• Korean Journal of Soil Science and Fertilizer
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• v.33 no.4
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• pp.266-274
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• 2000

Understanding of microbial community structure in soil-root system is necessary to use beneficial soil and rhizosphere microbes for improvement of crop production and biocontrol. The knowledge of behavior and function of microbes in soil-root system plays a key role for the application of beneficial inocula. Because the majority of the intact bacteria in soil are unable to grow on nutrient media, both culturable and nonculturable bacteria have to be studied together. In our study, culture-independent survey of bacterial community in the soil-root system of red pepper fields was conducted by the sequence analysis of three universal clone libraries of genes which code for small-subunit rRNA (rDNA). Universal small subunit rRNA primers were used to amplify DNA extracted from each sample and PCR products were cloned into pGEM-T. Out of 27 clones sequenced, 25 clones were from domain bacteria. Two of the rDNA sequences were derived from eukaryotic organelles. Within the domain bacteria, several kingdoms were represented : the Proteobacteria (16 clones). Cytophyga-Flexibacter-Bacteroides group (2 clones). the high G+C content gram-positive group(1 clone) and 4 unknown clones.

• Journal of Microbiology and Biotechnology
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• v.23 no.11
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• pp.1617-1626
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• 2013

The Bacterial community structure and its complexity of the enrichment culture during the isolation and screening of imidacloprid-degrading strain were studied using denaturating gradient gel electrophoresis analysis. The dominant bacteria in the original tea rhizosphere soil were uncultured bacteria, Rhizobium sp., Sinorhizobium, Ochrobactrum sp., Alcaligenes, Bacillus sp., Bacterium, Klebsiella sp., and Ensifer adhaerens. The bacterial community structure was altered extensively and its complexity reduced during the enrichment process, and four culturable bacteria, Ochrobactrum sp., Rhizobium sp., Geobacillus stearothermophilus, and Alcaligenes faecalis, remained in the final enrichment. Only one indigenous strain, BCL-1, with imidacloprid-degrading potential, was isolated from the sixth enrichment culture. This isolate was a gram-negative rod-shaped bacterium and identified as the genus Ochrobactrum based on its morphological, physiological, and biochemical properties and its 16S rRNA gene sequence. The degradation test showed that approximately 67.67% of the imidacloprid (50 mg/l) was degraded within 48 h by strain BCL-1. The optimum conditions for degradation were a pH of 8 and $30^{\circ}C$. The simulation of imidacloprid bioremediation by strain BCL-1 in soil demonstrated that the best performance in situ (tea soil) resulted in the degradation of 92.44% of the imidacloprid (100 mg/g) within 20 days, which was better than those observed in the ex situ simulations that were 64.66% (cabbage soil), 41.15% (potato soil), and 54.15% (tomato soil).

• Korean Journal of Soil Science and Fertilizer
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• v.44 no.6
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• pp.1158-1163
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• 2011

The present study was aimed to evaluate the soil microbial communities by fatty acid methyl ester (FAME) method in paddy soils at 20 sites in Gyeongnam Province. The soil microbial biomass carbon content of fan and valley $1,266mg\;kg^{-1}$ was higher than alluvial plain $578mg\;kg^{-1}$ (p<0.05). In addition, The dehydrogenase activity of fan and valley $204{\mu}g\;TPF\;g^{-1}\;24h^{-1}$ was higher than alluvial plain $93{\mu}g\;TPF\;g^{-1}\;24h^{-1}$ (p<0.05). The communities of total bacteria and Gram-negative bacteria in the fan and valley paddy soils were significantly higher than those in the alluvial plain paddy soils (p<0.05). Total bacteria communities should be considered as a potential responsible factor for the obvious microbial community differentiation that was observed between the fan and valley and alluvial plain in paddy soils.

