• Korean Journal of Soil Science and Fertilizer
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• v.45 no.5
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• pp.792-797
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• 2012

Glomalin-related soil protein has been suggested as an enhancer for soil stability by promoting the aggregation. In this study, we examined the concentrations of glomalin and characteristics of microbial community in 20 paddy soils sampled from Gyeongnam Province. Total soil glomalin as glomalin-related soil protein (GRSP) had a significant positive correlation with soil organic matter (p<0.01) and soil dehydrogenase activity (p<0.01). The concentration of GRSP significantly correlated to soil microbial biomass carbon (p<0.001) and the total bacterial community (p<0.01) in paddy soils. In addition, the GRSP had a significant positive correlation with gram-negative bacteria community (p<0.05) and ratio of cy19:0 to 18:$1{\omega}7c$ (p<0.05) in paddy soils. In conclusion, the concentration of GRSP could be an indicator of soil health that simplify the inspection steps for sustainable agriculture in paddy soils.

• Journal of Applied Biological Chemistry
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• v.52 no.3
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• pp.121-125
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• 2009

We measured the influence of antifungal antagonists Bacillus subtilis AH18 and Bacillus licheniformis K11 on soil microbial community in microcosms. Both antifungal antagonists were confirmed to suppress hot pepper phytophthora blight. Phospholipid fatty acids (PLFA) were analyzed to investigate the soil microbial community. B. subtilis AH18 changed the total PLFA composition and bio-indicators of PLFA, compared with other treatments. B. subtilis AH18 decreased the proportion of bacteria and gram negative/gram positive bacteria, and increased the fungi/bacteria and anaerobic/aerobic microorganisms. In addition cy19:0/18:$1{\omega}7c$, which means adaptation to unfavorable environmental conditions, was increased by the application of B. subtilis AH18. On the other hand the inoculation of B. licheniformis K11 or combined inoculation of both antifungal strains did not affect soil microbial community. The suppression of phytophthora blight and preservation of indigenous soil microbial community may be achieved by the combined application of B. subtilis AH18 and B. licheniformis K11.

• Journal of Microbiology and Biotechnology
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• v.24 no.3
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Korean Journal of Environmental Agriculture
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• v.30 no.4
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• pp.367-376
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• 2011

BACKGROUND: In order to develop effective assessment method for Korean paddy soil microbial community structure, reliable genomic DNA extraction method from paddy soil and quantitative real-time PCR (qRT-PCR) method are needed to establish METHODS AND RESULTS: Out of six conventional soil genomic DNA extraction methods, anion exchange resin purification method was turn to be the most reliable. Various PCR primers for distinguishing five bacterial phylum (${\alpha}$-Proteobacteria, ${\beta}$-Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes), all bacteria, and all fungi were tested. Various qRT-PCR temperature conditions were also tested by repeating experiment. Finally, both genomic DNA extraction and qRT-PCR methods for paddy soil were well established. CONCLUSION: Quantitative real-time PCR (qRT-PCR) method to assess paddy soil microbial community was established.

• Journal of Environmental Science International
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• v.20 no.4
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• pp.457-463
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• 2011

This study was carried out to compare the toxicity of nano and micrometer particles with Cu and Zn on soil microbial community and metal uptake of buck wheat. In microcosm system, soil was incubated for 14 days after soil aliquots were artificially contaminated with 1,000 mg/kg Cu, Zn nano and micro particles, respectively. After then, buck wheat was planted in incubating soils and non incubating soils. After 14 days, we compared bioaccumulation of metal, and microbial carbon substrate utilization patterns between incubating soils and non-incubating soils. The enrichment factor (EF) values of incubating samples were greater than non-incubating soils. Dehydrogenase activity had been inhibited by Cu and Zn nanoparticles in non-incubating soil, as well as it had been inhibited by Zn micro particles in incubating soils. Results of biolog test, it was not significant different between nano particles and micro particles. It cannot be generalized that nanoparticles of metal are always more toxic to soil microbial activity and diversity than micrometer-sized particles and the toxicity needs to be assessed on a case-by-case basis.

