• Journal of the Korea Organic Resources Recycling Association
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• v.24 no.4
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• pp.77-83
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• 2016

The objectives of this study was to investigate the difference between organic-farming and conventional-farming soils relatives to soil chemical properties and microbial flora. Fifteen soil sampling sites were chosen from the certified organic upland farm, considered with its location, crop and application of organic compost types. Soil chemical properties were analyzed by standard methods established by National Institute of Agricultural Sciences, Rural Development Administration. For the soil chemical properties, the values of pH were ranged from 4.5 to 7.3. The values of electrical conductivity (EC) in the sampling sites were below 2 dS/m of convention cultivation soil. For analyzing the microbial flora, the bacillus(16S rDNA) and cladothricosis(18S rDNA) were analyzed by using PCR-DGGE (Denaturing Gradient Gel Electrophoresis) in the soil of 15 sampling sites. Cluster analysis of biodiversity index was performed by using pattern of DGGE. DGGE patterns and clustering analysis of bacterial DNA from soil extracts revealed that the bacterial community was differentiated between less than 5 years and more than 5 years depending on the cultivation history. But there was no consistent tendency between cultivation history and regional trend in the case of molds. Therefore, it would be very effective to analyze bacterial clusters of organically cultivated soils in long - term cultivated soil for more than 5 years.

• Proceedings of the Korean Society of Soil Zoology Conference
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• 2003.06a
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• pp.1-2
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• 2003

• 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.

• Journal of the Korea Organic Resources Recycling Association
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• v.12 no.4
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• pp.139-147
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• 2004

We have isolated two bacterial strains, FM-02 and AL-02, which produced EPS from forest soil for the restoration of forest fire by promoting soil aggregation. FM-02 was found to be Gram negative rod and belong to Beta Proteobacterium sp. through 16s-rDNA sequence analysis, and AL-02 was Gram positive rod and showed 81% of similarity to Zoogloea sp. through the analysis of 16s-rDNA sequence. FM-02 and AL-02 produced about 1.8g and 8.3g of EPS, respectively, per 1L of culture as dry weight. Flocculation activity (FA) was also measured in two strains. FM-02 showed 2.31 FA against active carbon, and AL-02 showed 6.21 FA against kaolin clay. From these results, we expect that AL-02 strain will be applied as a good biological material for the reduction of forest soil erosion by wild and rain after fire through promoting coagulation of soil particles.

• Mycobiology
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• v.31 no.1
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• pp.23-31
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• 2003

With universal primer ITS1-F, the specific DHJ2 primer was developed to detect the Ectomycorrhizal(ECM) root tips in soil and to identify the species of ECM fungi, as based on DNA sequences of rDNA stored in GeneBank of NCBI. This primer was designed with the common sites of rDNA of Amanita and Boletus, and was also designed with several DNA programs provided by NCBI. The DNA fragments synthesized by PCR were calculated to be 1,000 to 1,200 bps of DNA located to 18s to 28s rDNA to contain two variable sites of ITS, indicating much diversities for specific species or ecotypes of ECM fungi. The primer DHJ2 reacted with the genomic DNA's extracted from the tissues of basidiocarp at the rate of 73 of 80 fungi collected produced single bands with a 1,100 bps length. The DNA fragment synthesized with the genomic DNA that extracted from eight ECM tips of Pinus densiflora was confirmed and analysized to the rDNAs of ECM in full sequences, and informed to be a ECM fungal species in the forest.

• Korean Journal of Environmental Biology
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• v.18 no.2
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• pp.205-213
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• 2000

Laboratory studies have revealed that naturally transformable bacteria develop competence under in situ conditions. Thus, the occurrence of competent bacteria in the environment can be considered as a certainty The persistence of free DNA in natural habitats is influenced by nucleolytic degradation and protection from degradation by adsorption to minerals. Although DNA seeded into natural environment was hydrolysed at substantial rates, but was still detectable at low levels after even several weeks. Compared to the number of laboratory based studies, only a few data have been published dealing with transformation of bacteria in the field. Recently, the potential transfer of recombinant DNA (rDNA) from deliberately or accidentally released bacteria to indigenous microbes has raised biosafety issues, since the persistence of rDNA becomes independent of the survival of its original host and leads to unpredictable, long-term ecological effects. The aim of the present review is to summarise recent literature on horizontal gene transfer (HGT) by transformation among bacteria in both soil and aquatic habitat and special emphasis is placed on recent reports which have addressed HGT among bacteria in the field. [Transformation, Horizontal gene transfer (HGT), recombinant DNA (rDNA), Genetically modified microorganisms (GMMs), Biosafety]

