Moon-Soo Rhee

Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo, Korea

A bacterial strain, designated YH12T, was isolated from a wetland sample collected from Woopo, Republic of Korea, and characterized using a polyphasic approach. Analysis of 16S rDNA indicated that the isolate formed a monophyletic clade with the members of the genus Comamonas. The closest phylogenetic relative among the valid species was Comamonas testosteroni, with 96.6% 16S rDNA similarity. The chemotaxonomic properties of the wetland isolate supported its membership of the genus Comamonas, as it contained ubiquinone Q-8 as a major respiratory quinone and hexadecanoic, methylene-hexadecanoic and octadecenoic acids as major cellular fatty acids. The G+C content of the DNA was 66 mol%. The isolate is a gram-negative, non-pigmented, rod-shaped, oxidase- and catalase-positive, non-motile, non-endospore-forming and non-fermentative bacterium. The phenotypic properties of the isolate were compared with those of the type strains of Comamonas terrigena, C. testosteroni and Delftia acidovorans. A number of tests, including motility, can differentiate our isolate from related taxa. On the basis of the 16S rDNA phylogenetic, chemotaxonomic and phenotypic evidence given in this study, it is proposed that strain YH12T (= KCTC 12005T = IMSNU 11158T) be assigned as the type strain of a novel species of the genus Comamonas, Comamonas koreensis sp. nov.

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle.

Three strictly anaerobic, methanogenic strains JH1(T), JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales, and Methanobrevibacter wolinii SH(T) was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1(T), JH4 and JH8 and M. wolinii SH(T) were 96.2 and 89.0 % respectively, and DNA-DNA hybridization of the isolates and M. wolinii DSM 11976(T) showed a 20 % reassociation. Strain JH1(T) exhibited 92 % DNA-DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5-1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37-40 °C and pH 6.5-7.0. The DNA G+C content of strain JH1(T) was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter, for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1(T) ( = KCTC 4102(T) = JCM 18376(T)).

Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle.

A strictly anaerobic, Gram-negative, non-spore-forming bacterium, designated GH1(T), was isolated from the rumen of Korean native cattle (HanWoo). Cells were straight to slightly curved rods (2.0-4.5 µm long) and were motile by peritrichous flagella. The isolate grew at 30-45 °C (optimum 40 °C), at pH 5.5-6.5 (optimum pH 6.0) and with up to 3.5% (w/v) NaCl. Strain GH1(T) produced acid from d-glucose, d-ribose and d-xylose, with butyric acid being the major end product. The genomic DNA G+C content was 54.6 mol%. Based on comparative 16S rRNA gene sequence analysis, strain GH1(T) was most closely related to Oscillibacter valericigenes Sjm18-20(T) (97.3% 16S rRNA gene sequence similarity). DNA-DNA hybridization between strain GH1(T) and O. valericigenes DSM 18026(T) showed 24% reassociation. The major fatty acids were iso-C13:0 (13.0%), iso-C15:0 (17.6%), anteiso-C15:0 (8.4%) and C14:0 (4.1%), and the cellular fatty acid methyl esters as dimethylacetals (DMAs) were C16:0 DMA (17.8%), iso-C15:0 DMA (15.2%) and C14:0 DMA (4.52%). The cell-wall peptidoglycan of strain GH1(T) contained meso-diaminopimelic acid and the major cell-wall sugar was galactose. Based on 16S rRNA gene sequence similarity, phylogenetic analysis, DNA G+C content, DNA-DNA relatedness and distinct phenotypic characteristics, strain GH1(T) is classified in the genus Oscillibacter as a member of a novel species, for which the name Oscillibacter ruminantium sp. nov. is proposed. The type strain is GH1(T) (=KCTC 15176(T)=NBRC 108824(T)=JCM 18333(T)).

Genome sequence of Methanobrevibacter sp. strain jh1, isolated from rumen of Korean native cattle.

ABSTRACT The Methanobrevibacter sp. strain JH1 was isolated from the rumen of Korean native cattle (HanWoo; Bos taurus coreanae). Here, we provide a 2.06-Mb draft genome sequence of strain JH1 that might provide more information about the lifestyle of rumen methanogens and about the genes and proteins that can be targeted to curb methane emissions.

Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea.

A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6T, was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C14:0 (17.8%), iso-C16:0 (15.8%), and iso-C12:0 (11.3%). The diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6T from the published Bacillus species. BL3-6T therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6T (=KCTC 13318T =JCM 15801T).

Paenibacillus pinihumi sp. nov., a cellulolytic bacterium isolated from the rhizosphere of Pinus densiflora

A novel cellulolytic bacterium, strain S23T, was isolated from the rhizosphere of the pine trees in Daejeon, Republic of Korea. This isolate was Gram-positive, strictly aerobic, rod-shaped, catalase-negative, oxidase-positive, motile by means of peritrichous flagella, and tested positive for alkaline phosphatase, esterase lipase, leucine arylamidase, α-galactosidase, and β-galactosidase activities. The DNA G+C content was 49.5 mol%. The main cellular fatty acids were anteiso-C15:0 (51.9%), iso-C16:0 (14.7%), and iso-C15:0 (13.2%). The major isoprenoid quinone was menaquinone 7 (MK-7). Diagnostic diamino acid in the cell-wall pepti-doglycan was meso-diaminopimelic acid. Comparative 16S rRNA gene sequence analysis showed that this strain clustered with Paenibacillus species. The 16S rRNA gene sequence similarity values between S23T and other Paenibacillus species were between 89.9% and 95.9%, and S23T was most closely related to Paenibacillus tarimensis SA-7-6T. On the basis of phylogenetic and phenotypic properties of strain S23T, the isolate is considered as a novel species belonging to the genus Paenibacillus. Therefore, the name, Paenibacillus pinihumi sp. nov., is proposed for the rhizosphere isolate; the type strain is S23T (=KCTC 13695T =KACC 14199T =JCM 16419T)

