KyungHwa Won

Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov., isolated from an ancient tree trunk, and emended description of the genus Pedobacter.

Two Gram-stain-negative, yellow, aerobic and rod-shaped bacterial isolates, designated THG-DN3.18(T) and THG-DN3.19(T), were isolated from an ancient tree trunk from Daejeon, South Korea. 16S rRNA gene sequence similarity showed that both strains belong to the genus Pedobacter within the family Sphingobacteriaceae . Strain THG-DN3.18(T) exhibited maximum sequence similarity with Pedobacter boryungensis KCTC 23344(T) (98.5%) while strain THG-DN3.19(T) exhibited maximum sequence similarity with Pedobacter nyackensis LMG 24260(T) (97.3%). In DNA-DNA hybridization tests, the two strains showed less than 35% relatedness with respect to closely related species of the genus Pedobacter . Both strains contained iso-C(15 : 0) and C(16 : 1)ω6c and/or C(16 : 1)ω7c (summed feature 3) as the predominant fatty acids and MK-7 as the major isoprenoid quinone. The DNA G+C contents of strains THG-DN3.18(T) and THG-DN3.19(T) were 35.5 and 40.1 mol%, respectively. The genotypic analysis, biochemical properties, and phenotypic and chemotaxonomic characteristics indicate that strains THG-DN3.18(T) and THG-DN3.19(T) represent novel species of the genus Pedobacter , for which the names Pedobacter daejeonensis sp. nov. and Pedobacter trunci sp. nov. are proposed. The type strains are THG-DN3.18(T) ( = KCTC 42230(T) = JCM 30352(T)) and THG-DN3.19(T) ( = KCTC 42233(T) = JCM 30353(T)), respectively.

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)).

Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.

A novel bacterial strain, designated THG-S11.7T, was isolated from garden soil in Incheon, South Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile cocci, and were catalase- and oxidase-positive. Colonies of the strain were white. Strain THG-S11.7T grew optimally at 28 °C, at pH 7.0 and in the presence of 2.0 % NaCl. 16S rRNA gene sequence analysis indicated that the strain was a member of the genus Nocardioides. Strain THG-S11.7T showed a 16S rRNA gene sequence similarity of 98.2 % to Nocardioides kongjuensis KCTC 19054T, 98.0 % to Nocardioides caeni KCTC 19600T, 97.9 % to Nocardioides daeguensis KCTC 19799T, 97.8 % to Nocardioides nitrophenolicus KCTC 047BPT, 97.6 % to Nocardioides aromaticivorans KACC 20613T, 97.5 % to Nocardioides simplex KACC 20620T and 97.0 % to Nocardioides ginsengisoli KCTC 19135T. DNA-DNA relatedness values between strain THG-S11.7T and the closest phylogenetic neighbours were below 45.0 % and the DNA G+C content of strain THG-S11.7T was 72.2 mol%. Strain THG-S11.7T was characterized chemotaxonomically as having ll-diaminopimelic acid in the cell-wall peptidoglycan and menaquinone MK-8(H4) as the predominant isoprenoid quinone. The major phospholipid was determined to be diphosphatidylglycerol. The major cellular fatty acids of strain THG-S11.7T were iso-C15 : 0, C16 : 0 and iso-C16 : 0. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the isolate represents a novel species of the genus Nocardioides, for which the name Nocardioides albidus sp. nov. is proposed. The type strain is THG-S11.7T ( = KCTC 39607T = CCTCC AB 2015297T).

Chryseobacterium solani sp. nov., isolated from field-grown eggplant rhizosphere soil.

Strain THG-EP9T, a Gram-stain-negative, aerobic, motile, rod-shaped bacterium was isolated from field-grown eggplant (Solanum melongena) rhizosphere soil collected in Pyeongtaek, Gyeonggi-do, Republic of Korea. Based on 16S rRNA gene sequence comparisons, strain THG-EP9T had closest similarity with Chryseobacterium ginsenosidimutans THG 15T (97.3 % 16S rRNA gene sequence similarity), Chryseobacterium soldanellicola PSD1-4T (97.2%), Chryseobacterium zeae JM-1085T (97.2%) and Chryseobacterium indoltheticum LMG 4025T (96.8%). DNA-DNA hybridization showed 5.7% and 9.1% DNA reassociation with Chryseobacterium ginsenosidimutans KACC 14527T and Chryseobacterium soldanellicola KCTC 12382T, respectively. Chemotaxonomic data revealed that strain THG-EP9T possesses menaquinone-6 as the only respiratory quinone and iso-C15 : 0 (29.0%), C16 : 0 (12.5%) and iso-C17 : 0 3-OH (11.9 %) as the major fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, an unidentified aminophospholipid, two unidentified glycolipids, six unidentified aminolipids and two unidentified polar lipids. The DNA G+C content was 35.3 mol%. These data corroborated the affiliation of strain THG-EP9T to the genus Chryseobacterium. Thus, the isolate represents a novel species of this genus, for which the name Chryseobacterium solani sp. nov. is proposed, with THG-EP9T ( = KACC 17652T = JCM 19456T) as the type strain.

Lysobacter novalis sp. nov., isolated from fallow farmland soil.

