• Korean Journal of Ecology and Environment
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• v.47 no.4
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• pp.342-349
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• 2014

This study was conducted to identify the bloom-forming Anabaena strains with two phenotypes (straight-type and coil-type) isolated from North Han River (Sambong-ri Joam-myun) using 16S rDNA sequence. The odor material producing potential was also examined using the geosmin-synthesizing gene cluster. Despite of striking morphological difference of the two stains, resembling A. circinalis and A. crassa species, the phylogenetic analysis using 16S rDNA identified the both strains as a single species of A. circinalis with high genetic similarity (98%~100%). Also, two Anabaena strains showed to possess the geosmin-synthesizing gene cluster, indicating that they are capable of producing the odor substance. This study is the first report that provides the direct evidence of geosmin production in the gene level by A. circinalis in Korea, and provides important basic information to identify the source alga of geosmin increase and its management in North Han River.

• The Plant Pathology Journal
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• v.17 no.6
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• pp.329-335
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• 2001

Yellowing disease of palms caused by phytoplasma is spreading in the Arabian Gulf region. Surveys were conducted to determine the occurrence of the disease. Electron and fluorescence microscopy, and polymerase chain reaction (PCR) techniques were used to detect the phytoplasma associated with the yellowing disease of ornamental palm Washingtonia sp. grown in Kuwait. An accumulation of phytoplasmal DNA was observed by fluorescence microscopy in phloem tissues of diseased palms. Electron microscopy showed that phytoplasma cells were primarily confined to the phloemsieve elements of tissue samples collected from infected mature palms in the field. The pathogen was identified on the basis of molecular analysis using universal and specific nested primers in PCR amplifications. Prokaryotic 16S rDNA gene was detected in amplified PCR products. Nested PCR resulted in DNA amplification of 1.2 kbp fragment. This is the first report of a phytoplasmal rDNA gene identified from the putative causal pathogen of yellows in ornamental palms in the Arabian Gulf region.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1743-1750
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• 2007

Two Gram-negative, nonmotile, coccobacilli, SW-$3^T$ and SW-$100^T$, were isolated from sea water of the Yellow Sea in Korea. Strains SW-$3^T$ and SW-$100^T$ contained ubiquinone-9 (Q-9) as the predominant respiratory lipoquinone and $C_{18:1}\;{\omega}9c$ and $C_{16:0}$ as the major fatty acids. The DNA G+C contents of strains SW-$3^T$ and SW- $100^T$ were 44.1 mol% and 41.9 mol%, respectively. A neighbor-joining tree based on l6S rRNA gene sequences showed that the two isolates fell within the evolutionary radiation enclosed by the genus Acinetobacter. Strains SW-$3^T$ and SW-$100^T$ exhibited a l6S rRNA gene similarity value of 95.7% and a mean DNA-DNA relatedness level of 9.2%. Strain SW-$3^T$ exhibited l6S rRNA gene sequence similarity levels of 93.5-96.9% to the validly described Acinetobacter species and fifteen Acinetobacter genomic species. Strain SW-$100^T$ exhibited l6S rRNA gene sequence similarity levels of less than 97.0% to the other Acinetobacter species except Acinetobacter towneri DSM $14962^T$ (98.0% similarity). Strains SW-$3^T$ and SW-$100^T$ exhibited mean levels of DNA-DNA relatedness of 7.3-l6.7% to the type strains of some phylogenetically related Acinetobacter species. On the basis of phenotypic, phylogenetic, and genetic data, strains SW-$3^T$ and SW-$100^T$ were classified in the genus Acinetobacter as two distinct novel species, for which the names Acinetobacter marinus sp. novo (type strain SW-$3^T$=KCTC $12259^T$=DSM $16312^T$) and Acinetobacter seohaensis sp. novo (type strain SW-$100^T$=KCTC $12260^T$=DSM $16313^T$) are proposed, respectively.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.643-650
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• 2000