Genome Sequence of Oscillibacter ruminantium Strain GH1, Isolated from Rumen of Korean Native Cattle

Oscillibacter ruminantium strain GH1 was isolated from the rumen of Korean native cattle (HanWoo; Bos taurus coreanae). Here, we present the 3.07-Mb draft genome of this strain, which could reveal the presence of certain fiber-specific glycoside hydrolases and butyric acid-producing genes.

Bacillus solimangrovi sp. nov., isolated from mangrove soil

Two novel bacterial strains, GH2-4T and GH2-5, were isolated from mangrove soil near the seashore of Weno island in Chuuk state, Micronesia, and were characterized by a polyphasic approach. The two strains were strictly aerobic, Gram-staining-positive, motile, endospore-forming rods that were catalase- and oxidase-positive. Colonies were circular, convex, stringy and transparent yellowish (GH2-4T) or opaque whitish (GH2-5). The 16S rRNA gene sequences of the two isolates were identical. The most closely related strains in terms of 16S rRNA gene sequence similarity were Bacillus kochii WCC 4582T, B. horneckiae DSM 23495T, B. azotoformans LMG 9581T, B. cohnii DSM 6307T and B. halmapalus DSM 8723T (95.6, 95.4, 95.4, 95.2 and 95.2% similarity, respectively). The partial groEL sequence of strain GH2-4T was identical to that of strain GH2-5 and showed <85% similarity to those of the most closely related strains. The isolates grew at pH 5-12 (optimal growth at pH 9), at 10-40 °C (optimum 30-35 °C) and at 0-9% (w/v) NaCl (optimum 1-3% NaCl). The cell-wall peptidoglycan of strains GH2-4T and GH2-5 contained meso-diaminopimelic acid and cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 36 mol%, and DNA-DNA relatedness between the isolates and five related reference strains was 20-24%. Strain GH2-4T exhibited 81% DNA-DNA relatedness with strain GH2-5. The major cellular fatty acids of both strains were iso-C15:0, iso-C16:0, iso-C14:0 and anteiso-C15:0 and the predominant menaquinone was MK-7. On the basis of the evidence from this polyphasic study, strains GH2-4T and GH2-5 (=KCTC 33143=JCM 18995=DSM 27084) represent a novel species of the genus Bacillus, for which the name Bacillus solimangrovi sp. nov. is proposed; the type strain is GH2-4T (=KCTC 33142T=JCM 18994T=DSM 27083T).

Arthrobacter siderocapsulatus Dubinina and Zhdanov 1975AL is a later subjective synonym of Pseudomonas putida (Trevisan 1889) Migula 1895AL.

The taxonomic position of Arthrobacter siderocapsulatus Dubinina and Zhdanov 1975AL was investigated using 16S rDNA, fatty acid and phenotypic analyses. The type strain (NCIMB 11286T) showed 99.85% 16S rDNA similarity to the type strain of Pseudomonas putida. Phenotypic properties of the two strains were compared using API 20NE and BIOLOG kits. Identical reactions were recorded for all tests, except for assimilation of malonic acid. The two strains also showed almost identical cellular fatty acid profiles. On the basis of evidence presented in this and earlier studies, it is proposed that Arthrobacter siderocapsulatus is a later subjective synonym of Pseudomonas putida (Trevisan 1889) Migula 1895AL.

Sunxiuqinia dokdonensis sp. nov., Isolated from Deep Sub-Seafloor Sediment §

A novel facultatively anaerobic strain DH1T was isolated from deep sub-seafloor sediment at a depth of 900 m below the seafloor off Seo-do (the west part of Dokdo Island) in the East Sea of the Republic of Korea. The new strain was characterized using polyphasic approaches. The isolate was Gram-stain-negative, motile by gliding, non-spore-forming rods, oxidase-negative, and catalase-positive; and formed colonies of orange-red color. The NaCl range for growth was 0.5–7.0% (w/v) and no growth was observed in the absence of NaCl. The isolate grew optimally at 30°C, with 2% (w/v) NaCl and at pH 7. The cell-wall hydrolysates contained ribose as a major sugar. The DNA G+C content was 40.8 mol%. The closest related strains are Sunxiuqinia faeciviva JAM-BA0302T and Sunxiuqinia elliptica DQHS-4T (97.9 and 96.3% sequence similarity, respectively). The level of DNA-DNA relatedness between strain DH1T and S. faeciviva JAM-BA0302T was around 41% (but only 6% between DH1T and S. elliptica DQHS-4T). The major cellular fatty acids of the isolate were contained iso-C15:0 (25.9%), anteiso-C15:0 (16.7%), and summed feature 9 (comprising C16:0 3-OH and/or unknown fatty acid of dimethylacetal ECL 17.157; 13.2%). The predominant menaquinone was MK-7. On the basis of polyphasic evidence from this study, the isolate was considered to represent a novel species of the genus Sunxiuqinia, for which the name Sunxiuqinia dokdonensis sp. nov. is proposed; the type strain is DH1T (=KCTC 32503T =CGMCC 1.12676T =JCM 19380T).