• Proceedings of the Microbiological Society of Korea Conference
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• 2003.05a
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• pp.26-33
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• 2003

We isolated and identifed culturable Arctic bacteria that have inhabited around Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 16S rDNA sequences. Out of total 227 strains, 198 strains were overlapped or unidentified, and 43 bacteria were finally identified: 31 strains belonged to Pseudomonas, 7 strains Arthrobacter, two Flavobacterium sp., an Achromobacter sp., a Pedobacter sp., and a Psychrobacter sp. For isolation of diverse bacteria, we need more effective transport method than 3M petri-films, which were used for convenience of transportation that was restricted by volume. We also need to use other culture media than nutrient media. We expect these Arctic bacteria can be used for screening to develop new antibiotics or industrial enzymes that are active at low temperature.

• Korean Journal of Microbiology
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• v.47 no.1
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• pp.56-65
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• 2011

Culture-independent microscopic observations and 16S rDNA analyses were applied to describe the bacterial community inherent to the biofilm structure of the RABC (Rotating Activated Bacillus Contactors) process for swine butchery wastewater treatment. The ratios of Gram-positive bacterial counts to total bacterial counts of the RABC process were significantly increased in the last aeration tank as well as returned sludge, while those of the existing A2O (Anaerobic-Anoxic-Oxic) process maintained constant from aeration tanks to returned sludge. Totally nine phyla were recovered by 16S rDNA analysis, two of which were major groups: the Proteobacteria (64.1%) and the Actinobacteria (18.4%). The third major group was the endospore-forming Firmicutes (5.4%). The remaining six minor groups are the Bacteroidetes (3.3%), the Chlorobi (2.2%), the Nitrospirae (1.1%), the Chlorofleix (1.1%), the Acidobacteria (1.1%), and the Fusobacteria (1.1%). The ratio of endospore-forming bacteria was 19.4%, which was composed of the members of the Firmicutes phylum (5.4%) and the Intrasporangiaceae family (14.0%) of the Actinobacteria phylum. Nitrifying and denitrifying related- and phosphorus accumulating related-sequences were composed of 6.5% and 5.4% of total community, respectively, these could mean the high capacity of the RABC process to remove odor compounds and reduce eutrophication by efficient removing inorganic nutrients.

• Korean Journal of Microbiology
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• v.51 no.1
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• pp.86-95
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• 2015

To study the halobacterial diversity at the rhizospheric soil of coastal plant native to Dokdo islands, several host plant were selected and its rhizospheric soil was sampled. Soil sample was diluted serially and pure isolation was done by sub-culture using marine agar media. 26 halophilic strains cultivable at the marine medium containig concentration of 9.0% sodium chloride were selected among total 161 isolates. Their partial 16S rRNA gene sequences extracted from genomic DNA were analyzed and partially identified. Furthermore, to identify their genetic relationship, phylogenetic tree was deduced. Total 26 strains were belongs to Firmicutes (30.8%), Gamma proteobacteria (53.8%), Bacteroidetes (7.7%), Alpha proteobacteria (7.7%), and Actinobacteria (7.7%). These results showed the specific difference from previous researches which has been reported the microbial flora of soil or sea water around the Dokdo islands. Furthermore, 4 among 26 halophilic strains grew at above 12.0% NaCl concentrated marine broth, and 2 strains Idiomarina abyssalis LM4H23 and Halomonas huangheensis AS4H13 grew at 15.0% concentration. These halophilic strains thought to overcoming the severe stress like high salt concentration or variation derived from Dokdo-specific climate and might have unknown, specific relationship with their host coastal plant native to Dokdo islands.

• Korean Journal of Microbiology
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• v.45 no.1
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• pp.26-31
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• 2009

This study was aimed at the analysis of prokaryote communities in Korean traditional fermented food, jeotgal, and isolation of a novel strain from jeotgal by using culture-dependent and molecular biological approaches. Seventeen kinds of jeotgal were selected on the basis of its origins and sources. The samples were inoculated on 12 kinds of media. 308 isolates were selected randomly by morphological features, and its 16S rRNA gene sequences was amplified by PCR technique with bacteria and archaea specific primers (8F, 21F, and 1492R). The 16S rRNA gene sequences were compared with those in EzTaxon and GenBank databases. DNA-DNA hybridization was performed to identify a novel strain. As a result, the majority of the isolates were lactic acid bacteria (Leuconostoc, Weisella, Lactococcus, Lactobacillus, Carnobacterium, Marinilactibacillus), Bacillus, Pseudomonas, Micrococcus, Brevibacterium, Microbacterium and Kocuria in 17 kinds of jeotgal. The strains belonging to Salinicoccus, Halomonas, Cobetia, Lentibacillus, Paracoccus, and Psychrobacter were isolated as minor ones. Fourteen novel species were identified based on phylogenetic analysis.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.12a
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• pp.55-55
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• 2020

