• Korean Journal of Environmental Agriculture
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• v.32 no.2
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• pp.148-154
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• 2013

BACKGROUND: Genetically modified(GM) trigonal cactus(Hylocereus trigonus Saff.) contained a coat protein gene of cactus virus X (CVX), which conferred resistance to the virus, phosphinothricin acetyltransferase (bar) gene, which conferred herbicide resistance, and a cauliflower mosaic virus 35S promoter (CaMV 35S). This study was conducted to evaluate the possible impact of GM trigonal cactus cultivation on the soil microbial community. METHODS AND RESULTS: Microorganisms were isolated from the rhizosphere of GM and non-GM trigonal cactus cultivation soils. The total numbers of bacteria, and actinomycete in the rhizosphere soils cultivated GM and non-GM trigonal cactus were similar to each other, and there was no significant difference. Dominant bacterial phyla in the rhizosphere soils cultivated with GM and non-GM trigonal cactus were Proteobacteria, Uncultured archaeon, and Uncultured bacterium. The denaturing gradient gel electrophoresis (DGGE) profiles show a similar patterns, significant difference was not observed in each other. DNA was isolated from soil cultivated GM and non-GM trigonal cactus, we analyzed the persistence of the inserted gene by PCR. Amplification of the inserted genes was not observed in the soil DNA, which was collected after harvest. CONCLUSION(S): This result suggests that the GM trigonal cactus cultivation does not change significantly the microbial community.

• Journal of Korean Society of Forest Science
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• v.101 no.3
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• pp.501-508
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• 2012

This study was carried out to compare species diversity of soil bacteria from Baekdudaegan mountain forests (Bonghwa-gun, Mungyeong-si and Sangju-si) in Gyeongsangbuk-do and to analyze the effects of soil environments on diversity and population of soil bacteria. Soil bacteria were isolated from soil samples by streak plate method, and identified by DNA extaction and 16S rDNA sequence analyses. The population of soil bacteria from the soil samples of Bonghwa-gun was the highest with $5.1{\times}10^5cfu/g$, and followed by those from Mungyeong-si and Sangju-si with $1.9{\times}10^5cfu/g$ and $1.1{\times}10^5cfu/g$, respectively. The population of soil bacteria from surface layer soil was the highest, and then gradually decreased according to soil depth. The increase in population of soil bacteria from soil samples of different sites was correlated with the increase of the altitude of soil sampling site, depth of A horizon, liquid phase among three phases of soil, water content and bulk density of soil. Two hundreds and sixty eight bacterial colonies from Bonghwa-gun were classified into 10 species, 8 genera. One hundred and thirty four bacterial colonies from Mungyeong-si were classified into 15 species, 9 genera. Forty four bacterial colonies from Sangju-si were classified into 5 species, 2 genera. The dominant species (occupancy rate) from Bonghwa-gun and Mungyeong-si were Bacillus weihenstephanensis (36% and 40%, respectively), and Sangju-si was Bacillus cereus (39%). The relationships between soil environment and community structure of soil bacteria were analyzed statistically by using ecological indices. The diversity, evenness and dominance indices of soil bacteria were 6.30, 2.04 and 0.59 in Bonghwa-gun, 9.09, 2.94 and 0.51 in Mungyeong-si, and 4.55, 2.34 and 0.71 in Sangju-si, respectively. The diversity and evenness indices were increased by the increase of water content, drainage condition and gravel content of soil, while the dominance index was decreased.

• Journal of Korean Society on Water Environment
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• v.22 no.4
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• pp.590-598
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• 2006

In-situ Air sparging (IAS) is a groundwater remediation technique, in which organic contaminants volatilize into air form the saturated to vadose zone. This study was carried out to evaluate the effect of sludge and soil microbial community structure on air sparging of Total Petroleum Hydrocarbons (TPH) contaminated groundwater soils. In the laboratory, diesel (10,000 mg TPH/kg) contaminated saturated soil. The Air was injected in intermittent (Q=1500 mL/min, 10 minute injection and 10 minute idle) modes. For Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of eubacterial communities in sludge of wastewater treatment plants and soil of experiment site, the 16S rDNA was amplified by Polymerase Chain Reaction (PCR) from the sludge and the soil. The obtained 16S rDNA fragments were digested with Msp I and separated by electrophoresis gel. We found various sequence types for experiment with sludge soil samples that were closely related to Agrococcus, Flavobacterium, Thermoanaerobacter, Flexibacter and Shewanella, etc, in the clone library. The results of the present study suggests that T-RFLP method may be applied as a useful tool for the monitoring in the TPH contaminated soil the fate of microorganisms in natural microbial community.

