• Korean Journal of Microbiology
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• v.52 no.1
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• pp.59-64
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• 2016

In this study, a pyrosequencing was performed and analyzed to verify the phylogenetic diversity of actinomycetes in the bamboo (Sasa borealis) soil as a base study to obtain the genetic resources of actinomycetes. It was found that the rhizosphere soil had much various distribution in bacterial communities showing a diversity of 8.15 with 2,868 OTUs, while the litter layer showed a diversity of 7.55 with 2,588 OTUs. The bacterial community in the bamboo soil was composed of 35 phyla and the predominant phyla were Proteobacteria (51-60%), Bacteroidetes (16-20%), Acidobacteria (4-16%) and Actinobacteria (4-14%). In particular, Actinobacteria including Micromonosporaceae and Streptomycetaceae had a diverse distribution of actinomycetes within the six orders, 35 families and 121 genera, and it was characterized that about 83% of actinomycetes within Actinomycetales belonged to the 28 families. Among the dominant actinobacterial populations, Micromonosporaceae, Pseudonocardiaceae and Streptomycetaceae were representative family groups in the bamboo soils.

• Journal of Microbiology and Biotechnology
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• v.17 no.5
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• pp.753-760
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• 2007

The diversity of Paenibacillus species was assessed in the rhizospheres of four cultivars of sorghum sown in Cerrado soil amended with two levels of nitrogen fertilizer(12 and 120 kg/ha). Two cultivars(IS 5322-C and IS 6320) demanded the higher amount of nitrogen to grow, whereas the other two(FBS 8701-9 and IPA 1011) did not. Using the DNA extracted from the rhizospheres, a Paenibacillus-specific PCR system based on the RNA polymerase gene(rpoB) was chosen for the molecular analyses. The resulting PCR products were separated into community fingerprints by DGGE and the results showed a clear distinction between cultivars. In addition, clone libraries were generated from the rpoB fragments of two cultivars(IPA 1011 and IS 5322-C) using both fertilization conditions, and 318 selected clones were sequenced. Analyzed sequences were grouped into 14 Paenibacillus species. A greater diversity of Paenibacillus species was observed in cultivar IPA 1011 compared with cultivar IS 5322-C. Moreover, statistical analyses of the sequences showed that the bacterial diversity was more influenced by cultivar type than nitrogen fertilization, corroborating the DGGE results. Thus, the sorghum cultivar type was the overriding determinative factor that influenced the community structures of the Paenibacillus communities in the habitats investigated.

• Korean Journal of Microbiology
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• v.51 no.2
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• pp.133-140
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• 2015

We have examined the correlation between the physicochemical and microbiological environment variables for the different layers of oak forest soil in Mt. Gyeryong, Korea. The result shows that there is a high correlation in the environment variables between the soil parameters of the fermented (F) layer and humus (H) layer. In particular, the pH level in the F layer shows a high correlation with C and N, while the various organic acids of the H layer turns out to be closely correlated with soil bacteria density. As we evaluated phylogenetic characteristics of bacterial populations by DGGE analysis with DNA extracted. Total of 175 bands including 43 bands from litter (L) layer, 42 bands from F layer, 43 bands from H layer and 47 bands from rhizosphere (A) layer were selected as the major DGGE band of oak forest soil. Based on the 16S rRNA gene sequences, 175 DGGE bands were classified into 32 orders in 7 phylum. The heat map was analyzed in order to compare the quantity of the base sequences of each order and based on the clustering of the different layers of oak forest soil, the result confirms that the F layer and H layer belong to a different cluster from that of L layer and A layer. Furthermore, it also showed that approximately 50% of the total microbial population in different layers is ${\alpha}$-proteobacteria, which indicates that they belong to the dominant system group. In particular, Rhizobiales, Burkholderiales and Actinobacteriales were observed in all the seasons and layers of oak forest soil, which confirms that they are the indigenous soil bacterial community in oak forest soil.

• Korean Journal of Environmental Biology
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• v.25 no.4
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• pp.356-362
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• 2007

The rhizobacterial diversity associated with 9 native plant species inhabiting coastal sand dunes in Tae-an area, Chungnam Province, was studied using the denaturing gradient gel electrophoresis (DGGE) fingerprinting analysis over three times from October 2003 to March 2004. One dominant band commonly occurred in all of the rhizosphere samples, which was identified as that of Lysobacter enzymogenes. The other common bands included those derived from species of Pseudomonas and Bacillus. It was notable that L. enzymogenes was dominant in all of the 9 plant species and such dominance was consistent throughout the whole sampling period, which confirms the previous study by Lee et al. (2006a). The Bacillus bands were detected in all of the three samplings, and those of Pseudomonas were notable in the samples of December 2003. By the DGGE analysis alone, the significance of Lysobacter to the sand dune plants is not clear. However, considering their presence in healthy plants and the dominance in all plant species, Lysobacter may have positive roles in the survival or growth of the plants in sand dune area.

• Weed & Turfgrass Science
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• v.4 no.2
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• pp.124-128
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• 2015

Large patch, caused by Rhizoctonia solani AG2-2 IV, is a soil-born disease that is the most important of warm season turfgrass such as zoysia and Bermuda grass. This study was conducted to analysis of the soil microbial community structure on large patch. Center of the large patch (CLC), edge (CLE) and healthy (CLH) part of microbial communities were examined using metagenomics in Phylum level. Distribution trends of the rhizosphere microorganisms were similar to the order Proteobacteria, Acidobacteria, Chloroflexi, Firmicutes, Planctomycetes, Gemmatimonadetes, Nitrospira, Cyanobactria and Verrucomicrobia in soil collections. Contrastively Actinobacteria was more 56% abundant in healthy part soil (16%) than in the center (9.28%) or edge (10.84%) parts. Taxonomic distributions were compared among the CLC, CLE and CLH, total 6,948 OTUs were detected in the CLC, 6,505 OTUs for the CLE and 5,537 OTUs were detected in the CLE. Distributions of Actinobacteria OTUs were appeared 615 OTUs in the CLC, 709 OTUs in the CLE and 891 OTUs in the CLH. Among Actinobacteria, 382 OTUs were overlapped in the all soils. Not matched OTUs of CLH (286 OTUs) was detected 23 times higher than CLC (91 OTUs) and CLE (126 OTUs).

• Korean Journal of Soil Science and Fertilizer
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• v.37 no.1
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• pp.46-53
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• 2004

In this study, we compared the levels of methylotrophic bacterial community diversity in the leaf, stem, grain, root and rhizosphere soil sainples of four rice cultivars collected from three regions of Korea. Thirty five pigmented and five non-pigmented isolates showing characteristic growth on methanul were obtained. When phylotypes were defined by performing numerical analysis of 42 characteristics, four distinct clusters were formed. While two clusters, I and IV diverged on the basis of nitrate and nitrite reduction, other two clusters, comprising only pink pigmented colonies, diverged on the basis of cellulase activity. Out of the two reference strains used in the analysis, Methyhbacterium extorquens AM1 diverged from all the clusters and M. fujisawaense KACC 10744 grouped under cluster III. All the isolates were positive for urease, oxidase, catalase and pectinase activity and negative for indole production, MR and VP test, $H_2S$ production, starch, and casein hydrolysis. No clusters were found to possess thermotolerant isolates, as no growth of the isolates was observed at $45^{\circ}C$. Two strains in cluster I were found to possess gelatin hydrolysis and methane utilizing properties respectively. Most of the isolates in all the four clusters utilized monosaccliarides, disaccharide and polyols as carbon source. Six isolates showed considerable nitrogenase activity ranging from 86.2 to $809.9nmol\;C_2H_4\;h^{-1}\;mg^{-1}$ protein.