• Korean Journal of Soil Science and Fertilizer
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• v.33 no.4
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• pp.266-274
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• 2000

Understanding of microbial community structure in soil-root system is necessary to use beneficial soil and rhizosphere microbes for improvement of crop production and biocontrol. The knowledge of behavior and function of microbes in soil-root system plays a key role for the application of beneficial inocula. Because the majority of the intact bacteria in soil are unable to grow on nutrient media, both culturable and nonculturable bacteria have to be studied together. In our study, culture-independent survey of bacterial community in the soil-root system of red pepper fields was conducted by the sequence analysis of three universal clone libraries of genes which code for small-subunit rRNA (rDNA). Universal small subunit rRNA primers were used to amplify DNA extracted from each sample and PCR products were cloned into pGEM-T. Out of 27 clones sequenced, 25 clones were from domain bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Within the domain bacteria, several kingdoms were represented : the Proteobacteria (16 clones). Cytophyga-Flexibacter-Bacteroides group (2 clones). the high G+C content gram-positive group(1 clone) and 4 unknown clones.

• Applied Biological Chemistry
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• v.50 no.4
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• pp.262-267
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• 2007

To access the natural product antibiotics produced by uncultured microorganisms, six cosmid libraries of DNA extracted directly from soil samples (environmental DNA, eDNA) were constructed and screened for the production of antibacterial active molecules. Of the approximately 60,000 clones screened, one antibacterial clone (YS92B) was detected. Ethyl acetate extracts of clone YS92B showed antibacterial activity against various pathogenic bacteria (Listeria monocytogenes, Bacillus subtilis, Pseudomonas syringae, Xanthomonas campestris pv. oryzae, Staphylococcus epidemis). Active constituents from cultures of YS92B were isolated and purified using a bioassay-guided fractionation against B. subtilis through a series of procedures (ethyl acetate extraction, Sephadex LH20 column chromatography, High Performance Liquid Chromatography). NMR (Nuclear Magnetic Resonance) spectral analysis of a major antibacterial active YS92B-VII indicated that it is a lauric acid linked to tyrosine. This report describes the characterization of antibacterially active long chain N-acyl derivatives of tyrosine that are produced by eDNA clones hosted in Escherichia coli from Korean soils.

• Korean Journal of Environmental Agriculture
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• v.26 no.4
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• pp.319-324
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• 2007

This study was conducted to evaluate the persistence of DNA in the transgenic chili pepper resistant to cucumber mosaic virus (CMV) in the field condition. We analyzed the persistence of genes in the leaf samples obtained from two field conditions, below and above soil. Transgenic and non-transgenic leaf tissues were buried in the soil at a depth of 10 cm or placed on the soil surface. Qualitative and quantitative PCR analysis showed that the amount of transferred genes from the transgenic peppers below and above soil was dropped to 28.3-42.7% one month after buried and it was rapidly reduced to 0.9-3.3% after two months. The transgenes were not detected three to four month after buried. In addition, DNA of the leaves placed below soil decomposed about 8%more than those on soil surface. The gene transfer from decomposing leaves of the transgenic pepper to soil was investigated by PCR analysis with the soil attached to the samples. The PCR result indicated that the gene transfer from the transgenic pepper to soil was not occurred.

• Journal of Korean Society of Forest Science
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• v.96 no.4
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• pp.425-431
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• 2007

To investigate genetic diversity and PCR detection of Rhizina undulata, PCR detection and sequence analysis of rDNA ITS region of R. undulata in soil were analyzed and developed. The length of partial 18S rDNA from four R. undulata isolates were 1,375 nt. The sequence similarity of R. undulata isolates was 100%. The rDNA ITS regions of R. undulata isolates were 585 nt long. Nucleotide sequencing of the ITS regions showed that PDK-1, PTT-1 and PDJ-9 isolates had 100% sequence identity. But, PDS-5 isolate differed from the three isolates by two nucleotide substitution. R. undulata-specific primers designed by the sequence of ITS region were used in PCR detection of R. undulata. PCR products about 525 bp size, which is specific to R. undulata, were amplified from total DNAs of R. undulata isolates. To assay the sensitivity of PCR detection by R. undulata ITS-specific primer, purely cultured mycelial suspension of R. undulata was serially diluted and mixed with 100g of sterile sandy loam soil, respectively. And then, PCR products of total DNAs extracted from each mycelium-soil mixtures were analysed. The PCR protocol could detected up to 1ng mycelium of R. undulata within 100g of soil.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 1986.12a
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• pp.514.1-514
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• 1986

토양으로부터 dextranase를 분비하는 균을 분리하였으며, 그 균이 Flavobacterium multivorum으로 동정되었다. 이 F. multivorum의 배치조건에 따른 dextran 이용과 dextranase 분비능을 조사하였고 아울러 성장조건도 알아보았다. 한편 위의 균은 plasmid를 갖고 있지 않았으며, 그에 따라 chromosomal DNA를 추출하여 Sau3Al 절단한 후

• Korean Journal of Ecology and Environment
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• v.54 no.3
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• pp.170-189
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• 2021