A new aniline-utilizing microorganism, strain HY1 obtained from an orchard soil, was characterized by using the BIOLOG system, an analysis of the total cellular fatty acids, and a 16S rDNA sequence. Strain HY1 was identified as a Burkholderia species, and was designated Burkholderia sp. HY1. GC and HPLC analyses revealed that Burkholderia sp. HY1 was able to degrade aniline to produce catechol, which was subsequently converted to cis,cis-muconic acid through an ortho-ring fission pathway under aerobic conditions. Strain HY1 exhibited a drastic reduction in the rate of aniline degradation when glucose was added to the aniline media. However, the addition of peptone or nitrate to the aniline media dramatically accelerated the rate of aniline degradation. A fatty acid analysis showed that strain HY1 was able to produce lipids 16:0 2OH, and 11 methyl 18:1 ${\omega}7c$ approximately 3.7-, 2.2-, and 6-fold more, respectively, when grown on aniline media than when grown on TSA. An analysison the alignment of a 1,435 bp fragment. A phylogenetic analysis of the 16S rDNA sequence based on a 1,420 bp multi-alignment sowed of the 16s rDNA sequence revealed that strain HY1 was very closely related to Burkholderia graminis with 95% similarity based that strain HY1 was placed among three major clonal types of $\beta$-Proteobacteria, including Burkholderia graminis, Burkholderia phenazinium, and Burkholderia glathei. The sequence GAT(C or G)${\b{G}}$, which is highly conserved in several locations in the 16S rDNA gene among the major clonal type strains of $\beta$-Proteobacteria, was frequently replaced with GAT(C or G)${\b{A}}$ in the 16S rDNA sequence from strain HY1.

• Food Engineering Progress
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• v.14 no.1
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• pp.7-13
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• 2010

A thermophilic microorganism, which is able to hydrolyze starch, was isolated from soil and compost in Korea. It was Gram-positive, rod-shaped, catalase positive, nonmotile, glucose and mannitol fermentative, xylose oxidative, and spore forming microorganism. It also has an ability to hydrolyze casein and gelatin. The color of colony was yellowish white. The sequence of 16S rDNA of strain 2719 showed 99.5% sequence homology with the sequence of 16S rDNA of Bacillus thermoglucosidasius. On the basis of biochemical and physiological properties and phylogenetic analysis, the isolated strain was named as Bacillus thermoglucosidasius 2719.

• Journal of Animal Science and Technology
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• v.47 no.3
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• pp.465-474
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• 2005

A two-step broad-range PCR method detecting gram-negative bacteria at the level as low as 2 CFU was developed by using primers of GNFI and GNRI and then semi-nested primer of GNF2 and GNRI. The nucleotide sequences of the primers were determined based on l6S rRNA gene. The DNA fragments of 1173 bp and 169 bp were amplified in one-step PCRs with primer sets of GNFI-GNRI and GNF2-GNRl, respectively, using template DNA from seven strains of gram-negative bacteria including Escherichia coli, Enterobacter aerogenes, Klebsiella pneumoniae, Pseudomonas spp., and Acinetobacter baumaii but not from Achromobacter lyticus, Alca/igens faecalis, and five strains of gram-positive bacteria. DNA fragments of 180 bp were amplified from LTLT-pasteurized milk and UHf-pasteurized milk in the two-step PCR. The DNA fragments were amplified from LTLT-pasteurized milk which was added with Pseudomonas j/uorescens and subsequently heated at 65 $^{\circ}C$, 80 $^{\circ}C$, and 100 $^{\circ}C$ for 30 min but they were not amplified from the milk autoclaved at 121$^{\circ}C$ for 15 min. It was suggested in PCR that Pseudomonas fluorescens heated at 65 $^{\circ}C$ for 30 min in milk was more sensitive to DNase treatment than viable bacteria.

• Microbiology and Biotechnology Letters
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• v.35 no.4
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• pp.347-351
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• 2007

Potato scab is prevalent in all potato-growing areas of Jeju Island and causes economically significant losses. Streptomyces species are known as pathogens of potato scab. In this study, we analyzed the 16S rRNA sequences of Streptomyces spp, which are isolated from potato scab lesions in Jeju Island, and constructed 16S rRNA phylogenetic tree. All isolates were clearly differentiated into the genus Streptomyces, and the tree also showed that new scab-causing Streptomyces spp or not yet named species of Streptomyces are existed in Jeju Island, Korea.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.21-29
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• 2010

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from the 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

• Korean Journal of Microbiology
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• v.42 no.1
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• pp.19-25
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• 2006

This study was undertaken to develop PCR primers for the identification and detection of Streptococcus mutans (by)using species-specific forward and universal reverse primers. These primers targeted the variable regions of the 16S ribosomal RNA coding gene (rDNA). The primer specificity was tested against 11S. mutans strains and 10 different species (22 strains) of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of S. mutans ATCC $25175^T$. The data showed that species-specific amplicons were obtained from all the S. mutans strains tested, which was not observed in the other species. The direct and nested PCR could detect as little as 2 pg and 2 fg of the chromosomal DNA from S. mutans ATCC $25175^T$, respectively. This shows that the PCR primers are highly sensitive and applicable to the detection and identification of S. mutans.