• Korean Journal of Soil Science and Fertilizer
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• v.49 no.2
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• pp.144-156
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• 2016

Soil is a dynamic biological system, in which it is difficult to determine the composition of microbial communities. Knowledge of microbial diversity and function in soils are limited because of the taxonomic and methodological limitations associated with studying the organisms. In this review, approaches to measure microbial diversity in soil were discussed. Research on soil microbes can be categorized as structural diversity, functional diversity and genetic diversity studies, and these include cultivation based and cultivation independent methods. Cultivation independent technique to evaluate soil structural diversity include different techniques such as Phospholipid Fatty Acids (PLFA) and Fatty Acid Methyl Ester (FAME) analysis. Carbon source utilization pattern of soil microorganisms by Community Level Physiological Profiling (CLPP), catabolic responses by Substrate Induced Respiration technique (SIR) and soil microbial enzyme activities are discussed. Genetic diversity of soil microorganisms using molecular techniques such as 16S rDNA analysis Denaturing Gradient Gel Electrophoresis (DGGE) / Temperature Gradient Gel Electrophoresis (TGGE), Terminal Restriction Fragment Length Polymorphism (T-RFLP), Single Strand Conformation Polymorphism (SSCP), Restriction Fragment Length Polymorphism (RFLP) / Amplified Ribosomal DNA Restriction Analysis (ARDRA) and Ribosomal Intergenic Spacer Analysis (RISA) are also discussed. The chapter ends with a final conclusion on the advantages and disadvantages of different techniques and advances in molecular techniques to study the soil microbial diversity.

• 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 Environmental Agriculture
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• v.27 no.2
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• pp.139-144
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• 2008

A field experiment was conducted to investigate the influence of cultivars and compost on soil microbial activities and diversities in a red pepper-grown field. Compost was applied with 0, 30, and 60M/T $ha^{-1}$ in April and then red pepper seedlings of "Yong-go 4" and "Koeun" were transplanted in May 2007. Soil samples were collected in early August 2007. Measurement of microbial activities was based on a dehydrogenase assay and a fluorescein diacetate hydrolysis. Soil microbial community was characterized with Biolog $EcoPlate^{TM}$ and phospholipid fatty acid(PLFA). Red pepper cultivars did not differentiate the selected soil chemical and microbial properties. Soil pH and soil microbial community changed by amending the soil with 30 and 60 M/T $ha^{-1}$ of compost, and the soil organic matter and potassium content, and soil microbial activities increased in soils amended with 60 M/T $ha^{-1}$ of compost. Red pepper cultivar induced a little different soil chemical properties and microbial activity in soils amended with 60 M/T $ha^{-1}$ of compost even though significant differences were not found in those properties. In conclusion the effects of compost on soil chemical and microbial properties were much higher than red pepper cultivars in short-term period but the effects of red pepper cultivars should be investigated in long-term field test.

• The Plant Pathology Journal
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• v.32 no.2
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• pp.136-144
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• 2016

Pseudomonas fluorescens pc78 is an effective biocontrol agent for soil-borne fungal diseases. We previously constructed a P43-gfp tagged biocontrol bacteria P. fluorescens pc78-48 to investigate bacterial traits in natural ecosystem and the environmental risk of genetically modified biocontrol bacteria in tomato rhizosphere. Fluctuation of culturable bacteria profile, microbial community structure, and potential horizontal gene transfer was investigated over time after the bacteria treatment to the tomato rhizosphere. Tagged gene transfer to other organisms such as tomato plants and bacteria cultured on various media was examined by polymerase chain reaction, using gene specific primers. Transfer of chromosomally integrated P43-gfp from pc78 to other organisms was not apparent. Population and colony types of culturable bacteria were not significantly affected by the introduction of P. fluorescens pc78 or pc78-48 into tomato rhizosphere. Additionally, terminal restriction fragment length polymorphism profiles were investigated to estimate the influence on the microbial community structure in tomato rhizosphere between non-treated and pc78-48-treated samples. Interestingly, rhizosphere soil treated with strain pc78-48 exhibited a significantly different bacterial community structure compared to that of non-treated rhizosphere soil. Our results suggest that biocontrol bacteria treatment influences microbial community in tomato rhizosphere, while the chromosomally modified biocontrol bacteria may not pose any specific environmental risk in terms of gene transfer.

• Journal of Soil and Groundwater Environment
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• v.12 no.5
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• pp.54-63
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• 2007

To examine the effects of amendments on heavy mineral oil degradation, a pilot scale experiment was conducted for over 105days. During the experiment, soil samples were collected and analyzed periodically for the determination of residual hydrocarbon and microbial activities. At the end of the experiment, the initial level of contamination ($6,205{\pm}173mgkg^{-1}$) was reduced by $33{\sim}45%$ in the amendment amended soil; whereas only 8% of the hydrocarbon was eliminated in the non-amended soil. Heavy mineral oil degradation was much faster and more complete in compost amended soils. Enhanced dissipation of heavy mineral oil in compost amended soil might be derived from increased microbial activities (respiration, microbial biomass-C) and soil enzyme activity(lipase, dehydrogenase, and FDA hydrolase) were strongly correlated with heavy mineral oil biodegradaton (P < 0.01).