Environmental DNA (eDNA) is a genetic material derived from organisms in various environments (water, soil, and air). eDNA has many advantages, such as high sensitivity, short investigation time, investigation safety, and accurate species identification. For this reason, it is used in various fields, such as biological monitoring and searching for harmful and endangered organisms. To collect eDNA from a freshwater ecosystem, it is necessary to consider the target organism and gene and a wide variety of items, such as on-site filtration and eDNA preservation methods. In particular, the method of collecting eDNA from the environment is directly related to the eDNA concentration, and when collecting eDNA using an appropriate collection method, accurate (good quality) analysis results can be obtained. In addition, in preserving and extracting eDNA collected from the freshwater ecosystem, when an accurate method is used, the concentration of eDNA distributed in the field can be accurately analyzed. Therefore, for researchers at the initial stage of eDNA research, the eDNA technology poses a difficult barrier to overcome. Thus, basic knowledge of eDNA surveys is necessary. In this study, we introduced sampling of eDNA and transport of sampled eDNA in aquatic ecosystems and extraction methods for eDNA in the laboratory. In addition, we introduced simpler and more efficient eDNA collection tools. On this basis, we hope that the eDNA technique could be more widely used to study aquatic ecosystems and help researchers who are starting to use the eDNA technique.

• 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.

• Microbiology and Biotechnology Letters
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• v.31 no.2
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• pp.177-181
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• 2003

Eleven bacterial strains which are able to utilize terephthalic acid as a carbon and an energy source for growth were isolated from the soil of 7 water quality evaluation points in Kyonggi area of Korea. Phthalic acid isomer degrading activity of the isolates from the 4 contaminated points was higher than those from the 3 clean points. Among 11 isolates, 4 isolates which have high terephthalic acid degrading activity and degrade two phthalic acid isomers were identified by partal 16S rDNA sequence determination. One of them was identified as Pseudomonas putida, and the others as Comamonas testosteroni. Thus a large number of phthalic acid isomer degrading bacteria in domestic soil were inferred as C. testosteroni. On the basis of these results, the PCR detection of C. testosteroni in soil was applied to monitor soil contamination by phthalic acid isomers. The DNA of C. test-osteroni extracted from 4 g soil was directly detected by PCR with C. testosteroni specific primer pair. The amount of PCR products was different according to sampling sites and more PCR products were obtained from contaminated sites than those from clean sites (Gulpo-chun＞Anyang-chun＞Hwangguji-chun>Shin-chun＞Huk-chun＞Pukhan-river>Kapyeong-chun). This result was coincided with that of the viable cell counts for terephthalic acid degrading bacteria.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.116-124
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• 2006

In this study was performed to analyze quantitatively the number of viable but non-culturable bacteria in the Pine and Quercus forest soil by improved direct viable count (DVC) and plate count (PC) methods. The number of living bacteria of Pine and Quercus forest soil by PC method were less then 1% of DVC method. This result showed that viable but non-culturable (VBNC) bacteria existed in the forest soil with high percentage. Diversity and structure of VBNC bacterial populations in forest soil were analyzed by direct extracting of DNA and 16S rDNA-ARDRA from Pine and Quercus forest soil. Each of them obtained 111 clones and 108 clones from Pine and Quercus forest soil. Thirty different RFLP types were detected from Pine forest soil and twenty-six different RFLP types were detected from Quercus forest soil by HeaIII. From ARDRA groups, dominant clones were selected for determining their phylogenetic characteristics based on 16S rDNA sequence. Based on the 16S rDNA sequences, dominant clones from ARDRA groups of Pine forest soil were classified into 7 major phylogenetic groups ${\alpha}$-proteobacteria (12 clones), ${\gamma}$-proteobacteria (3 clones), ${\delta}$-proteobacteria (1 clone), Flexibacter/Cytophaga (1 clone), Actinobacteria (4 clones), Acidobacteria (4 clones), Planctomycetes (5 clones). Also, dominant clones from ARDRA groups of Quercus forest soil were classified into 6 major phylogenetic groups : ${\alpha}$-proteobacte,ia (4clones), ${\gamma}$-proteobacteria (2 clones), Actinobacteria (10 clones), Acidobacteria (8 clones), Planctomycetes (1 clone), and Verrucomicobia (1 clone). Result of phylogeneric analysis of microbial community from Pine and Quercus forest soils were mostly confirmed at uncultured or unidentified bacteria, VBNC bacteria of over 99% existent in forest soil were confirmed variable composition of unknown micro-organism.

• Journal of Korean Society of Environmental Engineers
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• v.35 no.7
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• pp.503-508
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• 2013

The aim of this study was to investigate the microbial communities in animal carcass disposal soils to examine the possible threat of pathogens from leachate. DNA extraction was performed for the soils in three carcass disposal sites located in Gyeonggi-do, Korea, and then 16S rRNA pyrosequencing was conducted to identify the microbial communities. Results indicate that, according to phylum classification, Proteobacteria (100%) was identified in soil A, Actinobacteria (66.4%) > Proteobacteria (31.1%) > Bacteriodetes (2.1%) > Acidobacteria (0.3%) in soil B, and Actinobacteria (63.1%) > Proteobacteria (36.9%) in soil C. According to genus classification, Pseudomonas was dominant in soil A (98%), Arthrobacter in soil B (68%) and C (61%). There were no detections of pathogens such as Salmonella, Campylobacter and Clostridium perfringens. However, high concentration of Ralstonia pickettii causing bacteremia was observed. Although carcass disposal soils examined in this study were not highly contaminated with pathogens, further monitoring is still needed to examine the potential threat of pathogens in leachate derived from carcass disposal sites.