A report on 24 unrecorded bacterial species of Korea isolated in 2016, belonging to the orders Rhizobiales and Sphingomonadales in the class Alphaproteobacteria

정요찬,조장천,임완택,전체옥,조기성,김승범,김원용,이순동,차창준 국립생물자원관 2018 Journal of species research Vol.7 No.1

In 2016, as a part of the research program ‘Survey of Korean Indigenous Species’, diverse environmental samples were collected from various sources of freshwater, seawater, soil, wetland, reclaimed land, sand, pine forest, plant root, ginseng field, solar saltern, and caves. Thousands of bacterial strains were isolated from the diverse samples and identified based on 16S rRNA gene sequence analyses. The present study, as a phylogenetic subset of the primary research program, reports 24 unrecorded bacterial species in Korea that belong to the orders Rhizobiales and Sphingomonadales in the class Alphaproteobacteria. Based on the high 16S rRNA gene sequence similarities (>98.8%) and formation of a robust phylogenetic clade with the closest type species, it was determined that each strain belonged to each independent and predefined bacterial species. There is no official report that these 24 bacterial species have been described in Korea; therefore, 10 species of nine genera in the order Rhizobiales and 14 species of seven genera in the order Sphingomonadales are described for unreported alphaproteobacterial species in Korea. Gram reaction, colony and cell morphology, biochemical properties, and isolation sources are also provided in the species description section.

Pontibacter jeungdoensis sp. nov., Isolated from a Solar Saltern in Korea

정요찬,김한을,이범일,강희영,장태용,권오섭,조기성 한국미생물학회 2013 The journal of microbiology Vol.51 No.4

A Gram-staining-negative, rod-shaped and red-pigmented bacterial strain, HMD3125T, was isolated from a solar saltern in Jeungdo, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3125T formed a lineage within the genus Pontibacter and was similar to Pontibacter salisaro (96.1%) and P. korlensis (95.3%). The major fatty acids of strain HMD3125T were summed feature 4 (comprising iso-C17:1 I and/or anteiso-C17:1 B; 30.4%),iso-C15:0 (20.4%) and iso-C17:0 3OH (17.2%). The polar lipid profile of HMD3125T consisted of the phosphatidylethanolamine,four unidentified polar lipids, unidentified phospholipid,unidentified aminolipid and unidentified aminophospholipid. Strain HMD3125T contained MK-7 as the predominant menaquinone and sym-homospermidine as the major polyamine. The DNA G+C content of strain HMD3125T was 45.6 mol%. Strain HMD3125T assigned as a novel species in the genus Pontibacter, for which the name Pontibacter jeungdoensis sp. nov. is proposed. The type strain is HMD3125T (=KCTC 23156T =CECT 7710T).

Pedobacter yonginense sp. nov., Isolated from a Mesotrophic Artificial Lake in Korea

정요찬,Hanuel Kim,Kiseong Joh 한국미생물학회 2010 The journal of microbiology Vol.48 No.4

A non-motile red-pigmented bacterium, designated strain HMD1002T, was isolated from an artificial lake located on the campus of Hankuk University of Foreign Studies, South Korea. The major fatty acids were iso-C15:0 (29.6%), Summed Feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH; 17.5%) and iso-C17:0 3-OH (12.5%). The major isoprenoid quinone was menaquinone-7 (MK-7). The DNA G+C content was 41.0 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1002T formed a lineage in the genus Pedobacer and was closely related to Pedobacer terrae (96.3%) and Pedobacer suwonensis (95.8%) in sequence similarity. On the basis of the evidence presented in this study, strain HMD1002T represents a novel species of the genus Pedobacter, for which the name Pedobacter yonginense sp.nov. is proposed. The type strain is HMD1002T (=KCTC 22721T =CECT 7544T).

GFP를 이용한 autoinducer를 검출할 수 있는 새로운 vector 개발

정요찬,조기성 한국외국어대학교 외국학종합연구센터 부설 기초과학연구소 2003 기초과학연구 Vol.15 No.-

Quorum sensing은 미생물에 있어서 하나의 통신을 말한다. 미생물은 각각에 맞는 autionducer를 생산하며, autionducer는 세포에 여러 signal로 작용하여 세포의 2차적인 변화를 일어나도록 한다. 본 실험은 protease 생산 균주로 알려져 있는 JW1가 autionducer를 만들어 내는 여러가지 증거를 제시하고, 새로운 sensing strain을 만들고자 하였다. 그 결과, protease 생산 균주는 NTL4 sensing strain으로 검출이 가능한 autoinducer를 생산 하는 것을 plate assay 와 thin layer chromatography를 통해 확인 하였다. 또 sensing strain으로부터 autoinducer에 의해 유도되는 gene인 tragene의 일부를 PCR을 통해 얻었다. 또 gene product와 GFP를 Fusion하여 새로운 vector를 제작하였다. 이 vector는 새로운 기존의 autoinducer 검출 sensor보다 더 우수한 효과를 갖는 것으로 추측된다.

