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

Joung, Yochan,Jang, Hye-Jin,Kim, Myeong Woon,Hwang, Juchan,Song, Jaeho,Cho, Jang-Cheon The National Institute of Biological Resources 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.

Flavobacterium aquariorum sp. nov., isolated from freshwater of the North Han River

Yochan Joung,Hye-jin Jang,송재호,Jang-Cheon Cho 한국미생물학회 2019 The journal of microbiology Vol.57 No.5

A non-motile, yellow-pigmented bacterial strain, designated IMCC34762T, was isolated from a freshwater sample collected from Lake Cheongpyeong in Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC- 34762T formed a lineage within the genus Flavobacterium and was most closely related to F. pectinovorum DSM 6368T (98.3% sequence similarity), followed by F. piscis CCUG 60099T (98.3%), F. branchiicola 59B-3-09T (98.2%), and F. saccharophilum DSM 1811T (98.2%). The average nucleotide identity and the genome-to-genome distance between strain IMCC34762T and the closely related strains were 61–62% and 26–27%, respectively, indicating that IMCC34762T is a novel species of the genus Flavobacterium. The major fatty acids (> 5%) of strain IMCC34762T were summed feature 3 (C16:1 ω6c and/or C16:1 ω7c, 17.3%), iso-C15:0 (15.0%), iso-C15:0 G (9.0%), C15:0 ω6c (7.4%), iso-C15:0 (7.4%), and iso-C16:0 (5.3%). The major respiratory quinone and polyamine were MK-6 and sym-homospermidine, respectively. The major polar lipids were phosphatidylethanolamine, an unidentified aminophospholipid, and an unidentified lipid. The DNA G+C content of strain IMCC34762T was 34.4 mol%. Based on the taxonomic data presented in this study, strain IMCC34762T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium aquariorum, sp. nov. is proposed. The type strain is IMCC34762T (= KACC 19725T = NBRC 113425T).

<i>Cyclobacterium jeungdonense</i> sp. nov., isolated from a solar saltern

Joung, Yochan,Kim, Haneul,Kim, Seung Bum,Joh, Kiseong International Union of Microbiological Societies 2014 International journal of systematic and evolutiona Vol.64 No.1

<P>A horseshoe-shaped, orange-pigmented strain, HMD3055<SUP>T</SUP>, was isolated from a solar saltern in Korea. Strain HMD3055<SUP>T</SUP> grew optimally at 25 °C and with a salt concentration of 3–5 %. The predominant quinone of strain HMD3055<SUP>T</SUP> was menaquinone (MK)-7. The major fatty acids of strain HMD3055<SUP>T</SUP> were iso-C<SUB>15 : 0</SUB>, summed feature 3 (comprising C<SUB>16 : 1</SUB>ω6<I>c</I> and/or C<SUB>16 : 1</SUB>ω7<I>c</I>) and summed feature 9 (iso-C<SUB>17 : 1</SUB>ω9c and/or 10-methyl C<SUB>16 : 0</SUB>). The polar lipids of HMD3055<SUP>T</SUP> consisted of phosphatidylethanolamine, one unidentified phospholipid, one unidentified aminolipid and five unidentified polar lipids. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3055<SUP>T</SUP> formed a distinct lineage within the genus <I>Cyclobacterium</I>. Strain HMD3055<SUP>T</SUP> was closely related to <I>Cyclobacterium lianum</I> (95.8 %), <I>Cyclobacterium lianum</I> HY9<SUP>T</SUP> (95.8 %), <I>C. marinum</I> DSM 745<SUP>T</SUP> (93.2 %) and <I>C. amurskyense</I> KMM6143<SUP>T</SUP> (92.6 %) form a distinct lineage from other members of the genus <I>Cyclobacterium</I>. The DNA G+C content of strain HMD3055<SUP>T</SUP> was 45.6 mol%. On the basis of the evidence presented in this study, it is concluded that strain HMD3055<SUP>T</SUP> represents a novel species of the genus <I>Cyclobacterium</I>, for which the name <I>Cyclobacterium</I> <I>jeungdonense</I> sp. nov. is proposed. The type strain is HMD3055<SUP>T</SUP> ( = KCTC 23150<SUP>T</SUP> = CECT 7706<SUP>T</SUP>).</P>

Pontibacter salisaro sp. nov., Isolated from a Clay Tablet Solar Saltern in Korea

Yochan Joung,Haneul Kim,안태석,조기성 한국미생물학회 2011 The journal of microbiology Vol.49 No.2

A Gram-negative, aerobic, rod-shaped, and red-pigmented bacterial strain, HMC5104^T, was isolated from a solar saltern, found in Jeungdo, Republic of Korea (34°59′47′′N 126°10′02′′E). The major fatty acids were summed feature 4 (comprising iso-C_(17:1) I and/or anteiso-C_(17:1) B; 37.2%), iso-C_(15:0) (20.4%), and iso-C_(17:0)3OH (15.3%). The DNA G+C content was 46.0 mol%. The major isoprenoid quinone was menaquinone-7(MK-7). A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMC5104^T formed a lineage within the genus Pontibacter, and was closely related to Pontibacter korlensis (95.9%), P. roseus (94.9%), and P. actiniarum (94.3%). Similarities to all other Pontibacter species were between 95.9-93.9%. On the basis of the evidence presented in this study, strain HMC5104^T represents a novel species of the genus Pontibacter, for which the name Pontibacter salisaro sp. nov. is proposed. The type strain is HMC5104^T (=KCTC 22712^T =NBRC 105731^T).

