• Journal of Microbiology and Biotechnology
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• v.19 no.11
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• pp.1281-1287
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• 2009

The distribution pattern of the phylum Acidobacteria, a previously uncultured bacterial group, was investigated by molecular ecological analyses of global soil samples collected from pristine ecosystems across five continents. Acidobacterial 16S rDNAs were observed in almost all soil samples, and members of acidobacterial primer group A were detected in all samples that harbored the phylum Acidobacteria. Other primer groups, Y, G, and O, showed limited distribution patterns. We further divided the primer groups into acidobacterial subdivisions (class-level). Subdivisional distribution patterns were determined by comparing the observed T-RFs with theoretical T-RFs predicted by in silico digestion of acidobacterial 16S rDNAs. Consistent with the PCR results obtained with subgroup-specific primers, T-RFLP analyses showed that acidobacterial subdivision 1 belonging to primer group A was present in the majority of the soil samples. This study revealed that the phylum Acidobacteria could be globally distributed. At the subdivisional level, acidobacterial subdivision 1 might be the most widely distributed group in this phylum, indicating that members of subdivision 1 might be adapted to various soil environments, and members belonging to other subdivisions might be restricted to certain geographic regions or habitats.

• Journal of agriculture & life science
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• v.50 no.1
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• pp.117-124
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• 2016

Researches on soil microbial community are increasing to assess ecosystem responses to anthropogenic disturbances and to provide an indicator of ecosystem recovery. Microbial communities are able to respond more rapidly to environmental changes than plants and therefore they may provide an early indication of the ecosystem recovery trajectory. This study was conducted using 16S rRNA gene pyrosequencing of soil samples to compare soil bacterial community composition between artificially covered soils of the Baedudaegan ridgeline and their adjacent forest soils in two restoration project sites, Ihwaryeong and Yuksimnyeong, which were completed in 2012 and 2013, respectively. Richness of the Phylum level was 29.3 in Ihwaryeong and 32.3 in Yuksimnyeong. Significant difference in the richness between artificial restored soils and adjacent forest soils(p<0.01) was observed, however no significant difference was observed for site location and soil depth. Acidobacteria(37.3%) and Proteobacteria(31.1%) were more abundant than any other phylum in collected soil samples. Also, we found the significant difference in the relative abundance of the two abundant phyla between artificially restored soils and their adjacent forest soils (Proteobacteria, 38.1% in restored soils vs 24.2% in adjacent forest soils, p<0.01; Acidobacteria, 55.4% in restored soils vs 19.2% in adjacent forest soils, p<0.001). The results support the previous researches indicating that soil bacterial community composition is affected by nutritional status of soils and that Acidobacteria is also strongly influenced by pH, thus favoring soils with lower pH. This study could be utilized to monitor and evaluate restoration success of forest soil environment quantitatively.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.201-209
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• 2007

The CFDA (6-carboxyfluorescein diacetate) direct viable count method and plate count (PC) method using conventional nutrient broth (NB) medium and $10^{-2}$ diluted NB (DNB) medium were applied to samples collected from Mt. Yongdoo In Andong, in an effect to determine the number of living bacteria pine mushroom forest soil. The number of living bacteria determined via plate count in NB medium comprised $5{\sim}8%$ of the CFDA direct viable count, and the bacteria in the DNB medium comprised $40{\sim}47%$. This result indicated that viable but nonculturable (VBNC) bacteria existed in the pine mushroom forest soil at a high percentage. The phylogenetic characteristics of the VBNC bacterial populations in the samples of pine mushroom (Tricholoma matsutake) forest soil were analyzed via the direct extraction of DNA and 16S rDNA-ARDRA. The 115 clones from pine mushroom forest soil were clustered into 31 different RFLP phylotypes by ARDRA. Based on the 16S rDNA sequences, the 31 ARDRA clusters were classified into 6 phylogenetic groups: ${\alpha}-,\;{\beta}-,\;{\gamma}-Proteobacteria$, Acidobacteria, Actinobacteria and Firmicutes. Among these bacterial populations, approximately 85% were classified as members of phylum Acidobacteria. The Acidobacteria phylum was shown to exist abundantly in the pine mushroom forest soil.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.210-216
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• 2007

The principal objective of this study was to analyze 16S rDNA-ARDRA of the humus forest soil via an improved manual method and an ISOIL kit on the basis of the UPGMA clustering of the 16S rDNA combined profile, 44 ARDRA clusters of 76 clones via the ISOIL kit method and 45 ARDRA clusters of 136 clones via the improved manual method. On the basis of the 16S rDNA sequences, 44 clones from the ARDRA clusters by the ISOIL kit were classified into 3 phyla : ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria and Actinobacteria. Using the improved manual method, the specimens were classified into 6 phyla : the ${\alpha}-,\;{\beta}-,\;{\gamma}-,\;{\delta}-Proteobacteria$, Acidobacteria, Bacteroides, Verrucomicrobia, Planctomycetes and Gemmatomonadetes. As a result, the modified manual method indicated greater phylogenetic diversity than was detected by the ISOIL kit. Approximately 40 percent of the total clones were identified as ${\alpha}-Proteobacteria$ and 30 percent of the total clones were ${\gamma}-Proteobacteria$ and assigned to dominant phylogenetic groups using the ISOIL kit. Using the modified manual method, 41 percent of the total clones were identified as Acidobacteria and 28 percent of total clones were identified as ${\alpha}-proteobacteria$ and assigned to dominant phylogenetic groups.