다양한 중금속에서 mer operon의 발현

정요찬,김혜원,조기성 한국외국어대학교 기초과학연구소 2001 기초과학연구 Vol.11 No.-

mer gene product는 수은에 의해서 발현되어 수은의 독성을 제거하는 데 관련된 gene으로 알려져 있다. 우리는 mer gene에 reporter로써 GFP를 사용하여 수은과 여러 가지 중금속에 의해 mer gene의 발현을 알아 보고자 하여 새로운 plasmid를 제작하였다. 이 plasmid는 GFP가 mer operon의 promter뒤에 위치하여 수은에 의해 GFP가 유도될 수 있었다. 결국 plasmid는 수은이 존재하면 GFP를 발현하므로 수은의 존재 유무를 확인할 수 있었다. 또 여러가지 중금속 (Co2+, Cd2+, Zn2+ etc.)에서도 수은과 같이 GFP의 발현을 확인하였다. 그 중에서 다른 중금속에 비해 가장 많은 GFP를 발현한 중금속은 Cobalt였으며, 다른 중금속도 대부분 수은과 비교하면 같은 수준의 GFP를 발현함을 확인하였다. 이러한 결과는 분리한 mer operon은 수은에 의해서만 유도되는 것이 아니라 여러가지 중금속에 의해서도 조절 받고 있음을 나타내었다. mer gene reported that Hg2+ was removed mercury toxin effect by mer gene product. New plasmid for the determination of reducible mercury compound was constructed. It utilized GFP gene as a reporter under the control of the mercury-inducible mer promoter and merRTP sequence in mer operon. Using new plasmid, the GFP-based assay was evaluated for selectivity of the detection of mercury. Using new vector, GFP-based assay measured for other heavy metals (Co2+, Cd2+, Zn2+etc.). Expression level of mer operon was highest induction of cobalt than other heavy metals. These observations established that mer operon is regulated to variours heavy metals.

Pedobacter soyangensis sp. nov., Isolated from Lake Soyang in Korea

정요찬,강희영,김한을,이범일,권오섭,조기성 한국미생물학회 2014 The journal of microbiology Vol.52 No.1

Strain HME6451T was isolated from Lake Soyang in Korea. Phylogenetic tree based on 16S rRNA gene sequence showed that strain HME6451T formed a lineage within the genus Pedobacter. The strain HME6451T was closely related to Pedobacter daechungensis (95.4% sequence similarity), Pedobacter lentus (94.4%), and Pedobacter glucosidilyticus (93.8%). And strain HME6451T was a Gram-staining-negative, short rodshaped,strictly aerobic bacterium. The major fatty acids were iso-C15:0 (41.2%), summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c; 23.1%), and iso-C17:0-3OH (10.1%). The polar lipids of HME6451T were consisted of one phosphatidylethanolamine,one unidentified aminolipid, one unidentified phospholipid and four unidentified polar lipids. The DNA G+C content was 36.0 mol%. On the basis of the evidence presented in this study, strain HME6451T represent a novel species of the genus Pedobacter, for which the name Pedobacter soyangensis sp. nov., is proposed the type strain HME6451T (=KCTC 23467T =CECT 7865T).

A report of 22 unrecorded bacterial species in Korea, isolated from the North Han River basin in 2017

정요찬,조장천,장혜진,정일석,박미리 국립생물자원관 2018 Journal of species research Vol.7 No.3

Culturable bacterial diversity was investigated using freshwater and sediment samples collected from the North Han River basin in 2017, as a part of the research program ‘Survey of freshwater organisms and specimen collection’. Over a thousand bacterial strains were isolated from the samples and identified based on 16S rRNA gene sequences. Among the bacterial isolates, 22 strains showing higher than 98.7% sequence similarity with validly published bacterial species, but not reported in Korea, were classified as unrecorded species in Korea. The 22 bacterial strains were phylogenetically diverse and assigned to 6 classes, 11 orders, 15 families, and 21 different genera. At the generic level, the unreported species were affiliated with Flavobacterium of the class Flavobacteria, Flexibacter of the class Cytophagia, Blastomonas, Brevundimonas, Elstera, Rhizobium, Roseomonas, Sphingomonas, and Xanthobacter of the class Alphaproteobacteria, Albidiferax, Cupriavidus, Curvibacter, Ferribacterium, Hydrogenophaga, Iodobacter, Limnohabitans, Polaromonas, Undibacterium, and Variovorax of the class Betaproteobacteria, Pseudomonas of the class Gammaproteobacteria, and Arcobacter of the class Epsilonproteobacteria. The unreported bacterial species were further characterized by examining Gram reaction, colonial and cellular morphology, and biochemical properties. The detailed descriptions of 22 strains of the unreported bacterial species are also provided.