A novel bacterial strain, designated THG-PC7(T), was isolated from fallow farmland soil in Yongin, South Korea. Cells of strain THG-PC7(T) were Gram-stain-negative, dark yellow, aerobic, rod-shaped and had gliding motility. Strain THG-PC7(T) grew optimally at 25-35 °C, at pH 7 and in the absence of NaCl. Comparative 16S rRNA gene sequence analysis identified strain THG-PC7(T) as belonging to the genus Lysobacter, exhibiting highest sequence similarity with Lysobacter ximonensis KCTC 22336(T) (98.7%) followed by Lysobacter niastensis KACC 11588(T) (95.7%). In DNA-DNA hybridization tests, DNA relatedness between strain THG-PC7(T) and its closest phylogenetic neighbour L. ximonensis was below 25%. The DNA G+C content of the novel isolate was determined to be 62.5 mol%. Flexirubin-type pigments were found to be present. The major cellular fatty acids were determined to be iso-C15 : 0, iso-C16 : 0, anteiso-C15 : 0 and iso-C17 : 1ω9c. The major respiratory quinone was identified as ubiquonone-8 (Q8). The predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospolipid. On the basis of results from DNA-DNA hybridization and the polyphasic data, strain THG-PC7(T) represents a novel species of the genus Lysobacter, for which the name Lysobacter novalis sp. nov. is proposed. The type strain is THG-PC7(T)( = KACC 18276(T) = CCTCC AB 2014319(T)).

Sphingobacterium mucilaginosum sp. nov., isolated from rhizosphere soil of a rose.

A Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, designated strain THG-SQA8(T), was isolated from rhizosphere soil of rose in PR China. Strain THG-SQA8(T) was closely related to members of the genus Sphingobacterium, showed the highest sequence similarities with Sphingobacterium multivorum KACC 14105(T) (98.0%) and Sphingobacterium ginsenosidimutans KACC 14526(T) (97.4%). DNA-DNA hybridization showed values of 35.2 ± 0.9% and 8.8 ± 0.3% DNA reassociation with S. multivorum KACC 14105(T) and S. ginsenosidimutans KACC 14526(T), respectively. Chemotaxonomic data revealed that strain THG-SQA8(T) possesses menaquinone-7 as the only respiratory quinone, and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C1 : 0 and C16 : 0 as the major fatty acids. The major polar lipid was phosphatidylethanolamine. The DNA G+C content was 40.7 mol%. These data corroborated the affiliation of strain THG-SQA8(T) to the genus Sphingobacterium. Thus, the isolate represents a novel species, for which the name Sphingobacterium mucilaginosum sp. nov. is proposed, with THG-SQA8(T) as the type strain ( = CCTCC AB 2014317(T) = KCTC 42503(T)).

Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower)

A Gram-stain-negative, aerobic, short-rod-shaped bacterium, motile by means of one flagellum (THG-T2.8T), was isolated from the rhizosphere of Mugunghwa flower. Growth occurred at 10-37 °C (optimum 28 °C), at pH 6-8 (optimum 7) and with 0-5 % NaCl (optimum 1 %). The major quinone was ubiquinone-10 (Q-10). The major fatty acids were C10 : 0 3-OH, C16 : 0, C18 : 0 and C18 : 1ω7c. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, one unidentified aminolipid, two unknown phospholipids, one unknown glycolipid and one unidentified lipid. The DNA G+C content of strain THG-T2.8T was 65.5 mol%. Based on 16S rRNA gene sequence analysis, the nearest phylogenetic neighbours of strain THG-T2.8T were identified as Paracoccus tibetensis Tibet-S9a3T (98.6 %), Paracoccus aestuarii B7T (98.4 %), Paracoccus rhizosphaerae CC-CCM15-8T (98.3 %) and Paracoccus beibuensis JLT1284T (98.2 %). Levels of sequence similarity among strain THG-T2.8T and other species of the genus Paracoccus were lower than 98.0 %. DNA-DNA hybridization values between strain THG-T2.8T and P. tibetensis Tibet-S9A3TT, P. aestuarii B7T, P. rhizosphaerae CC-CCM15-8T and P. beibuensisJLT1284T were 36.5 % (38.8 %, reciprocal analysis), 32.8 % (34.8 %), 31.6 % (33.8 %) and 15.3 % (24.8 %), respectively. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-T2.8T represents a novel species of the genus Paracoccus, for which the name Paracoccus hibisci sp. nov. is proposed. The type strain is THG-T2.8T (=KACC 18932T=CCTCC AB 2016181T).

Massilia arvi sp. nov., isolated from fallow-land soil previously cultivated with Brassica oleracea, and emended description of the genus Massilia.

A novel bacterial strain, designated THG-RS2OT, was isolated from fallow-land soil previously cultivated with Brassica oleracea in Yongin, South Korea. Cells were Gram-stain-negative, aerobic, non-motile rods, catalase- and oxidase-positive. Strain THG-RS2OT grew optimally at 25–37 °C, at pH 7.0 and in the absence of NaCl. 16S rRNA gene sequence analysis demonstrated that strain THG-RS2OT shows highest sequence similarity with Massilia kyonggiensis KACC 17471T followed by Massilia aerilata KACC 12505T, Massilia niastensis KACC 12599T, Massilia tieshanensis KACC 14940T and Massilia haematophila KCTC 32001T. Levels of DNA–DNA relatedness between strain THG-RS2OT and the closest phylogenetic neighbours were below 55.0 % and the DNA G+C content of strain THG-RS2OT was 63.2 mol%. Major fatty acids were C16 : 0, cyclo-C17 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The major respiratory quinone was identified as ubiquonone-8 and predominant polar lipids were determined to be diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Characterization by 16S rRNA gene sequence analysis, DNA–DNA hybridization, ubiquinone, polar lipid, fatty acid composition, and physiological and biochemical parameters revealed that strain THG-RS2OT represents a novel species of the genus Massilia. Hence, the present study describes a novel species for which the name Massilia arvi sp. nov. is proposed. The type strain is THG-RS2OT ( = KCTC 42609T = CCTCC AB 2015115T).

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)).