• Applied Biological Chemistry
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• v.48 no.4
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• pp.345-351
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• 2005

To access the natural products of uncultured microorganisms, we constructed and screened the metagenomic DNA libraries by using a cosmid vector and DNA inserts isolated directly from soil. Initial screening of the libraries in Escherichia coli resulted in the isolation of several clones that produce a dark brown color when grown in LB medium. One of the positive clones, designed pYS85C, was transposon mutagenized and the DNA surrounding the transposon insertions in cosmids that no longer conferred the production of brown pigment to E. coli was sequenced. Annotation of the pYS85C sequence obtained from the transposon mutagenesis experiment indicated a single 393 amino acid open reading frame (ORF) with a molecular mass of about 44.5 kDa, predicted to be a 4-hydroxyphenylpyruvate dioxygenases (HPPDs), was responsible for the observed brown pigment. In a BLAST search against deposited sequence, the translated protein from this ORF showed moderate-level identity (>60%) to the other known HPPDs and was most conserved in the C-terminal region of the protein. These results show that genes involved in natural product synthesis can be cloned directly from soil DNA and expressed in a heterologous host, supporting the idea that this technology has the potential to provide novel natural products from the wealth of environmental microbial diversity and is a potentially important new tool for drug discovery.

• Korean Journal of Soil Science and Fertilizer
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• v.47 no.1
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• pp.28-35
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• 2014

Due to recent interest of the consumers on safe farm products and the government's political support for eco-friendly agriculture, organic fruit production has been growing continuously. This research was conducted in order to study the effect of cover plants on soil microbial community on cover plants and establish an organic fruit cultivation method through choosing optimal cover plant. As a result of investigating soil microbial population density, the bacterial density in soil showed an increasing trend in June compared to April, and there was a decreasing trend in bacterial density of the soil in August compared to June. The density of actinomycetes in soil increased around 1.6 times in June compared to April when the soil was covered with hairy vetch. The increase of filamentous fungus in crimson clover group was 6.1 times higher in June compared to April and in hairy vetch group, the increase was 4.9 times higher in June compared to April. As a result of analyzing DNA extracted from the soil categorized by different types of cover plants using DGGE method, soil collected from April had higher number of bands detected from different locations according to different types of cover plants. Diversity of the bands from the soil collected from August showed higher range of reduction. As a result of analyzing soil microbial community by different period and the types of cover plants using Pyrosequencing method, microbes were detected in the order of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Distribution rate of Firmicutes increased in the soil collected in August compared to June and this was shown in all types of cover plants by twice the amount.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2005.10a
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• pp.85-86
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• 2005

• Korean Journal of Microbiology
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• v.20 no.4
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• pp.210-222
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• 1982

Coliphages isolated from Han-River from September 1980 to August 1981 were classified by morphological and physiological characteristics. Effects of soil metrial on the fate of coliphage in nature were investigated. 1. The correlation coefficient between coliphage and E.coli which was host of coliphages in nature was 0.7173 (p=0.004). 2. Coliphage I isolated from Han-River of which DNA molecular weight was $27{\times}10^6$ daltons was identified as $T_1$ phage and coliphage II of which DNA molecular weight $72{\times}10^6$ daltons was classified as $T_5$ phage. 3. Soil material SW was composed of 63.65% silt and 21.92% clay. Clay was consisted of illite, kaolinite and chlorite evenly. Soil material J was composed of 68.92% silt and 11.67% clay. Clay consisted of smectite only. 4. Coliphage was absorbed to soil material J more than soil material SW, and $T_1$ coliphage was absorbed to soil material more than $T_5$ coliphage was. 5. The phage adsorption efficiency to soil material was enhanced at lower pH : the phage adsorption efficiency at pH 4 was 27 time higher than at pH 7. 6. Divalent $(Ca^{2+})\;and\;trivalention\;(Al^{3+})$ enhanced the phage adsorption efficiency to soil material from 4 to 39 and from 17 to 91 times higher than monovalent $ion(Na^+)$, respectively. 7. The concentration of organic compound was inversely related to the phage adsorption efficiency to soil. 8. Adsorption of phage onto soil material, and elution efficiency of elutants was in the order of D.D.W>tap water>river water>seawater. 9. The higher the concentration of organic compound was, the more were adsorbed phages to soil eluted. 10. Coliphages survived longer in sterile soil suspension than in nonsterile soil material suspension.

• Korean journal of applied entomology
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• v.53 no.1
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• pp.85-91
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• 2014

In this study, we analyzed the phylogenetic characterization of root-knot nematodes (Meloidogyne spp.) in soils from fruits and vegetables greenhouses in Korea. Soil samples were collected from 12 greenhouse fields in which tomato, cucumber, watermelon, and Oriental melon were being cultivated. Meloidogyne spp. were detected in all the soil samples at an average number of $72{\pm}6$ nematodes/300 g of soil to $2,898{\pm}468$ nematodes/300 g of soil. Phylogenetic analysis using polymerase chain reaction-restriction fragment length polymorphism was attempted for the second-stage juveniles (J2) of Meloidogyne spp. collected from the greenhouse soils. Twelve Meloidogyne spp. from the greenhouse soils were classified into two groups by using HinfI digestion of mitochondrial DNA, resulting in 900, 410, 290, and 170 bp fragments (group A) and 900, 700, and 170 bp fragments (group B). Phylogenetic analysis based on mitochondrial DNA sequences (1,483-1,521 bp) showed that nine group A isolates were identified as Meloidogyne incognita (99.73-99.93%) and three group B isolates showed 99.54-99.73% similarity to Meloidogyne arenaria.