Pentachlorophenol 대사물과 세포내 거대분자물의 반응에 관한 연구

정요찬,윤병수,이영순,조명행 한국독성학회 1997 Toxicological Research Vol.13 No.3

Pentachlorophenol(PCP) which ks widely used in wood preservation, pulp and paper mills, has led to a substantial envirortmental contamination. To get the reliable data for the effective health risk assessment with PCP, covalent binding potential of PCP to cellular macromolecules and glutathione(GSH) was investigated after intraperitoneal administration of $^{14}C-PCP$ to rats. PCP metabolites were able to bind covalently to serum albumin and hepatic protein in a dose- and time-dependent manner. Hepatic protein adducts of PCP metabolites were increased as a function of cytochrome P-450 activities, whereas, albumin adducts significantly decreased. Covalent binding of PCP metabolites with DNA or hemoglobin was not observed. GSH levels in liver tissue decreased over 12hrs, however, the level was recovered after 48hrs. Tetrachloro-1,4-benzoquinone (1,4-TCBQ), one of the most reactive PCP metabolites, conjugated with GSH very rapidly. Base on our results, we could conclude that PCP metabolized to reactive electrophilic metabolites by cytochrome P-450 isoenzymes and conjugated rapidly with neighboring protein or nonprotein sulfhydryl before reacting with DNA or hemoglobin. We propose that albumin adducts and mercapturic acids of PCP metabolites can be used good biomarker of recent PCP exposure.

A report of 26 unrecorded bacterial species in Korea, isolated from urban streams of the Han River watershed in 2018

정요찬,장혜진,김명운,황주찬,송재호,조장천 국립생물자원관 2019 Journal of species research Vol.8 No.3

Owing to a distinct environmental regime and anthropogenic effects, freshwater bacterial communities of urban streams are considered to be different from those of large freshwater lakes and rivers. To obtain unrecorded, freshwater bacterial species in Korea, water and sediment samples were collected from various urban streams of the Han River watershed in 2018. After plating the freshwater samples on R2A agar, approximately 1000 bacterial strains were isolated from the samples as single colonies and identified using 16S rRNA gene sequence analyses. A total of 26 strains, with >98.7% 16S rRNA gene sequence similarity with validly published bacterial species but not reported in Korea, were determined to be unrecorded bacterial species in Korea. The unrecorded bacterial strains were phylogenetically diverse and belonged to four phyla, six classes, 12 orders, 16 families, and 21 genera. At the generic level, the unreported species were assigned to Nocardioides, Streptomyces, Microbacterium, Kitasatospora, Herbiconiux, Corynebacterium, and Microbacterium of the class Actinobacteria; Paenibacillus and Bacillus of the class Bacilli; Caulobacter, Methylobacterium, Novosphingobium, and Porphyrobacter of the class Alphaproteobacteria; Aquabacterium, Comamonas, Hydrogenophaga, Laribacter, Rivicola, Polynucleobacter, and Vogesella of the class Betaproteobacteria; Arcobacter of the class Epsilonproteobacteria; and Flavobacterium of the class Flavobacteriia. The details of the 26 unreported species, including Gram reaction, colony and cell morphology, biochemical properties, and phylogenetic position are also provided in the strain descriptions.

Pedobacter aquicola sp. nov., isolated from freshwater

정요찬,장혜진,박미리,송재호,조장천 한국미생물학회 2018 The journal of microbiology Vol.56 No.7

A non-motile, pink-pigmented bacterial strain designated IMCC25679T, was isolated from freshwater Lake Chungju of Korea. Phylogenetic trees based on 16S rRNA gene sequences showed that the strain IMCC25679T formed a lineage within the genus Pedobacter. The strain IMCC25679T was closely related to Pedobacter daechungensis Dae 13T (96.4% sequence similarity), Pedobacter rivuli HME8457T (95.3%) and Pedobacter lentus DS-40T (94.3%). The major fatty acids of IMCC- 25679T were iso-C15:0, iso-C16:0 and summed feature 3 (comprising C16:1 ω6c and/or C16:1 ω7c). The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine (PE), an unidentified sphingolipid (SL), an unidentified aminolipid (AL) and three unidentified polar lipids (PL). The DNA G + C content of IMCC25679T was 32.2 mol%. Based on the evidence presented in this study, the strain IMCC25679T represents a novel species within the genus Pedobacter, with the proposed name Pedobacter aquicola, sp. nov. The type strain is IMCC25679T (= KACC 19486T = NBRC113131T).