Journal of Microbiology

Duck-Chul Oh

6 Articles

Lysinibacillus jejuensis sp. nov., Isolated from Swinery Waste: Ji-Young Kim , So-Hyun Park , Duck-Chul Oh , Young-Ju Kim; J. Microbiol. 2013;51(6):872-876. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-2500-7

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A Gram-positive, endospore-forming, rod-shaped bacterium, designated strain N2-5T, was isolated from swinery waste collected in Jeju, Republic of Korea. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain N2-5T formed a phyletic group within the phylum Firmicutes with less than 97.0% similarities to members of the genus Lysinibacillus, its nearest phylogenetic neighbors. The highest levels of sequence similarity to the isolate were observed against Lysinibacillus xylanilyticus XDB9T (96.8%), Lysinibacillus macroides LMG 18474T (95.6%), and Lysinibacillus parviboronicapiens BAM-582 T (95.6%). The organism grew optimally at 30°C and pH 7 and in the presence of 1–3% (w/v) NaCl. Strain N2-5T was chemotaxonomically characterized by possessing menaquinone-7 (MK-7) as the major menaquinone, and iso-C15:0 (54.9%), iso-C17:1ω10c (12.0%), and C16:1ω7c alcohol (11.8%) as the predominant fatty acids. The genomic DNA G+C content of the novel strain was 43.3 mol% and the cell-wall peptidoglycan was type A4α. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Based on its phenotypic properties and phylogenetic data, strain N2-5T (=DSM 28310T =KCTC13837 T) represents a novel species in the genus Lysinibacillus, for which the name Lysinibacillus jejuensis sp. nov. is proposed.

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Winogradskyella jejuensis sp. nov., a Marine Bacterium Isolated from a Brown Alga Carpopeltis affinis: Ji-Young Kim , Duck-Chul Oh; J. Microbiol. 2012;50(5):888-892. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2447-0

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A Gram-negative, orange-pigmented, rod-shaped bacterium, designated strain CP32T was isolated from a brown alga Carpopeltis affinis collected on the coast of Jeju Island, Republic of Korea. The isolate grew at 10–37°C (optimum 25°C) and at pH 6.5–9.5 (optimum pH 7.0). The 16S rRNA gene sequence of the isolate showed much similarity with the type strains of recognized species of the genus Winogradskyella (94.0–96.6%). The most closely related species were Winogradskyella echinorum KMM 6211T, Winogradskyella ulvae KMM 6390T, Winogradskyella thalassocola KMM 3907T, Winogradskyella poriferorum UST030701-295T, and Winogradskyella eximia KMM 3944T. The major respiratory quinone was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:1 G (24.8%), iso-C15:0 (23.4%), and iso-C17:0 3-OH (11.6 %). The DNA G+C content was 33.3 mol%. The polar lipid profile was composed of phosphatidylethanolamine, two aminolipids, and five unknown lipids. On the basis of phenotypic features, and the result of 16S rRNA gene sequence analysis, strain CP32T (=KCTC 23835T =JCM 18454T) represents a novel species of the genus Winogradskyella, for which the name Winogradskyella jejuensis sp. nov. is proposed.

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Isolation and genome analysis of Winogradskyella algicola sp. nov., the dominant bacterial species associated with the green alga Dunaliella tertiolecta
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Winogradskyella eckloniae sp. nov., a marine bacterium isolated from the brown alga Ecklonia cava
Ji-Young Kim, So-Hyun Park, Ga-Young Seo, Young-Ju Kim, Duck-Chul Oh
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List of new names and new combinations previously effectively, but not validly, published
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Aquimarina litoralis sp. nov., Isolated from a Coastal Seawater: You-Sung Oh , Hyung-Yeel Kahng , Young Sun Lee , Byoung-Jun Yoon , Sang-Bin Lim , Jae Sung Jung , Duck-Chul Oh , Dong-Heon Lee; J. Microbiol. 2010;48(4):433-437. Published online August 20, 2010; DOI: https://doi.org/10.1007/s12275-010-0088-8

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A strictly aerobic, red-pigmented, non-motile, catalase- and oxidase-positive, Gram-staining-negative bacterium, designated strain CNURIC011T, was isolated from seawater off the coast of Jeju Island in Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain CNURIC011T belongs to the genus Aquimarina in the family Flavobacteriaceae. 16S rRNA gene sequence analysis revealed that the close relatives of the novel strain are Aquimarina latercula ATCC 23177T, Aquimarina marcrocephali JAMB N27T, Aquimarina intermedia KMM 6258T, Aquimarina muelleri KMM 6020T, and Aquimarina brevivitae SMK-19T, with sequence similarities of 97.6, 96.6, 96.0, 95.6, and 94.2%, respectively. DNA-DNA hybridization revealed that the level of relatedness between strain CNURIC011T and Aquimarina latercula ATCC 23177T (=KCTC 2912T) was 4.9%. The DNA G+C content was 35.8 mol% and the major respiratory quinone was MK-6. The major fatty acids were iso-C15:0 (14.9%), C15:0 (13.9%), iso-C17:0 3-OH (12.6%), iso-C15:1 G (7.3%), and iso-C17:1 ω9c (7.2%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC011T represents a novel species within the genus Aquimarina, for which the name Aquimarina litoralis sp. nov. is proposed. The type strain is CNURIC011T (=KCTC 22614T =JCM 15974T).