• Korean Journal of Soil Science and Fertilizer
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• v.33 no.4
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• pp.275-282
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• 2000

Among the fluorescent pseudomonad isolates from soil- root system of red pepper in Chinju, Kyunsangnam-Do, the phylogenetic analysis for 35 isolates were conducted. The partial 16S ribosomal DNA sequences were used as taxonomic key for phylogenetic analyses, and these sequences were enabled to identification of the fluorescent pseudomonad isolates on the species level. The 17 isolates among them were classified into Pseudomonas putida group, and consisted of the strains isolated mainly from soil. This group were subdivided into 4 subgroups (I, II, III, and IV). The subgroup I and IV were unique ones which were relatively remotely related with subgroup II and III including the type strain of P. putida. The 15 isolates among 35 isolates were grouped along with the type strain of Pseudomonas fluorescens, and 3 isolate were characterized as intermediates of P. fluorescens and Pseudomonas chlororaphis. Most of strain isolateds from the rhizosphere soil and rhizoplane of red pepper were identified as P. fluorescens and closely related with each other. In this study, root of red pepper was supposed to be colonized by a specific strain or strains of P. fluorescens.

• Journal of Microbiology and Biotechnology
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• v.17 no.11
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• pp.1765-1771
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• 2007

A polymerase chain reaction (PCR)-based method was developed to detect the DNA of Ralstonia solanacearum, the causal agent of bacterial wilt in various crop plants. One pair of primers (RALSF and RALSR), designed using cytochrome c1 signal peptide sequences specific to R. solanacearum, produced a PCR product of 932 bp from 13 isolates of R. solanacearum from several countries. The primer specificity was then tested using DNA from 21 isolates of Ralstonia, Pseudomonas, Burkholderia, Xanthomonas, and Fusarium oxysporum f. sp. dianthi. The specificity of the cytochrome c1 signal peptide sequences in R. solanacearum was further confirmed by a DNA-dot blot analysis. Moreover, the primer pair was able to detect the pathogen in artificially inoculated soil and tomato plants. Therefore, the present results indicate that the primer pair can be effectively used for the detection of R. solanacearum in soil and host plants.

• Korean journal of applied entomology
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• v.34 no.4
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• pp.373-377
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• 1995

Four Bacillus thuringiensis isolates obtained from soil samples in Korea produce parasporal inclusions non-toxic to 10 insect species of three orders, Lepidopera, Diptera and Coleoptera. These four isolates are named NTB-1, NTB-2, NTB-3 and NTB-4, respectively. The morphology of parasporal inclusions of four isolates observed by phase contrast- and scanning electron microscope was all ovoid. Characterization of four non-toxic B. thuringiensis isolates was determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and restriction endonuclease analysis. The results showed that parasporal inclusion proteins and total plasmid DNA profiles of four isolates are different from other known non-toxic B. thuringiensis strains', suggesting that four isolates are novel.

• Korean Journal Plant Pathology
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• v.14 no.2
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• pp.164-170
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• 1998

This study was carried out to develop DNA probe for specific detection of Erwinia carotovora subsp. carotovora. Universal rice primer (URP, 20 mer) developed from repetitive sequence of rice was applied for producing PCR DNA fingerprints of Erwinis spp. In E. carotovora subsp. carotovora strains, primer URP2F amplyfied polymorphic bands which are distinguisable from other Erwinia spp. A PCR band of 0.6 kb selected from PCr polymorphic bands of E. carotovora subsp. carotovora strains was cloned and evaluated as a diagnostic DNA probe. Among 28 bacterial strains including 22 Erwinia spp, the probe (pECC2F) only hybridized to total DNAs from e. carotovora subsp. carotovora strains and E. carotovora subsp. wasabiae, but sizes of hybridized bands were different between these subspecies, 10.0 kb and 3.5 kb respectively. In dot blot assays using probe pECC2F, as few as 103 colony forming units (CFU) of E. carotovora subsp. carotovora could be detected in a suspension containing about 1$\times$103 CFU of soil bacteria.

• Proceedings of the Korean Society of Soil and Groundwater Environment Conference
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• 2003.09a
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• pp.438-441
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• 2003

The present study reports the novel physiological function of dissimilatory perchlorate reduction by two strains JB101 and JB109 isolated from a sewage treatment facility in Incheon, South Korea. The physiological data of the isolates showed good correspondence with the members of the family Enterobacteriaceae. The partial 16S rRNA and 16S rDNA sequence of strains JB101 and JB109 showed similarity of 99.8% to Citrobacter amalonaticus and 98% to Citrobacter farmari, respectively. The study infers toward possibility of Citrobacter spp. to form an important group of dissimilatory perchlorate reducers within the (equation omitted) subclass of Proteobacteria because the majority of the known. members belong to two monophyletic groups namely Dechloromonas and Dechlorosoma in $\beta$ subclass of Proteobacteria.

• Journal of Microbiology and Biotechnology
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• v.7 no.1
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• pp.32-36
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• 1997

An adenosine deaminase inhibitor-producing bacterium was isolated from soil. An isolate exhibiting high adenosine deaminase inhibitory activity, was designated J-89, and classified as a strain of Bacillus subtilis on the basis of its morphological, phenotypic characteristics, the menaquinone content and cellular fatty acid composition. To confirm the taxonomic position of the strain we need more information such as DNA-DNA homology and other chemotaxonomic characteristics. In this paper we provisionally named strain J-89 as Bacillus sp. J-89 pending further chemotaxonomic study and analysis of adenosine deaminase inhibitor.

• BMB Reports
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• v.43 no.1
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• pp.1-8
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• 2010

The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs.