• Korean Journal of Microbiology
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• v.51 no.2
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• pp.97-107
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• 2015

Wetlands constitute a transitional zone between terrestrial and aquatic ecosystems and have unique characteristics such as frequent inundation, inflow of nutrients from terrestrial ecosystems, presence of plants adapted to grow in water, and soil that is occasionally oxygen deficient due to saturation. These characteristics and the presence of vegetation determine physical and chemical properties that affect decomposition rates of organic matter (OM). Decomposition of OM is associated with activities of various extracellular enzymes (EE) produced by bacteria and fungi. Extracellular enzymes convert macromolecules to simple compounds such as labile organic carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) that can be easily taken up by microbes and plants. Therefore, the enzymatic approach is helpful to understand the decomposition rates of OM and nutrient cycling in wetland soils. This paper reviews the physical and biogeochemical factors that regulate extracellular enzyme activities (EEa) in wetland soils, including those of ${\beta}$-glucosidase, ${\beta}$-N-acetylglucosaminidase, phosphatase, arylsulfatase, and phenol oxidase that decompose organic matter and release C, N, P, and S nutrients for microbial and plant growths. Effects of pH, water table, and particle size of OM on EEa were not significantly different among sites, whereas the influence of temperature on EEa varied depending on microbial acclimation to extreme temperatures. Addition of C, N, or P affected EEa differently depending on the nutrient state, C:N ratio, limiting factors, and types of enzymes of wetland soils. Substrate quality influenced EEa more significantly than did other factors. Also, drainage of wetland and increased temperature due to global climate change can stimulate phenol oxidase activity, and anthropogenic N deposition can enhance the hydrolytic EEa; these effects increase OM decomposition rates and emissions of $CO_2$ and $CH_4$ from wetland systems. The researches on the relationship between microbial structures and EE functions, and environmental factors controlling EEa can be helpful to manipulate wetland ecosystems for treating pollutants and to monitor wetland ecosystem services.

• Microbiology and Biotechnology Letters
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• v.41 no.1
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• pp.105-111
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• 2013

Biofilm formation of multifunctional plant growth promoting rhizobacterium (PGPR), Pseudomonas fluorescens 2112 is necessary for P. fluorescens 2112 to have a positive impact on the rhizosphere of red-pepper. This study investigated whether signal molecules of the quorum sensing AHLs are produced in order to confirm biofilm formative ability. Through the use of Petri dish bioassays a blue circle formed evidence of AHLs. It was confirmed that P. fluorescens 2112 produced six-carbon-chain-long AHLs by TLC bioassay. The bacterial density of P. fluorescens 2112 on the top and bottom of pepper plant roots was estimated as $3{\times}10^5$ and $8{\times}10^3$ CFU/g root, respectively. P. fluorescens 2112 exist more with high-density of $3.5{\times}10^6$ CFU/g soil at a depth of 1 cm but at a low-density of $1.1{\times}10$ CFU/g soil at a depth of 5 cm, from the surface of rhizosphere soil. In addition, biofilm formation of P. fluorescens 2112 on the epidermises and the tips of the red-pepper roots were confirmed visually by SEM. Thus, the production of AHLs by P. fluorescens 2112 brings about quorum sensing signaling and the formation of biofilm on the roots which has a positive effect on economically important crops such as red-pepper by additionally producing a variety of antifungal substances and auxin.

• Korean Journal of Microbiology
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• v.39 no.1
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• pp.16-20
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• 2003

A phylogenetic analysis of bacterial populations inhabiting soil derived from serpentine was conducted. The samples were collected from adjacent metamorphic rocks and serpentinite soil at Kwangcheon. The pH of the serpentine areas ranged from 8.5 to 9.2. The number of bacteria on the DAL medium which was diluted with $10^{-2}$ of AL medium was 10~100 fold higher than that from the full strength of AL medium, and which indicates that oligotrophs are distributed in the serpentinite soil. Of a total of 76 isolates, 42 isolates were oligotrophic bacteria, which grew only on the DAL medium. Based on a phylogenetic analysis using 16S rDNA sequences, these isolates are found to fall within five major phylogenetic groups: proteobacteria $\alpha$-subdivision (3 strains), $\alpha$-subdivision (7 strains), $\gamma$-subdivision (2 trains); high G+C gram-positive bacteria (19 strains); low G+C grampositive bacteria (14 strains). Bacteria of the genus Streptomyces (high G+C division) and Bacillus (low G+C division) have been considered to form a numerically important fraction of serpentinite soil. Oligotrophic strains categorized as Afipia ($\alpha$-subdivision), Ralstonia, Variovorax ($\beta$-subdivision), Pseudomonas ($\gamma$ -subdivision), Arthrobacter (high G+C division), and Streptomyces (low G+C division).

