• Korean Journal of Environmental Agriculture
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• v.32 no.2
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• pp.95-101
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• 2013

BACKGROUND: Rice (Oryza sativa) is the most important staple food of over half the world's population. This study was conducted to evaluate the possible impact of transgenic rice cultivation on the soil microbial community. METHODS AND RESULTS: Microorganisms were isolated from the rhizosphere of GM and non-GM rice cultivation soils. Microbial community was identified based on the culture-dependent and molecular biology methods. The total numbers of bacteria, fungi, and actinomycete in the rhizosphere soils cultivated with GM and non-GM rice were similar to each other, and there was no significant difference between GM and non-GM rice. Dominant bacterial phyla in the rhizosphere soils cultivated with GM and non-GM rice were Actinobacteria, Firmicutes, and Proteobacteria. The microbial communities in GM and non-GM rice cultivated soils were characterized using the denaturing gradient gel electrophoresis (DGGE). The DGGE profiles showed similar patterns, but didn't show significant difference to each other. DNAs were isolated from soils cultivating GM and non-GM rice and analyzed for persistence of inserted gene in the soil by using PCR. The PCR analysis revealed that there were no amplified protox gene in soil DNA. CONCLUSION(S): These data suggest that transgenic rice does not have a significant impact on soil microbial communities, although continued research may be necessary.

• Journal of Korean Society of Environmental Engineers
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• v.32 no.2
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• pp.113-120
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• 2010

Air-cathode microbial fuel cell consisted of 4 unit cells were operated under batch condition and electricity generation and microbial community structure variation were investigated, depending on separator types and cathode characteristics: A) PEM(Proton Exchange Membrane)-30% Wet proofing Carbon Cloth(WC), B) AEM(Anion Exchange Membrane-WC, C) CEM(Cation Exchange Membrane)-WC, D) PEM-No Wet proofing Carbon Cloth(NC). Maximum power densities of PEM-WC, AEM-WC and CEM-WC were 510.9, 522.1 and 504.8 $mW/m^2$, respectively. But PEM-NC showed relatively lower maximum power density of 218.3 $mW/m^2$. And PEM-WC, AEM-WC and CEM-WC showed similar internal resistances(20.0-28.2 ${\Omega}$). PCRDGGE, PCA and diversity indices showed that uncultured bacteria which reported in previous MFC studies were detected in suspended growth bacteria and attached growth bacteria would be affected not by separator type but by cathode characteristic. Thus, cathode characteristic can be one of the critical factors for power generation in air-cathode MFC using PEM, AEM, and CEM as separator.

• The Journal of Engineering Geology
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• v.33 no.1
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• pp.15-25
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• 2023

The effects of forest fires on the activity of microbial communities in topsoil and subsoil were investigated. Samples were collected from Korean forest soils comprising mainly igneous and sedimentary rocks. Analysis of beta-glucosidase, found higher microbial activity in sedimentary rocks than in igneous rocks. Enzyme activity was not observed immediately after fire, but was restored over time. The enzyme activity of subsoil was inhibited by 33~46% compared with that in the topsoil, regardless of soil damage. The effect of fire on the availability of microbial substrate was investigated using EcoPlate. The percentages of average well color development values of damaged and normal topsoil were 52.7~56.8% and 62.3~83.6%, respectively. Forest fires appear to affect the diversity and substrate availability of the subsoil microbial community by accelerating the decomposition of soil organic matter. The Shanon index, representing microbial biodiversity, was high in the topsoil of all samples; it was higher for soil microorganisms in sedimentary rocks than in igneous rocks, and higher in topsoil than in subsoil.

• Korean Journal of Microbiology
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• v.45 no.1
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• pp.26-31
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• 2009

This study was aimed at the analysis of prokaryote communities in Korean traditional fermented food, jeotgal, and isolation of a novel strain from jeotgal by using culture-dependent and molecular biological approaches. Seventeen kinds of jeotgal were selected on the basis of its origins and sources. The samples were inoculated on 12 kinds of media. 308 isolates were selected randomly by morphological features, and its 16S rRNA gene sequences was amplified by PCR technique with bacteria and archaea specific primers (8F, 21F, and 1492R). The 16S rRNA gene sequences were compared with those in EzTaxon and GenBank databases. DNA-DNA hybridization was performed to identify a novel strain. As a result, the majority of the isolates were lactic acid bacteria (Leuconostoc, Weisella, Lactococcus, Lactobacillus, Carnobacterium, Marinilactibacillus), Bacillus, Pseudomonas, Micrococcus, Brevibacterium, Microbacterium and Kocuria in 17 kinds of jeotgal. The strains belonging to Salinicoccus, Halomonas, Cobetia, Lentibacillus, Paracoccus, and Psychrobacter were isolated as minor ones. Fourteen novel species were identified based on phylogenetic analysis.

