• Korean Journal of Microbiology
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• v.49 no.3
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• pp.282-285
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• 2013

Microbial diversities in the 300 m and 500 m deep seawaters near Goseong, Gangwon Province (South Korea), were investigated. Pyrosequencing of 16S rRNA genes of marine microbes resulted in 19,474 reads from the 300 m deep seawaters, which consisted of Alphaproteobacteria (57.41%) and Gammaproteobacteria (38.85%), and 82,806 reads from the 500 m deep seawaters, which consisted of Gammaproteobacteria (99.64%) mostly. Rhodobacterales (57.31%) were dominant in the 300 m deep seawaters, but Alteromonadales (45.65%) and Oceanospirillales (34.61%) were dominant in the 500 m deep seawaters. On the bases of operational taxonomic units and diversity indexes (Shannon and Simpson), biodiversity of marine bacteria in the 500 m deep seawaters was shown to be higher than that in the 300 m deep seawaters.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2005.11a
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• pp.523-526
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• 2005

계통발생학적 분석기법은 서열의 유사성을 비교하여 이들의 유연관계를 알아내는 것으로, 각각의 관계를 시각적으로 표현하는 것이 매우 중요하다. 일반적으로 2차원 계통수를 사용한다. 그러나 2차원으로 시각화했을 때 서로 유사성이 높은 OTU(Operational Taxonomic Unit)들을 서로 멀리 떨어뜨려 놓는 경우도 생기게 된다. 이 논문에서는 이러한 점을 보완하고자 3차원 공간에 OTU들을 배치시키기 위한 2단계 좌표 배치 기법을 제안한다. 단계는 유클리디안 거리를 3차원 좌표로 변환하는 것이다. 1단계 방법은 서열의 비교 순서에 영향을 받기 때문에 2단계를 통해 유전자 알고리즘 기법을 적용하여 보다 적절한 좌표를 찾는다.

• Parasites, Hosts and Diseases
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• v.29 no.1
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• pp.55-66
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• 1991

A numerical taxonomy was studied on a group of heterophyid trematodes and analysis was made on the following species: Metagonimus yokogawai (3 OTU, Operational Taxonomic Unit) , Metagcnimus Miyata Type (3 OTU), Metagonimus takahashii (2 OTU), Heterophyes dispar (2 OTU), Heterephyes heterophyes (1 OTU), Heterophyes nocens (2 OTV), Heterophyopsis continua (1 OTU), Pygidiopsis summa (3 OTU), Stellantchasmus falcatus (2 OTU) and Stictodora sari (2 OTU). Twenty-six morphological characters were measured and their values were expressed as relative ratios. Similarity and correlation matrix among each individuals were calculated. Clustering analysis by Ward's method and factor analysis were performed using the SAS (Statistical Analysis System) package. As a results, the groups belonging to the genus of Metegenimus were divided into three phonons (Awetegonimus yokogawai, Metegcnimus Miyata Type, M. takahashii) , and Metagonimus Miyata Type was classified as the level of subspecies of M. takahashii. The groups belonging to the genus Heterophyes were clearly divided into three phonons (Heterophyes dispar, H. heterephyes, H. nocens), and H. nccens was classified as not a subspecies level of H. heterophyes but a distinct species. Other species were classified as distinct phonons. From these results, the appllcr lion of numerical taxonomy on trematode classification is considered to be a great aid to determine the limit of taxa.

• Journal of Applied Biological Chemistry
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• v.59 no.4
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• pp.299-304
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• 2016

When used for amplicon sequencing, Illumina platforms produce more than hundreds of sequence artefacts, which affects operational taxonomic units based analyses such as differential abundance and network analyses. Nevertheless it has become a major tool for fecal microbial community analysis. In addition, results from sequence-based fecal microbial community analysis vary depending on conditions of samples (i.e., freshness, time of storage and quantity). We investigated if freeze-drying samples could improve quality of sequence data. Our results showed reduced number of possible artefacts while maintaining overall microbial community structure. Therefore, freeze-drying feces prior to DNA extraction is recommended for Illumina-based microbial community analysis.

• Journal of Microbiology and Biotechnology
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• v.26 no.5
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• pp.867-875
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• 2016

Archaea substantially contribute to global geochemical cycling and energy cycling and are impacted by land-use change. However, the response of archaeal communities to a change from upland field to paddy field has been poorly characterized. Here, soil samples were collected at two depths (0-20 cm and 20-40 cm) from one upland field and six paddy fields that were established on former upland fields at different times (1, 5, 10, 20, 30, and 40 years before the study). Barcoded pyrosequencing was employed to assess the archaeal communities from the samples at taxonomic resolutions from phylum to genus levels. The total archaeal operational taxonomic unit (OTU) richness showed a significant positive correlation with the land-use change duration. Two phyla, Euryarchaeota and Crenarchaeota, were recorded throughout the study. Both the relative abundance and OTU richness of Euryarchaeota increased at both depths but increased more steadily at the subsurface rather than at the surface. However, these data of Crenarchaeota were the opposite. Additionally, the archaeal composition exhibited a significant relationship with C/N ratios, total phosphorus, soil pH, Olsen phosphorus, and the land-use change duration at several taxonomic resolutions. Our results emphasize that after a change from upland fields to paddy fields, the archaeal diversity and composition changed, and the duration is an important factor in addition to the soil chemical properties.

• Korean Journal of Microbiology
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• v.52 no.3
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• pp.365-374
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• 2016

In high-latitude regions, temperature has risen ($0.6^{\circ}C$ per decade) and this leads to the increase in microbial degradability against soil organic carbon (SOC). Furthermore, the decomposed SOC is converted into green-house gases ($CO_2$ and $CH_4$) and their release could further increase the rate of climate change. Thus, understanding the microbial diversity and their functions linked with SOC degradation in soil-thawing model is necessary. In this study, we divided tundra soil from Council, Alaska into two depth regions (30-40 cm and 50-60 cm of depth, designated as SPF and PF, respectively) and incubated that for 108 days at $0^{\circ}C$. A total of 111,804 reads were obtained through a pyrosequencing-based metagenomic study during the microcosm experiments, and 574-1,128 of bacterial operational taxonomic units (OTUs) and 30-57 of archaeal OTUs were observed. Taxonomic analysis showed that the distribution of bacterial taxa was significantly different between two samples. In detail, the relative abundance of phyla Actinobacteria and Firmicutes largely increased in SPF and PF soil, respectively, while phyla Crenarchaeota was increased in both soil samples. Weight measurement and gel permeation chromatography of the SOC extracts demonstrated that polymerization of humic acids, main component of SOC, occurred during the microcosm experiments. Taken together our results indicate that these bacterial and archaeal phyla could play a key function in SOC degradation and utilization in cold tundra soil.

• Journal of Life Science
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• v.14 no.3
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• pp.400-405
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• 2004

Morphological characteristics of Kalopanox pictus Nakai were studied to examine population differentiation of this species. Based on a phenogram of using 23 morphological characteristics, differentiation of regions were distinct. Collections of 138 specimens from nine populations served as operational taxonomic unit (OTU's) were examined for phenotypic similarity and morphological variation using clustering (Ward's minimum variance method) and principal component analysis (PCA). The first three principal components were responsible for 77.0% of the total variance. Principal component 1 explained 52% of the total variance and was contributed to by the number of palmately parted, the number of pinnately lobed, and width between two lateral lobe apex.

• Journal of Conservation Science
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• v.37 no.4
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• pp.357-361
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• 2021

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple's soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple's soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

• Journal of Environmental Science International
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• v.30 no.12
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• pp.1015-1025
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• 2021

Our research work aimed to evaluate cover crop effects of winter rye on soil characteristics, soil conservation, and yield productivities on potato fields with 15% slope during a fallowed period. There were two controls of bared field without any cultivation and conventional potato cultivation without winter rye. Potato cultivation increased soil pH, organic matter, available phosphate, and exchangeable cation regardless of cover crop cultivation. Sub-soil, particularly, all components of soil chemical properties showed higher value in winter rye cultivation than conventional cultivation. Higher soil density was observed on cover crop cultivation than conventional cultivation resulting from root residues of the cover crop both topsoil and subsoil. Cover crop residues positively affected plant growth and reduced the amount of soil erosion by holding the soil. Although severe soil erosion was seen in conventional cultivation, winter rye cultivation declined soil erosion by 47% during the fallow period on potato slope fields. Distinct soil bacterial communities were detected among treatments and some OTU(Operational Taxonomic Unit)s showed significantly higher abundance in winter rye treatment. Total yield and commercial rate demonstrated no significant differences while higher tuber phosphate, K⁺, and Mg²⁺ contents were observed in winter rye cultivation.

• The Plant Pathology Journal
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• v.37 no.4
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• pp.396-403
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• 2021

Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.