뫼제비꽃(Viola selkirkii)의 엽록체 DNA 염기서열을 차세대염기서열분석법(NGS)을 이용하여 분석하였다. 재료는 강원도 화천군 일산과 제주도 한라산의 2개체를 사용하였다. 분석결과, 염기서열의 길이는 일산의 뫼제비꽃이 156,774 bp (GC content: 36.30%), 한라산의 뫼제비꽃이 157,451 bp(GC content: 36.30%)로 한라산 개체가 길게 분석되었다. 구간별로 LSC(Large single copy)지역은 한라산 개체(85,950 bp)가 일산 개체(85,930 bp)보다 20 bp 길었으며, SSC(Small single copy)지역은 한라산 개체(17,261 bp)보다 일산 개체가 17,982 bp로 길게 분석되었다. IR(Inverted repeat)지역은 한라산 개체가 27,120 bp로 일산 개체(26,431 bp)보다 길게 분석되었다. 이러한 염기서열 길이의 차이는 종내 개체 간 빈번하게 발생하는 현상으로 IGS와 intron 구간에서 확인 된 단순반복서열의 일부 누락과 IR지역 내의 수축과 확장에 의한 것으로 판단된다. 뫼제비꽃 2개체의 엽록체 게놈을 구성하는 유전자 수는 총 111개로 동일하였으며, protein coding gene 77개, tRNA(transfer RNA) gene 30개, 그리고 rRNA (ribosomal RNA) gene 4개로 구성되어 있었다. 이는 기 발표된 엽록체 DNA 전체 염기서열이 밝혀진 제비꽃속 (Viola) 종류들과 동일한 결과이다.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.6
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• pp.888-895
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• 2015

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and subsequent sub-cloning and sequencing were used in this study to analyze the molecular phylogenetic diversity and spatial distribution of bacterial communities in different spatial locations during the cooling stage of composted swine manure. Total microbial DNA was extracted, and bacterial near full-length 16S rRNA genes were subsequently amplified, cloned, RFLP-screened, and sequenced. A total of 420 positive clones were classified by RFLP and near-full-length 16S rDNA sequences. Approximately 48 operational taxonomic units (OTUs) were found among 139 positive clones from the superstratum sample; 26 among 149 were from the middle-level sample and 35 among 132 were from the substrate sample. Thermobifida fusca was common in the superstratum layer of the pile. Some Bacillus spp. were remarkable in the middle-level layer, and Clostridium sp. was dominant in the substrate layer. Among 109 OTUs, 99 displayed homology with those in the GenBank database. Ten OTUs were not closely related to any known species. The superstratum sample had the highest microbial diversity, and different and distinct bacterial communities were detected in the three different layers. This study demonstrated the spatial characteristics of the microbial community distribution in the cooling stage of swine manure compost.

• Journal of Microbiology and Biotechnology
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• v.31 no.9
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• pp.1210-1217
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• 2021

Two gram-negative, catalase-positive, strictly aerobic, and white colony-forming bacteria, strains H242^T and B156^T, were isolated from soil in South Korea. Cells of strain H242^T were oxidase-positive and non-motile short rods, while those of strain B156^T were oxidase-negative and long non-motile rods. Ubiquinone-8 was identified as the sole isoprenoid quinone in both strains. C_16:0, cyclo-C_17:0, andsummed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol were identified in both strains as the major cellular fatty acids and polar lipids, respectively. The DNA G+C contents of strains H242^T and B156^T were 69.4 mol% and 69.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA and 92 concatenated core gene sequences revealed that strains H242^T and B156^T formed distinct phylogenic lineages from other Ramlibacter type strains. The DNA-DNA hybridization (DDH) value between strains H242^T and B156^T was 24.6%. Strains H242^T and B156^T were most closely related to Ramlibacter ginsenosidimutans BXN5-27^T and Ramlibacter monticola G-3-2^T with 98.4% and 98.6% 16S rRNA gene sequence similarities, respectively. Digital DDH values between strain H242^T and R. ginsenosidimutans and between strain B156^T and R. monticola were 23.5% and 26.1%, respectively. Phenotypic, chemotaxonomic, and molecular analyses indicated that strains H242^T and B156^T represent two novel species of the genus Ramlibacter, for which the names Ramlibacter terrae sp. nov. and Ramlibacter montanisoli sp. nov., respectively, are proposed. The type strains of R. terrae and R. montanisoli are H242^T (=KACC 21667^T=JCM 33922^T) and B156^T (=KACC 21665^T=JCM 33920^T), respectively.