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.262-269
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• 2010

To investigate a quantitative evaluation of the actinobacteria, we have collected samples from various kinds of bamboo forest soil. Each different layers contained $2.7{\times}10^6-2.7{\times}10^8$ CFU/g of actinobacteria which was the highest in litter layers of Sasa boreali forest soil. We obtained 330 actinobacteria from different layers of bamboo forest soil; litter (100 strains), humus (70 strains), and rhizosphere soil (160 strains). Based on the colony morphology (aerial mycelium, substrate mycelium, and soluble pigment), isolates were divided into thirty-six groups and we selected 50 representative isolates. 16S rRNA gene sequence analysis showed Streptomyces was major actinobacteria (94%) and they were categorized as cluster I (2 strains), II (35 strains), III (6 strains), and IV (7 strains), respectively. The diversity index of 50 Streptomyces collected from the bamboo forest soil was calculated with the Shannon-Wiener method. Bamboo litter showed higher diversity index level of 3.33 than that of humus and rhizosphere soil. Also, antibiotic activities of our isolates were investigated against Botrytis cinerea, Xanthomonas campestris, Xanthomonas axonopodis pv. vesicatoria, and Bacillus cereus and found in 74, 16, 25, and 24 strains, respectively.

• Journal of Soil and Groundwater Environment
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• v.25 no.1
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• pp.25-36
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• 2020

In a redox transition zone, geochemical reactions are facilitated by active bacteria that mediate reactions involving electrons, and arsenic (As) and iron (Fe) cycles are the major electron transfer reactions occurring at such a site. In this study, the effect of repetitive redox changes on soil bacterial community in As-contaminated soil was investigated. The results revealed that bacterial community changed actively in response to redox changes, and bacterial diversity gradually decreased as the cycle repeated. Proportion of strict aerobes and anaerobes decreased, while microaerophilic species such as Azospirillum oryzae group became the predominant species, accounting for 72.7% of the total counts after four weeks of incubation. Bacterial species capable of reducing Fe or As (e.g., Clostridium, Desulfitobacterium) belonging to diverse phylogenetic groups were detected. Indices representing richness (i.e., Chao 1) and phylogenetic diversity decreased from 1,868 and 1,926 to 848 and 1,121, respectively. Principle component analysis suggests that repetitive redox fluctuation, rather than oxic or anoxic status itself, is an important factor in determining the change of soil bacterial community, which in turn affects the cycling of As and Fe in redox transition zones.

• Journal of Korean Society of Environmental Engineers
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• v.36 no.4
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• pp.277-285
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• 2014

The usage of efficient microorganism (EM) is increasing in concern for server purposes including odor removal during carcasses degradation. In this study, we have studied the type of soil and its effect on efficient microorganisms for the removal of odorous gases during buried carcasses degradation in lab-scale reactor. The carcasses are buried in the reactor with various soil types such as normal soil, 20% sandy and 20% clay soil with the efficient microorganism KEM. The efficient microorganisms KEM have the ability to stabilize the degradation of carcasses of the burial site. We have focused on the analysis of odorous gases such tri-methylamine (TMA), hydrogen sulfide ($H_2S$), methyl mercaptan (MM), dimethyl sulfide (DMS), dimethyl disulfide (DMDS), carbon dioxide ($CO_2$), and methane ($CH_4$) along with the changes of microbial community changed during complete degradation of buried carcasses for a year. The results suggested that the 20% sandy soil contain lesser level of $H_2S$ and MM (0.09 and 0.35 mg) but 20% clay has higher nitrogen compound removing effect and leave only less amount of ammonia and TMA (0.31 and 2.06 mg). The 20% sandy soil also has the ability to breakdown the carcasses more quality compared with other types of soil. Based on the data obtained in this study suggesting that, the use of 20% sandy soil can effectively control sulfur compounds whereas 20% clay soil controls nitrogen compounds in the buried soil. Depending on the type of the soil, the dominant of microbial communities and the distribution was change.