• Journal of Microbiology and Biotechnology
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• v.32 no.10
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• pp.1275-1283
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• 2022

Understanding soil microbial community structure in the Arctic is essential for predicting the impact of climate change on interactions between organisms living in polar environments. The hypothesis of the present study was that soil microbial communities and soil chemical characteristics would vary depending on their associated plant species and local environments in Arctic mature soils. We analyzed soil bacterial communities and soil chemical characteristics from soil without vegetation (bare soil) and rhizosphere soil of three Arctic plants (Cassiope tetragona [L.] D. Don, Dryas octopetala L. and Silene acaulis [L.] Jacq.) in different local environments (coal-mined site and seashore-adjacent site). We did not observe any clear differences in microbial community structure in samples belonging to different plant rhizospheres; however, samples from different environmental sites had distinct microbial community structure. The samples from coal-mined site had a relatively higher abundance of Bacteroidetes and Firmicutes. On the other hand, Acidobacteria was more prevalent in seashore-adjacent samples. The relative abundance of Proteobacteria and Acidobacteria decreased toward higher soil pH, whereas that of Bacteroidetes and Firmicutes was positively correlated with soil pH. Our results suggest that soil bacterial community dissimilarity can be driven by spatial heterogeneity in deglaciated mature soil. Furthermore, these results indicate that soil microbial composition and relative abundance are more affected by soil pH, an abiotic factor, than plant species, a biotic factor.

• Proceedings of the Korea Water Resources Association Conference
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• 2022.05a
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• pp.139-139
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• 2022

Nature-based solutions (NBS) involved conservation or rehabilitation of natural ecosystems or the creation of natural processes in modified or artificial ecosystems to mimic natural processes for the improved management of water (UN-Water, 2018). This study investigated the relationship between microbial presence and survival to the pollutant treatment performance of seven different stormwater NBS managing urban stormwater runoff. In this study, seven different stormwater nature-based solution (NBS) was investigated to identify the relationship of microbial community to the pollutant removal performance of stormwater NBS. Based on this study, Proteobacteria was found to be the most dominant microorganism for all stormwater NBS and IS followed by Acidobacteria and Actinobacteria. Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, WS3, and AF234118_p were found to have high positive correlation to most pollutant removal efficiency of different stormwater NBS (r-value: 0.62 to 0.68). Using Proteobacteria and Acidobacteria count in stormwater NBS, equations predicting pollutant removal performance were also developed and may be used in minimizing the cost for stormevent monitoring to identify the pollutant removal performance of stormwater NBS.

• Journal of Microbiology
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• v.45 no.6
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• pp.479-484
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• 2007

Bacterial communities at 10 cm, 100 cm, and 200 cm depths in a 100-year-old lead-zinc tailing heap were evaluated by constructing 16S rRNA gene libraries. In total, 98 operational taxonomic units (OTUs) were identified from 193 clones at a 3% sequence difference level. The OTU number and species richness decreased with the depth. Species composition was significantly different between the three libraries. Fifty-seven percent of the examined clones were Acidobacteria and 27% belonged to Proteobacteria. Other sequences included Chloroflexi, Firmicutes, Chlamydiae, Actinobacteria, Gemmatimonadetes, Nitrospira, and three unclassified OTUs. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria were mainly distributed in the rhizosphere of naturally colonizing plants; however, Deltaproteobacteria, Acidobacteria, and Chloroflexi tended to inhabit the deeper tailings (below the 100 cm-depth).

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.61-61
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• 2020