• Korean Journal of Soil Science and Fertilizer
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• v.17 no.3
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• pp.289-298
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• 1984

These studies were carried out to investigate the effects of rice straw on microflora in relation to the decomposition of organic matter, and the rate of rice straw decomposition. The number of total bacteria was increased in the first stage, and the number of microorganisms in upper layer was generally larger than lower layer. The number of fungi tended to decline as rice plant grew. Aerobacter among cellulose decomposition bacteria decreased with time, and the number of microorganisms in lower layer was higher than upper layer. The number of glucose decomposition bacteria and sulfate reducing bacteria increased in the submerged soil to which rice straw was applied, but decreased by percolation. the change of manganese oxidizing bacteria seemed not to be affected by rice straw application while they tend to increase as the rice plant grew. The aspect of microorganisms in the percolated water was same that of lower layer, but the number was low as much $10^{-1}$ during the whole stages. The decomposition rate of rice straw applied to submerged soil was about 40 per cent during the rice grew. The decomposition rate of cellulose contained rice straw was about 30 per cent, and lignin was about 60 per cent. The 70-80 per cent of nitrogen remained in the rice straw applied to soil.

• Journal of Ginseng Research
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• v.40 no.2
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• pp.97-104
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• 2016

Background: Rhizobacteria play an important role in plant defense and could be promising sources of biocontrol agents. This study aimed to screen antagonistic bacteria and develop a biocontrol system for root rot complex of Panax notoginseng. Methods: Pure-culture methods were used to isolate bacteria from the rhizosphere soil of notoginseng plants. The identification of isolates was based on the analysis of 16S ribosomal RNA (rRNA) sequences. Results: A total of 279 bacteria were obtained from rhizosphere soils of healthy and root-rot notoginseng plants, and uncultivated soil. Among all the isolates, 88 showed antagonistic activity to at least one of three phytopathogenic fungi, Fusarium oxysporum, Fusarium solani, and Phoma herbarum mainly causing root rot disease of P. notoginseng. Based on the 16S rRNA sequencing, the antagonistic bacteria were characterized into four clusters, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetesi. The genus Bacillus was the most frequently isolated, and Bacillus siamensis (Hs02), Bacillus atrophaeus (Hs09) showed strong antagonistic activity to the three pathogens. The distribution pattern differed in soil types, genera Achromobacter, Acidovorax, Brevibacterium, Brevundimonas, Flavimonas, and Streptomyces were only found in rhizosphere of healthy plants, while Delftia, Leclercia, Brevibacillus, Microbacterium, Pantoea, Rhizobium, and Stenotrophomonas only exist in soil of diseased plant, and Acinetobacter only exist in uncultivated soil. Conclusion: The results suggest that diverse bacteria exist in the P. notoginseng rhizosphere soil, with differences in community in the same field, and antagonistic isolates may be good potential biological control agent for the notoginseng root-rot diseases caused by F. oxysporum, Fusarium solani, and Panax herbarum.

• 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.

• Microbiology and Biotechnology Letters
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• v.49 no.3
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• pp.391-402
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• 2021

Earthworms play an important role in soil fertilization, interacting continually with microorganisms. This study aims to demonstrate the existence of beneficial microorganisms living in the earthworm's immune system, the coelomic fluid. To achieve this goal, a molecular identification technique was performed, using cytochrome c oxidase I (COI) barcoding to identify abundant endogenic earthworms inhabiting the temperate zone of Rabat, Morocco. Then, 16S rDNA and ITS sequencing techniques were adopted for bacteria and fungi, respectively. Biochemical analysis, showed the ability of bacteria to produce characteristic enzymes and utilize substrates. Qualitative screening of plant growth-promoting traits, including nitrogen fixation, phosphate and potassium solubilization, and indole acetic acid (IAA) production, was also performed. The result of mitochondrial COI barcoding allowed the identification of the earthworm species Aporrectodea molleri. Phenotypic and genotypic studies of the sixteen isolated bacteria and the two isolated fungi showed that they belong to the Pseudomonas, Aeromonas, Bacillus, Buttiauxella, Enterobacter, Pantoea, and Raoultella, and the Penicillium genera, respectively. Most of the isolated bacteria in the coelomic fluid showed the ability to produce β-glucosidase, β-glucosaminidase, Glutamyl-β-naphthylamidase, and aminopeptidase enzymes, utilizing substrates like aliphatic thiol, sorbitol, and fatty acid ester. Furthermore, three bacteria were able to fix nitrogen, solubilize phosphate and potassium, and produce IAA. This initial study demonstrated that despite the immune property of earthworms' coelomic fluid, it harbors beneficial microorganisms. Thus, the presence of resistant microorganisms in the earthworm's immune system highlights a possible selection process at the coelomic fluid level.