• Korean Journal of Environmental Agriculture
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• v.35 no.1
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• pp.39-45
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• 2016

BACKGROUND: This study aimed to evaluate the combined effects of three components (NPK) of chemical fertilizers with basal application of compost on soil organisms.METHODS AND RESULTS: The soil was treated with five treatments continuously for 15 years: control, PK, NK, NP and NPK. The application of N increased plant growth or biomass, and enhanced organic matter content in the soils. Levels of microbial phospholipid fatty acids (PLFAs) in the soils did not show marked differences among the soils treated with different treatments. However, the principal component analysis showed the changes in the structure of the microbial community in the soil, depending on treatments added. Nitrogen application caused a decrease of pH and an increase of EC in the soils, and these environmental stresses appeared to offset the promoting effect of increased organic matter content on microbial abundance. The abundance of bacterivorous nematodes was the highest in the soils after treating NPK; however, the abundance of fungivorous nematodes was unaffected. There was no significant correlation between the abundances of microbial groups and their feeders. Organic matter content was significantly correlated with the abundance of nematodes in the soils.CONCLUSION: Our results showed that chemical fertilizers affect the soil food chains through both biotic and abiotic factors, and a trophic cascade in the soils may not occur in response to long-term fertilization.

• Journal of the Korea Organic Resources Recycling Association
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• v.26 no.3
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• pp.23-31
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• 2018

This study was carried out to investigate the effects of livestock manure compost and fish-meal liquid fertilizer on the growth of cucumber and the soil properties for the stable production of organic cucumber. Cucumber was transplanted in greenhouse on the $6^{th}$ of April in 2017, and this experiment contained five treatments: livestock manure compost 100% (LC 100%), livestock manure compost 50% + fish-meal liquid fertilizer 50% (LC50 + LF50), livestock manure compost 50% (LC50), chemical fertilizer (NPK), and no fertilizer (NF). As a result, it was shown that soil chemical properties of LC50 + LF50 plot is not different from that of LC100 plot except for the EC content, but soil chemical properties of LC50 + LF50 plot is statistically significantly different from that of NPK plot except for pH. As a result of evaluating the functional diversity of soil microbial communities using Biolog system, the substrate richness (S) and the diversity index (H) were the highest in LC50 + LF50 plot. As a result of comparing the cucumber growth and yield, it was found that there was no statistically significant difference between the plant height and the fresh weight of LC100, LC50 + LF50, and NPK plot, but the plant height and the fresh weight of LC100, LC50 + LF50, and NPK plot were different from that of LC50 and NF plot. The yield of cucumber was the highest in NPK plot r(7,397 kg/10a), but there was no statistically significant difference in the yield of cucumber between NPK plot and LC100, LC50 + LF50 plot. The above-described results suggested that the livestock manure compost and fish meal liquid fertilizer can be used for organic cucumber production under greenhouse condition.

• KSBB Journal
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• v.28 no.5
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• pp.275-281
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• 2013

Soil microbial community analysis of farmland soil sprayed with lye in order to use fertilizer in Nigeria was performed. As a control, two kinds of soils not sprayed with lye, located in Eungo and Lagos with general practice in agriculture was selected. Soil sprayed with lye was pH 8.25 through alkalization reaction, while the other soil samples were pH 6.22 and 5.94. Substrate utilization and species diversity index of soil sprayed with lye were low than that of the other soils with the analysis of Biolog ecoplate. As a result of principal component analysis, the relationship between three samples was low. Microbial community analysis was performed by DGGE and most of them were soil uncultured bacterium. Especially, Uncultured Acidobacteria and Uncultured Methylocystis sp., which had been isolated from the rhizosphere of soybean grown in that site were discovered in the soil sprayed with lye.

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.336-342
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• 2013

Trichloroethylene (TCE) is a widely used substance in commercial and industrial applications, yet it must be removed from the contaminated soil and groundwater environment due to its toxic and carcinogenic nature. We investigated bacterial community structure, dominant bacterial strain, and removal efficiency in a TCE contaminated groundwater treatment system using immobilized carrier. The microbial diversity was determined by the nucleotide sequences of 16S rRNA gene library. The major bacterial population of the contaminated groundwater treatment system was belonging to BTEX degradation bacteria. The bacterial community consisted mainly of one genus of Pseudomonas (Pseudomonas putida group). The domination of Pseudomonas putida group may be caused by high concentration of toluene and TCE. Furthermore, we isolated a toluene and TCE degrading bacterium, named Pseudomonas sp. DHC8, from the immobilized carrier in bioreactor which was designed to remove TCE from the contaminated ground water. Based on the results of morphological and physiological characteristics, and 16S rRNA gene sequence analysis, strain DHC8 was identified as a member of Pseudomonas putida group. When TCE (0.83 mg/L) and toluene (60.61 mg/L) were degraded by this strain, removal efficiencies were 72.3% and 100% for 12.5 h, respectively. Toluene removal rate was 2.89 ${\mu}mol/g$-DCW/h and TCE removal rate was 0.02 ${\mu}mol/g$-DCW/h. These findings will be helpful for maintaining maximum TCE removal efficiency of a reactor for bioremediation of TCE.