids of strain THG-A18(T) were phosphatidylethanolamine, four unidentified aminolipids and seven unidentified lipids. A number of physiological and biochemical tests allowed phenotypic differentiation of strain THG-A18(T) from recognized species of the genus Chryseobacterium. The name Chryseobacterium gwangjuense sp. nov. is proposed, with THG-A18(T) ( = KACC 16227(T) = LMG 26579(T)) as the type strain.

Taibaiella koreensis sp. nov., isolated from soil of a ginseng field.

A Gram-staining-negative, strictly aerobic, motile (by gliding), non-spore-forming and rod-shaped bacterial strain, designated THG-DT86(T), was isolated from soil of a ginseng field of Pocheon province in the Republic of Korea and its taxonomic position was investigated by a polyphasic approach. Growth occurred at 10-35 °C, at pH 6.5-8.5 and with 0-1.5 % (w/v) NaCl on trypticase soy agar. Flexirubin-type pigments were found to be present. On the basis of 16S rRNA gene sequence similarity, strain THG-DT86(T) was shown to belong to the genus Taibaiella and was related to Taibaiella smilacinae PTJT-5(T) (95.3 %). The G+C content of the genomic DNA was 50.1 mol%. The only isoprenoid quinone detected in strain THG-DT86(T) was menaquinone-7 (MK-7) and the only polyamine was homospermidine. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, iso-C15 : 1 G and iso-C17 : 0, and the major polar lipids were phosphatidylethanolamine, an unidentified aminophosphoglycolipid and an unidentified aminophospholipid. Phenotypic data and phylogenetic inference supported the affiliation of strain THG-DT86(T) to the genus Taibaiella, and a number of biochemical tests differentiated strain THG-DT86(T) from the recognized species of the genus Taibaiella. Therefore, the novel isolate represents a novel species, for which the name Taibaiella koreensis sp. nov. is proposed, with THG-DT86(T) as the type strain ( = KACC 17171(T) = JCM 18823(T)).

Rhodanobacter koreensis sp. nov., a bacterium isolated from tomato rhizosphere.

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, designated THG-DD7(T), was isolated from tomato plant rhizosphere soil. Strain THG-DD7(T) grew optimally at 25-30 °C, at pH 7.0-7.5 and in the presence of 0.5% (w/v) NaCl. According to the results of 16S rRNA gene sequence comparisons, strain THG-DD7(T) was most closely related to Rhodanobacter umsongensis GR24-2(T) (98.2%), Rhodanobacter panaciterrae LnR5-47(T) (98.0%), Rhodanobacter soli DCY45(T) (97.9%), Rhodanobacter terrae GP18-1(T) (97.9%) and Dyella ginsengisoli Gsoil 3046(T) (97.7%). The DNA G+C content was 65.2 mol%. In DNA-DNA hybridization, the DNA relatedness levels between strain THG-DD7(T) and its closest phylogenetically neighbours were below 40.0%. The predominant isoprenoid quinone was ubiquinone Q-8. The major polar lipids were diphosphatidylglycerol, phosphtidylethanolamine, phosphatidyl-N-methylethanolamine and phosphatidylglycerol. The major fatty acids were iso-C(15 : 0), iso-C(16 : 0), iso-C(17 : 0), anteiso-C(15 : 0) and iso-C(17 : 1)ω9c and/or C(16 : 0) 10-methyl (summed feature 9). These data supported the affiliation of strain THG-DD7(T) to the genus Rhodanobacter . The results of physiological and biochemical tests enabled strain THG-DD7(T) to be differentiated genotypically and phenotypically from the species of the genus Rhodanobacter with validly published names. Therefore, the novel isolate represents a novel species, for which the name Rhodanobacter koreensis sp. nov. is proposed. The type strain is THG-DD7(T) ( = KACC 17650(T) = JCM 19614(T)).