• Asian Journal of Turfgrass Science
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• v.10 no.3
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• pp.247-262
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• 1996

In this study, the distribution of dictyostelid cellular slime molds was investigated from F, H and $A_1$ horizon of pinus, oak forests in Mt. Puk'an, Mt. Nam and Mt. Kwanak. The relationship of cellular slime molds with other soil microorganisms and abiotic factors were analyzed. The six species were isolated as follows: Polysphondlium pallidurn, Dictyostelium purpureum, D. mucoroides, D. crassicaule, D. capitatum, D. implicatum. The dominant species in pinus forests was P. pallidum, and in oak forests it was D. macro ides. In Mt. Nam, D. mucoroides and P. pallidum were isolated at only oak forest. The Correlations of slime mold abundance with bacteria were significant. Even though positive correlations of cellular slime molds with actinomycetes or fungi were not significant, correlations between soil microorganisms were analyzed. Correlation coefficients were high in Mt. Kwanak(r=0.5921) and Mt. Nam(r=0.7243) at significant level P<0.01. There were significant correlations between total slime molds and abiotic factors. It supports that cellular slime molds are limited by foods in nature. In low level of pH, water content and organic matter, that community diversity is more affected by bacteria whose organic degradation capacity is regulated by interactions of soil microorgaisms. Key words: Cellular slime molds, Soil microorganisms, Correlations, Abiotic factors.

• Journal of Food Hygiene and Safety
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• v.31 no.6
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• pp.414-419
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• 2016

The aims of this study were to investigate microbial contamination levels and to survey sanitation management between Good Agricultural Practices (GAP) and non-GAP farms of lettuce and cucumber. The samples (lettuce, cucumber, soil, agricultural water, gloves, and packing plastic bag) were tested to analyze sanitary indicator bacteria (total aerobic bacteria, coliforms and Escherichia coli) and major pathogenic bacteria (Staphylococcus aureus, Bacillus cereus). In the lettuce farms, the contamination levels of total aerobic bacteria and coliforms in GAP farms were little lower than non-GAP farms or similar. Staphylococcus aureus and Bacillus cereus in soil and agricultural water of GAP farms were detected at higher levels than non-GAP farms in soil and agricultural water. In the case of cucumber farms, levels of total bacteria and Bacillus cereus in soil and total bacteria and coliform in gloves of GAP farms were higher than those of non-GAP farms, and other bacteria contamination levels in collected samples were similar. These results indicate that agricultural products produced from GAP farm still exhibited potential microbial risks. According to the field survey, a sanitation management in GAP farms was insufficient. These results could be useful as basic data to suggestion of plan for preventing microbial contamination and to improvement of GAP certification.

• Korean Journal of Weed Science
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• v.15 no.1
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• pp.63-72
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• 1995

This study was carried out to isolate the soil bacteria degrading herbicide napropamide [N,N-diethyl-2-(1-naphthoxy)-propionamide] from the clayey loam soil tested and to clarify the characteristics of the napropamide-degrading bacteria. Twenty strains of the gram-positive and the gram-negative bacteria were isolated and identified from the clayey loam soil tested. Most of them were vigorously proliferated at 100ppm of napropamide and two strains of Staphylococcus spp., Corynebacterium spp. II and Other spp. II were very tolerated to napropamide even at the concentration of 1500ppm. Staphylococcus spp. II and Actinobacillus spp. II of the isolated bacteria degraded more than 20% of the treated napropamide. These two strains could not utilize napropamide as sole nitrogen sources, but could use this compound as sole carbon sources. Napropamide was rapidly decomposed by Staphylococcus spp. II at one-time application and at three-time application of napropamide, but wasn't at two-time application of napropamide.