• The Journal of Engineering Geology
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• v.33 no.2
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• pp.257-273
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• 2023

Hydrochemical characteristics and microbial communities of spring (Samtong), surface water, and groundwater in Cheorwon, Korea, were analyzed. Field surveys and water quality analyses were undertaken at 10 sampling points for five spring, two surface, and three groundwater samples on 15 December 2022. Hydrochemical analysis revealed that most water samples were Ca-HCO₃ type and that water-rock interactions were the predominant mineral source. Radon concentrations were <1 kBq m^-3 for surface water, 1~10 kBq m^-3 for spring water, and 1~1,000 kq m^-3 for groundwater. Microbial cluster analysis showed that the main phyla were Proteobacteria, Planctomyceta, Verrucomicrobia, Acidobacteria, and Actinomycetota.Non-metric multidimensional scaling (NMDS) analysis indicated that water temperature, pH, and Si content were closely related to microorganism content. NMDS and canonical correspondence analysis results revealed that environmental factors affecting spring water were temperature, and Mg and Si concentrations, particularly for Acidobacteria and Proteobacteria, and Pseudomonas brenneri. Both hydrochemical and microbial community analyses yielded similar results at some spring and groundwater sampling points, likely due to the effects of a basalt aquifer.

• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.171-179
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• 2016

Recent succession of soil microorganisms and vegetation has occurred in the glacier foreland, because of glacier thawing. In this study, whole microbial communities, including bacteria, archaea, and eukaryotes, from the glacier foreland of Midtre Lovénbreen in Svalbard were analyzed by metagenome sequencing, using the Ion Torrent Personal Genome Machine (PGM) platform. Soil samples were collected from two research sites (ML4 and ML7), with different exposure times, from the ice. A total of 2,798,108 and 1,691,859 reads were utilized for microbial community analysis based on the metagenomic sequences of ML4 and ML7, respectively. The relative abundance of microbial communities at the domain level showed a high proportion of bacteria (about 86−87%), whereas archaeal and eukaryotic communities were poorly represented by less than 1%. The remaining 12% of the sequences were found to be unclassified. Predominant bacterial groups included Proteobacteria (40.3% from ML4 and 43.3% from ML7) and Actinobacteria (22.9% and 24.9%). Major groups of Archaea included Euryarchaeota (84.4% and 81.1%), followed by Crenarchaeota (10.6% and 13.1%). In the case of eukaryotes, both ML4 and ML7 samples showed Ascomycota (33.8% and 45.0%) as the major group. These findings suggest that metagenome analysis using the Ion Torrent PGM platform could be suitably applied to analyze whole microbial community structures, providing a basis for assessing the relative importance of predominant groups of bacterial, archaeal, and eukaryotic microbial communities in the Arctic glacier foreland of Midtre Lovénbreen, with high resolution.

• Applied Biological Chemistry
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• v.39 no.5
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• pp.403-408
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• 1996

Total bacterial community DNA, which was extracted from microcosm soil and field soil after 2,4-D amendments, was analyzed on Southern blots, using the tfdA gene probe derived from plasmid pJP4 and the Spa probe from Sphingomonas paucimobilis. Southern blot analyses with total bacterial DNA extracted from soils Inoculated with Pseudomonas cepacia/pJP4 revealed that DNA probe method could detect the 2,4-D degrading bacteria down to $10^5\;cells/g$ dry soil. In the microcosm experiment, there was a good correlation between 2,4-D degradation and banding patterns in hybridization analyses performed after each 2,4-D treatment using the two probes. When bacterial DNA extracted from microcosm soil was hybridized with the Spa probe, a change in the position of hybrid bands was observed over time in a Southern blot, suggesting that population change or possibly genetic rearrangement in 2,4-D degrading microbial populations occurred in this soil. With the Spa probe, one hybrid DNA band was persistently observed throughout the five 2,4-D additions. When bacterial DNA isolated from the field soil was probed with the tfdA and Spa, strong hybridization signal was observed in the 100 ppm-treated subplot, weak signal In the 10 ppm-treated subplot, and no significant signal in the 1 ppm-treated and control subplots. The data show that DNA probe analyses were capable of detecting and discriminating the indigenous 2,4-D degrading microbial populations in soil amended with 2,4-D under laboratory and field conditions.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.26 no.6B
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• pp.695-701
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• 2006