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Mei C. Ooi, Evan F. Goulden, Andrew J. Trotter, Gregory G. Smith, Andrew R. Bridle
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Robert A. Quinn, Suchandra Hazra, Roxanna Smolowitz, Andrei Y. Chistoserdov
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Gaetbulibacter jejuensis sp. nov., Isolated from Seawater: You-Sung Oh , Sang-Bin Lim , Hyung-Yeel Kahng , Byoung-Jun Yoon , Duck-Chul Oh , Jae-Ho Joa , Dong-Heon Lee; J. Microbiol. 2010;48(3):307-311. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9232-8

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A novel marine bacterium, designated strain CNURIC014T was isolated from coastal seawater of Jeju Island in Korea. Strain CNURIC014T formed yellow colonies on marine agar 2216 and the cells were Gram-negative, non-motile, strictly aerobic, rod-shaped. The temperature, pH and NaCl ranges for growth were 15-37°C, pH 6.0-9.0 and 1.0-7.0% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CNURIC014T was most closely related to Gaetbulibacter marinus and Gaetbulibacter saemankumensis, with a sequence similarity of 95.1% and 94.6%, respectively. The DNA G+C content of the strain was 33.1 mol% and the major respiratory quinone was menaquinone-6. The major cellular fatty acids were iso-C15:1 (22.8%), iso-C15:0 (18.8%), summed feature 3 (iso-C15:0 2-OH/C16:1 ω7c, 12.9%) and iso-C17:0 3-OH (11.5%). On the basis of phenotypic, phylogenetic, and genotypic data, strain CNURIC014T represents a novel species within the genus Geatbulibacter, for which the name Gaetbulibacter jejuensis sp. nov. is proposed. The type strain is CNURIC014T (=KCTC 22615T =JCM 15976T).

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Purification and Characterization of a Catalase from Photosynthetic Bacterium Rhodospirillum rubrum S1 Grown under Anaerobic Conditions: Yoon-Suk Kang , Dong-Heon Lee , Byoung-Jun Yoon , Duck-Chul Oh; J. Microbiol. 2006;44(2):185-191.; DOI: https://doi.org/2366 [pii]

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Abstract PDF: The photosynthetic bacterium, Rhodospirillum rubrum S1, when grown under anaerobic conditions, generated three different types of catalases. In this study, we purified and characterized the highest molecular weight catalase from the three catalases. The total specific catalase activity of the crude cell extracts was 88 U/mg. After the completion of the final purification step, the specific activity of the purified catalase was 1,256 U/mg. The purified catalase evidenced an estimated molecular mass of 318 kDa, consisting of four identical subunits, each of 79 kDa. The purified enzyme exhibited an apparent Km value of 30.4 mM and a Vmax of 2,564 U against hydrogen peroxide. The enzyme also exhibited a broad optimal pH (5.0~9.0), and remained stable over a broad temperature range (20°C~60°C). It maintained 90% activity against organic solvents (ethanol/chloroform) known hydroperoxidase inhibitors, and exhibited no detectable peroxidase activity. The catalase activity of the purified enzyme was reduced to 19% of full activity as the result of the administration of 10 mM 3-amino-1,2,4-triazole, a heme-containing catalase inhibitor. Sodium cyanide, sodium azide, and hydroxylamine, all of which are known heme protein inhibitors, inhibited catalase activity by 50% at concentrations of 11.5 μM, 0.52 μM, and 0.11 μM, respectively. In accordance with these findings, the enzyme was identified as a type of monofunctional catalase.

Analysis of Catalases from Photosynthetic Bacterium Rhodospirillum rubrum S1: Hee-Kyoung Lim , Young-Mi Kim , Dong-Heon Lee , Hyung-Yeel Kahng , Duck-Chul Oh; J. Microbiol. 2001;39(3):168-176.

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Abstract PDF: Five different types of catalases from photosynthetic bacterium Rhodospirillum rubrum S1 grown aerobically in the dark were found in this study, and designated Cat1 (350 kDa), Cat2 (323 kDa), Cat3 (266 kDa), Cat4 (246 kDa), and Cat5 (238 kDa). Analysis of native PAGE revealed that Cat2, Cat3, and Cat4 were also produced in the cells anaerobically grown in the light. It is notable that only Cat2 was expressed much more strongly in response to the anaerobic condition. Enzyme activity staining demonstrated that Cat3 and Cat4 had bifunctional catalase-peroxidase activities, while Cat1, Cat2, and Cat5 were typical monofunctional catalases. S1 cells grown aerobically in the presence of malate as the sole source of carbon exhibited an apparent catalase Km value of 10 mM and a Vmax of about 705 U/mg protein at late stationary growth phase. The catalase activity of S1 cells grown in the anaerobic environment exhibited a much lower Vmax of about 109 U/mg protein at late logarithmic growth phase. The catalytic activity was stable in the broad range of temperatures (30 C-60 C), and pH (6.0-10.0). R. rubrum S1 was much more resistant to H_2 O_2 in the stationary growth phase than in the exponential growth phase regardless of growth conditions. Cells of stationary growth phase treated with 15 mM H 2 O 2 for 1 h showed 3-fold higher catalase activities than the untreated cells. In addition, L-glutamate induced an 80-fold increase in total catalase activity of R. rubrum S1 compared with malic acid. Through fraction analyses of S1 cells, Cat2, Cat3, Cat4 and Cat5 were found in both cytoplasm and periplasm, while Cat1 was localized only in the cytoplasm.

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