Soonwooa buanensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater

Joung, Yochan,Song, Jaeho,Lee, Kiyoung,Oh, Hyun-Myung,Joh, Kiseong,Cho, Jang-Cheon Microbiology Society 2010 International journal of systematic and evolutiona Vol.60 No.9

<P>A Gram-negative, non-motile, non-gliding, strictly aerobic, pale yellow colony-forming, rod-shaped bacterial strain, designated HM0024<SUP>T</SUP>, was isolated from coastal seawater of the Yellow Sea and subjected to a polyphasic taxonomy study. Based on 16S rRNA gene sequence similarities, strain HM0024<SUP>T</SUP> was most closely related to <I>Chryseobacterium balustinum</I> LMG 8329<SUP>T</SUP> (94.4 %), <I>Chryseobacterium scophthalmum</I> LMG 13028<SUP>T</SUP> (94.4 %), <I>Chryseobacterium piscium</I> LMG 23089<SUP>T</SUP> (94.3 %) and <I>Elizabethkingia meningoseptica</I> ATCC 13253<SUP>T</SUP> (94.0 %) and shared less than 92 % sequence similarity with other members of the family <I>Flavobacteriaceae</I>. Phylogenetic analyses showed that strain HM0024<SUP>T</SUP> formed an independent phyletic line of descent within the family <I>Flavobacteriaceae</I>. The DNA G+C content of the strain was 29.6 mol% and its major cellular fatty acids (>10 %) were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 1<I>ω</I>7<I>c</I> and summed feature 3 (C16 : 1<I>ω</I>6<I>c</I> and/or C16 : 1<I>ω</I>7<I>c</I>). The major isoprenoid quinone was MK-6 and the major polar lipids were phosphatidylethanolamine and several aminolipids. Strain HM0024<SUP>T</SUP> was differentiated from phylogenetically related members of the family by having lower DNA G+C content, larger proportions of summed feature 3, anteiso-C15 : 0 and iso-C16 : 0 3-OH and particular phenotypic characteristics. On the basis of phenotypic and phylogenetic data, strain HM0024<SUP>T</SUP> is classified as a representative of a novel genus and species, for which the name <I>Soonwooa buanensis</I> gen. nov., sp. nov. is proposed. The type strain of <I>Soonwooa buanensis</I> is HM0024<SUP>T</SUP> (=KCTC 22689<SUP>T</SUP> =CECT 7503<SUP>T</SUP>).</P>

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

Joung, Yochan,Park, Miri,Jang, Hye-Jin,Jung, Ilsuk,Cho, Jang-Cheon The National Institute of Biological Resources 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.

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

Yochan Joung,Haneul Kim,장태용,안태석,조기성 한국미생물학회 2011 The journal of microbiology Vol.49 No.6

A non-motile, Gram- stain-negative, yellow pigmented, rod-shaped bacterium, strain HMD3159^T, was isolated from a solar saltern in Korea. The major fatty acids were iso-C_(15:0) (26.3%), iso-C_(17:0) 3OH (12.1%), iso-C_(16:0) (12.0%), summed feature 3 (comprising C_(16:1) ω7c and/or C_(16:1) ω6c; 11.0%) and summed feature 9 (iso-C_(17:1) ω9c and/or 10-methyl C_(16:0); 10.0%). The major respiratory quinone was MK-6. The DNA G+C content was 40.9 mol%. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD3159^T formed a lineage within the genus Gramella and closely related to Gramella gaetbulicola (95.5% sequence similarity), Gramella portivictoriae (94.9%), Gramella echinicola (94.6%), and Gramella marina (93.6%). On the basis of the evidence presented in this study, strain HMD3159T represents a novel species of the genus Gramella, for which the name Gramella jeungdoensis sp. nov., is proposed. The type strain is HMD3159^T (=KCTC 32123^T =CECT 7683^T).

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

Joung, Yochan,Cha, Chang-Jun,Im, Wan-Taek,Jeon, Che Ok,Joh, Kiseong,Kim, Seung-Bum,Kim, Wonyong,Lee, Soon Dong,Cho, Jang-Cheon The National Institute of Biological Resources 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.

Flavobacterium paronense sp. nov., isolated from freshwater of an artificial vegetated island

Joung, Yochan,Kang, Heeyoung,Kim, Haneul,Kim, Tae-Su,Han, Ji-Hye,Kim, Seung Bum,Ahn, Tae-Seok,Joh, Kiseong Microbiology Society 2016 International journal of systematic and evolutiona Vol.66 No.-

<P>A Gram-stain-negative, motile by gliding, yellow-pigmented bacterial strain, designated KNUS1(T), was isolated from Lake Paro in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain KNUS1(T) formed a distinct lineage within the genus Flavobacterium. Strain KNUS1(T) was closely related to Flavobacterium cheonhonense ARSA-15(T) (96.8 %16S rRNA gene sequence similarity), Flavobacterium pectinovorum DSM 6368(T) (96.3 %) and Flavobacterium dankookense ARSA-19(T) (96.1 %). The major fatty acids of strain KNUS1(T) were iso-C-15 : 0, and iso-C-15 : 1 G. The major polyamine was sym-homospermidine. The major polar lipids of strain KNUS1(T) were phosphatidylethanolamine, five unidentified aminolipids and three unidentified polar lipids. The major respiratory'quinone was menaquinone 6 (MK-6). The DNA G+C content of strain KNUS1(T) was 34.2 mol%. On the basis of the evidence presented in this study, strain KNUS1(T) represents a novel species of the genus Flavobacterium, for which the name Flavobacterium paronense sp. nov. is proposed. The type strain is KNUS1(T) (=KACC 17692(T)=CECT 8460(T)).</P>

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.