• The Korean Journal of Malacology
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• v.28 no.4
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• pp.377-384
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• 2012

The importance of biological resources has been gradually increasing, and mollusks have been utilized as main fishery resources in terrestrial ecosystems. But little is known about genomic and transcriptional analysis in mollusks. This is the first report on the transcriptomic profile of Meretrix lusoria. In this study, we constructed cDNA library and determined 542 of distinct EST sequences composed of 284 singletons and 95 contigs. At first, we identified 180 of EST sequences that have significant hits on protein sequences of the exclusive Mollusks database through BLASTX program and 343 of EST sequences that have significant hits on NCBI NR database. We also found that 211 of putative sequences through local BLAST (blastx, E < e-10) search against KOG database were classified into 16 functional categories. Some kinds of immune response related genes encoding allograft inflammatory factor 1 (AIF-1), B-cell translocation gene 1 (BTG1), C-type lectin A, thioester-containing protein and 26S proteasome regulatory complex were identified. To determine phylogenetic relationship, we identified partial sequences of four genes (COX1, COX2, 12S rRNA and NADH dehydrogenase) that significantly matched with the mitochondrial genomes of 3 species-Ml (Meretrix lusoria), Mp (Meretrix petechialis) and Mm (Meretrix meretrix). As a result, we found that there was a little bit of a difference between sequences of Korean isolates and other known isolates. This study will be useful to develop breeding technology and might also be helpful to establish a classification system.

• Journal of Animal Science and Technology
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• v.46 no.6
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• pp.909-916
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• 2004

CCAAT/enhancer binding proteins(C/EBP) are a group of transcription factors expressed during preadipocyte differentiation. In the C/EBPs, C/EBPa plays an important role in lipid deposition and adipocyte differentiation. In this studies, we report the identification, characterization, and expression of a Hanwoo CIEBP$\alpha$ The Hanwoo C/EBP$\alpha$DNA includes a 1059 bp open reading frame encoding a protein of 353 amino acids. The CIEBPa amino acid sequences of the Hanwoo show strong conservation with the corresponding sequences reported in other species. The distribution of C/EBP$\alpha$ mRNA in various tissues of Hanwoo aged 12 months were investigated using Northern blotting analysis. The highest expression was detected in adipose tissue and more lower expression was detected in colon and lung. We also identified expression of C/EBPa mRNA in Hanwoo sirloin and adipose tissue aged 12, 26, and 30 months by real-time RT-PCR. The higest expression were detected at 26 months in the sirloin and at 12 and 26 months in the adipose tissue.

• Journal of Mushroom
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• v.14 no.1
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• pp.21-26
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• 2016

The mannanase-producing bacteria, designated YJ17, was isolated from spent mushroom (Flammulina velutipes) substrates. The isolate YJ17 was a facultative anaerobic and was grown at temperatures ranging from $20^{\circ}C$ to $50^{\circ}C$ with an optimal temperature of $40^{\circ}C$. The DNA G+C content of the YJ17 was 44 mol%. The major fatty acids were anteiso-15:0 (38.9%), 17:0 (7.6%), and iso-15:0 (36.5%). The 16S rRNA gene sequence similarity between the isolate YJ17 and other Bacillus strains was from 98% to 99%. In the phylogenetic analysis based on these sequences, the isolate YJ17 and Bacillus amyloliquefaciens clustered within a group together and separated from other species of Bacillus. Based on the physiological and molecular properties, the isolate YJ17 was classified within the genus Bacillus as B. amyloliquefaciens YJ17. The optimal pH and temperature for mannanase activity of B. amyloliquefaciens YJ17 were pH 7.0 and $50^{\circ}C$, respectively.