A toluene-degrading bacterial strain was isolated from a mixed culture that was maintained using toluene as a sole carbon and energy source. The isolated bacterium was classified as Pseudomonas sp. TBD4 based on the close relationship to bacteria belonging to this genus. A bottle study to determine biodegradation rates of individual aromatic compounds showed that the biodegradation was faster in the order of toluene, benzene, styrene, and p-xylene. However, when various mixtures were subjected to TDB4, styrene was degraded at the highest rate, indicating that both toluene and p-xylene could stimulate the degradation of other substrates whereas styrene played as an inhibitor. In addition, the mixed culture and TDB4 were inoculated to the bioactive foam reactor (BFR), and the reactor performance and the corresponding change of microbial community were monitored using the fluorescent in situ hybridization (FISH) method. When an inlet concentration of the VOC mixture increased to greater than 250 ppm, the overall removal efficiency dropped significantly. The FISH measurement demonstrated that the ratio of TDB4 to the total bacteria also decreased to less than 20% along with the decline in removal efficiency in the BFR. As a result, the periodic addition of the pre-grown TDB4 might have been beneficial to achieve a stable performance in the BFR operated over an extended period.

• Korean Journal of Microbiology
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• v.50 no.3
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• pp.191-200
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• 2014

Gas hydrates play a significant role in the global carbon cycle and climate change because methane, a greenhouse gas, can be released from the dissociation of gas hydrate. Anaerobic oxidation of methane (AOM) is an important process that consumes more than 90% of the methane released into the hydrosphere and atmosphere. In this study, the microbial community associated with the methane gas hydrate sediment in the Ulleung basin, East Sea of Korea (UBGH) was analyzed by phylogenetic analysis of the mcrA and 16S rRNA gene libraries. A vertical stratification of the dominating anaerobic methane oxidizer (ANME)-1 group was observed at the surface and the sulfate methane transition zone (SMTZ). The ANME-2c group was found to be dominant in the high methane layer. The archaea of marine benthic group B, which is commonly observed in the AOM region, accounted for more than 50% of the identifications in all sediments. Nitrate reducing bacteria were predominant at SMTZ (Halomonas: 56.5%) and high methane layer (Achromobacter: 52.6%), while sulfate reducing bacteria were not found in UBGH sediments. These results suggest that the AOM process may be carried out by a syntrophic consortium of ANME and nitrate reducing bacteria in the gas hydrates of the Ulleung Basin of the East Sea.

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.3
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• pp.479-484
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• 2011

Fatty acid methyl ester (FAME) profiles were used to describe differences in soil microbial communities influenced by conventional farming system (CFS), conventional farming system without pesticides (CFSWP), and organic farming system (OFS) for strawberry cultivation in controlled horticultural land. In comparison to the CFS soils, the average soil microbial biomasses of in the OFS soils were approximately 1.2 times for total FAMEs ($195nmol\;g^{-1}$), 1.4 times for total bacteria ($58nmol\;g^{-1}$), 1.5 times for Gram-negative bacteria ($27.3nmol\;g^{-1}$), 1.2 times for Gram-positive bacteria ($26.1nmol\;g^{-1}$), and 1.5 times for actinomycetes ($2.8nmol\;g^{-1}$). The microbial communities of total bacteria (p<0.05) and Gram-negative bacteria (p<0.05) in the OFS and CFSWP soils were significantly higher larger than those in the CFS soils. However, fungal structure was significantly greater in CFS than in OFS and CFSWP (p<0.05). In principal component analyses of soil microbial communities, our findings suggest that actinomycetes should be considered as potential factor responsible for the clear microbial community differentiation observed between OFS and CFS in controlled horticultural land.