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.498-502
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• 2004

The current study was conducted to monitor the possibility of the gene transfer among soil bacteria, including the effect of drift due to rain and surface water, in relation to the release of genetically modified organisms into the environment. Four types of bacteria, each with a distinct antibiotic marker, kanamycin-resistant P. fluorescens, rifampicin-resistant P. putida, chloramphenicol-resistant B. subtilis, and spectinomycin-resistant B. subtilis, were plated using a small-scale soil-core device designed to track drifting microorganisms. After three weeks of culture in the device, no Pseudomonas colonies resistant to both kanamycin and rifampicin were found. Likewise, no Bacillus colonies resistant to both chloramphenicol and spectinomycin were found. The gene transfer from glyphosate-tolerant soybeans to soil bacteria, including Rhizobium spp. as a symbiotic bacteria, was examined by hybridization using the DNA extracted from soil taken from pots, in which glyphosate-tolerant soybeans had been growing for 6 months. The results showed that 35S, T-nos, and EPSPS were observed in the positive control, but not in the DNA extracted from the soilborne microorganisms. In addition, no transgenes, such as the 35S promoter, T-nos, and EPSPS introduced into the GMO soybeans were detected in soilborne bacteria, Rhizobium leguminosarum, thereby strongly rejecting the possibility of gene transfer from the GMO soybeans to the bacterium.

• Mycobiology
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• v.40 no.3
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• pp.151-158
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• 2012

Very few studies have addressed the phylogenetic diversity of fungi from Northeast India under the Eastern Himalayan range. In the present study, an attempt has been made to study the phylogenetic diversity of culturable soil fungi along the altitudinal gradients of eastern Himalayas. Soil samples from 24 m above sea level to 2,000 m above sea level altitudes of North-East India were collected to investigate soil micro-fungal community structure and diversity. Molecular characterization of the isolates was done by PCR amplification of 18S rDNA using universal primers. Phylogenetic analysis using BLAST revealed variation in the distribution and richness of different fungal biodiversity over a wide range of altitudes. A total of 107 isolates were characterized belonging to the phyla Ascomycota and Zygomycota, corresponding to seven orders (Eurotiales, Hypocreales, Calosphaeriales, Capnodiales, Pleosporales, Mucorales, and Mortierellales) and Incertae sedis. The characterized isolates were analysed for richness, evenness and diversity indices. Fungal diversity had significant correlation with soil physico-chemical parameters and the altitude. Eurotiales and Hypocreales were most diverse and abundant group of fungi along the entire altitudinal stretch. Species of Penicillium (D=1.44) and Aspergillus (D=1.288) were found to have highest diversity index followed by Talaromyces (D=1.26) and Fusarium (D=1.26). Fungal distribution showed negative correlation with altitude and soil moisture content. Soil temperature, pH, humidity and ambient temperature showed positive correlation with fungal distribution.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.521-532
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• 2021

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2001.06a
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• pp.118-119
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• 2001

A Southern-hybridization analysis and size-selected DNA library screening led to the isolation of a 6.3-kbp S. setonii DNA fragment, from which the Cl20-encoding genetic locus was found to be located within a 1.4-kbp DNA fragment. A complete nucleotide sequencing analysis of the 1.4-kbp DNA fragment revealed a 0.84-kbp ORF, which showed a strong overall amino acid similarity to the known high－G＋C gram-positive bacterial mesophilic C120s. The heterologous expression of the cloned 1.4-kbp DNA fragment in E. coli demonstrated that this Cl20 possessed a thermophilic activity within a broad temperature range and showed a higher activity against 3-methy1catechol than catechol or 4-methy-catechol, but no activity against protocatecuate.