• 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.

• Research in Plant Disease
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• v.10 no.4
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• pp.310-312
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• 2004

Pseudomonas syringae pv. actinidiae is the causative agent of bacterial canker in kiwifruit. A nested PCR detection method that uses primers designed from the cfl gene, involved in production of the phytotoxin coronatine, was applied on soil samples. These primers yielded 665 and 310-bp fragments in consecutive PCR amplification step with DNA from soil inoculated with Korean strain of P. syringae pv. actinidiae. This system was applied to survey soil samples from a kiwifruit orchard destroyed by bacterial canker. A specific 310-bp PCR product was obtained from all six samples of soil tested.

• Korean Journal of Environmental Biology
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• v.22 no.1
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• pp.213-219
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• 2004

The bacterial community of water stream, soil and guano in Gossi cave was examined by using PCR amplified the 16S rDNA-denaturing gradient gel electrophoyesis (DGGE). In this study, the genetic diversity and the similarity of bacterial community between open area and non - open area toy cave tour were investigated, and the seasonable variation pattern was compared each other. DGGE is attractive technique, as it sepayate same length dsDNA according to sequence variation typical 16S rDNA genes. The diversity and similarity of bacterial community in cave was analyzed by GC341f and PRUN518r primer sets foy amplification of V3 region of eubacteria 16S rDNA. The specific DGGE band profile of the cave water gives the possibility that the specific bacterial cell can be adapting to the specific cave environment and living in the cave. The DGGE band profiles of all samples with guano were compared and analyzed by image analyzer, in which mutual band profile was compared to be and the band intensity of guano was the highest. From these result, it is thought that the guano was main nutrient source and influenced on the community structure of the cave environment where is nutritionally limited. Pseudomonas sp. NZ060, Pseudomonas pseudoalcaligenes, uncultured Variovorax sp. and soli bacterium NS7 were identified to be on some sample from analysing DNA sequence of some DGGE band.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.15-20
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• 2010

A Gram negative, aerobic, nonspore-forming, straight or curved rod-shaped bacterium, designated Gsoil $317^T$, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Cells were dimorphic, with stalk (or prostheca) and nonmotile or nonstalked and motile, by means of a single polar flagellum. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil $317^T$ was most closely related to Caulobacter mirabilis LMG $24261^T$ (97.2%), Caulobacter fusiformis ATCC $15257^T$ (97.1 %), Caulobacter segnis LMG $17158^T$ (97.0%), Caulobacter vibrioides DSM $9893^T$ (96.8%), and Caulobacter henricii ATCC $15253^T$ (96.7%). The sequence similarities to any other recognized species within Alphaproteobacteria were less than 96.0%. The detection of Q-10 as the major respiratory quinone and a fatty acid profile with summed feature 7 ($C_{18:1}\;{\omega}7c$ and/or $C_{18:1}\;{\omega}9t$ and/or $C_{18:1}\;{\omega}12t;$ 56.6%) and $C_{16:0}$ (15.9%) as the major fatty acids supported the affiliation of strain Gsoil $317^T$ to the genus Caulobacter. The G+C content of the genomic DNA was 65.5 mol%. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil $317^T$ and its closest phylogenetic neighbors were below 11%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $317^T$ should be classified as representing a novel species in the genus Caulobacter, for which the name Caulobacter ginsengisoli sp. novo is proposed. The type strain is Gsoil $317^T$ (=KCTC $12788^T=DSM\;18695^T$).

• 보존과학연구
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• s.31
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• pp.69-77
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• 2010

Preservation of artifacts that are excavated from archeological sites is closely related to soil environment. Biological remains are especially influenced by degradation activity of microorganism from soil environment. In this study a preserved human bone in archaeological tomb, Tou-kwang-myo from Joseon Period was analyzed to characterize bacteria groups by molecular genetic tools using 16S rDNA sequences. 117 clones were identified and classified 9 phylogenetic groups : ${\alpha}$-, ${\beta}$-, ${\gamma}$-, ${\delta}$-Proteobacteria, Sphingobacteria, Clostridia, Actinobacteridae, Nitrospiraceae, and Gemmatimonadetes according to homologous 16S rDNA sequences submitted in NCBI. ${\gamma}$-Proteobacteria group appears the highest ratio in bones (about 35%) while about 19.6% belong to the Actinobacteria group. The results may contribute to study on the effect of microorganisms on the human remains with burial method.