본 연구는 우리나라 임상 중에서 침엽수림과 침활혼효림으로 구성된 산양삼 시험포지를 선정하고, 임상별 토양의 토양세균군집을 분석하여 산양삼 생육특성과의 상관관계 구명하고자 수행하였다. 산양삼 시험포지는 침염수림으로 구성된 충주 산양삼 종자공급단지와 침활혼효림으로 구성된 함양 산양삼 종자공급단지를 선정하여 각각 조성하였다. 토양세균군집 분석은 pyrosequencing analysis (Illumina platform)를 이용하였고, 토양세균군집과 생육특성 간의 상관관계는 Pearson's correlation을 이용하여 분석하였다. 임상별 시험포지의 토양세균은 두 시험포지 모두 Acidobacteria가 우점종으로 확인되었다. 주좌표 분석을 통해 임상별 산양삼 시험포지에서 우점하는 토양세균 군집을 확인한 결과, 먼저 토양세균 군집은 임상별 시험포지에 따라 군집화를 이루는 것으로 확인되었고, Pearson's 상관관계 분석 결과, 토양세균 군집의 상대적 빈도수는 수종 비율에 따라 상이한 상관관계를 보이는 것으로 확인되었다. 이 중에서 Proteobacteria, Alphaproteobacteria, Actinobacteria_class, Phycisphaerae는 침엽수의 비율과 유의적인 정의 상관관계를 보였고, Nitrospirae, Chlamydiae, Planctomycetia, Acidobacteria_6는 활엽수의 비율과 유의적인 정의 상관관계를 보이는 것으로 나타났다. 또한 임상별 산양삼 시험포지의 토양세균 군집과 산양삼 생육특성 간의 상관관계를 분석한 결과, Nitrospirae, Chlorobi, Planctomycetia, Acidobacteria_6가 산양삼의 생육과 유의적인 정의 상관관계를 보였다. 본 연구결과를 바탕으로 다양한 산림환경에서 토양세균군집과 산양삼 생육특성 간의 상관관계를 명확하게 구명할 수 있다면 향후 산양삼의 최적 재배지를 선정하는데 있어 도움을 줄 수 있을 것으로 사료된다.

• Journal of Life Science
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• v.25 no.3
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• pp.323-328
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• 2015

The study of microbial diversity and richness in soil samples from a volcanic island named Ulleungdo, located east of South Korea. The soil bacterial communities on the Ulleungdo were analyzed using pyrosequencing method based on 16S rRNA gene. There were 1,613 operational taxonomic units (OUT) form soil sample. From results of a BLASTN search against the EzTaxon-e database, the validated reads (obtained after sequence preprocessing) were almost all classified at the phylum level. Proteobacteria was the most dominant phylum with 48.28%, followed by acidobacteria (26.30%), actionbacteria (6.89%), Chloroflexi (4.58), Planctomycetes (4.56%), Nitrospirae (1.83%), Bacteroidetes (1.51%), Verrucomicrobia (1.48%), and Gemmatimonadetes (1.11%). α-proteobacteria was the most dominant class with 36.07% followed by Acidobacteria_c (10.65%), Solibacteres (10.64%), δ-proteobacteria (4.42%), γ-proteobacteria (4.29%), Planctomycetacia (4.16%), Actinobacteria_c (4.00%), Betaproteobacteria (3.50%), EU686603_c (2.97%), Ktedonobacteria (2.91%), Acidimicrobiia (1.32%), Verrucomicrobiae (1.27%), Gemmatimonadetes_c (1.11%), Sphingobacteria (1.09%), and GU444092_c (1.06%). Bradyrhizobiaceae was the most dominant family with 22.83% followed by Acidobacteriaceae (10.62%), EU445199_f (5.72%), Planctomycetaceae (4.03%), Solibacteraceae (3.63%), FM209092_f (3.58%), Steroidobacter_f (2.81%), EU686603_f (2.73%), Hyphomicrobiaceae (2.33%), Ktedonobacteraceae (1.75%), AF498716_f (1.46%), Rhizomicrobium_f (1.03%), and Mycobacteriaceae (1.01%). Differences in the diversity of bacterial communities have more to do with geography than the impact on environmental factors and also the type of vegetation seems to affect the diversity of bacterial communities.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.103-110
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• 2006

T-RFLP analysis and clone sequencing analysis based on bacterial 16S rDNA were conducted to assess bacterial community structure and diversity in Zoysia japonica soil treated with liquid fertilizer containing amino acids(LFcAA) after spray with herbicide. The results of T-RFLP (terminal restriction fragment length poly-morphism) analysis using restriction enzyme Hae III showed that the T-RFs of various size appeared evenly in the 32 clones of KD3 and 38 clones of KD4 respectively that had been treated with liquid fertilizer containing amino acid(LFcAA) compared to 23 clones of KD2 hat had not been treated with LFcAA. The microbial com- munity structure in KD2 appeared less diverse than those in KD3 and KD4. Analysis of partial sequences for 110 clones from KDI (control), KD2 (non-treated), KD3 (LFcAA 1X), KD4 (LFcAA 2X), respectively, revealed that most bacteria were related with uncultured bacteria in a 16S rDNA sequence similarity range of 91-99% through blast search. Otherwise, the other clones were members of proteobacteria, Acidobacteria, Act-inobacteria, Sphingobacteria and Planctomyces groups. Especially in KD4, members of Alpha Proteobacteria, Rhizobiales, Sphigomonadales, Caulobacterales, Gamma Proteobacteria, the genus Pseudomonas, Betapro-teobacteria, Nitrosomonadales and genus Nitrosospira appeared to be dominant. In addition, Acidobacteria group, Actinobacteria group, Planctomycetacia and Sphingobacteria were also shown. The microbial com-munity structure in Z. japonica soil sprayed with herbicide was affected by LFcAA.