• Applied Biological Chemistry
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• v.33 no.2
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• pp.133-137
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• 1990

The effects of soil environmental conditions on the rate of degradation of fungicide IBP (Iprobenfos, S-benzyl O, O-diisopropyl phosphorothioate) in the soils under flooded condintions were examined in the laboratory. IBP in soil was degraded more slowly under flooded conditions than under upland conditions. The degradation greatly varied among soils, and the degradation rate was negatively correlated with the content of soil organic matter. Degradation of IBP was influenced by the soil temperature and the amount of IBP applied. The rate of degradation in soil was remarkably inhibited by the amendment of rice straw but not affected by the treatment of mixed-fertilizer, and insecticide fenitrothion and herbicide butachlor. The degradation of IBP was assumed to be due to microorganisms, especially aerobic microbes, as no degradation was observed in sterilized soil.

• Journal of Microbiology and Biotechnology
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• v.31 no.8
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• pp.1045-1059
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• 2021

Various abiotic stressors like drought, salinity, temperature, and heavy metals are major environmental stresses that affect agricultural productivity and crop yields all over the world. Continuous changes in climatic conditions put selective pressure on the microbial ecosystem to produce exopolysaccharides. Apart from soil aggregation, exopolysaccharide (EPS) production also helps in increasing water permeability, nutrient uptake by roots, soil stability, soil fertility, plant biomass, chlorophyll content, root and shoot length, and surface area of leaves while also helping maintain metabolic and physiological activities during drought stress. EPS-producing microbes can impart salt tolerance to plants by binding to sodium ions in the soil and preventing these ions from reaching the stem, thereby decreasing sodium absorption from the soil and increasing nutrient uptake by the roots. Biofilm formation in high-salinity soils increases cell viability, enhances soil fertility, and promotes plant growth and development. The third environmental stressor is presence of heavy metals in the soil due to improper industrial waste disposal practices that are toxic for plants. EPS production by soil bacteria can result in the biomineralization of metal ions, thereby imparting metal stress tolerance to plants. Finally, high temperatures can also affect agricultural productivity by decreasing plant metabolism, seedling growth, and seed germination. The present review discusses the role of exopolysaccharide-producing plant growth-promoting bacteria in modulating plant growth and development in plants and alleviating extreme abiotic stress condition. The review suggests exploring the potential of EPS-producing bacteria for multiple abiotic stress management strategies.

• Journal of Plant Biotechnology
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• v.34 no.1
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• pp.75-80
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• 2007

The release of genetically modified organisms ($GMO_{s}$) into the environment has the potential risks regarding the possibility of gene transfer from $GMO_{s}$ to natural organisms and this needs to be evaluated. This study was conducted to monitor the possible horizontal gene transfer from herbicide-resistant zoysiagrass (Zoysia japonica Steud.) to indigenous microorganisms. We have first examined the effect of field-released GM zoysiagrass on the microbial flora in the gut of locust (Locusts mlgratoria). The microbial flora was analyzed through determining the 165 rDHA sequences of microorganisms. The comparison of the microbial flora in the gut of locusts that were captured at the field of GM zoysiagrass and of wild-type revealed that there is no noticeable difference between these two groups. This result indicates that the GM zoysiagrass does not have negative impact on microbial flora in the gut of locust. We then investigated whether the horizontal gene transfer occurred from GM zoysiagrass to microbes in soil, rhizosphere and faecal pellets from locusts by utilizing molecular tools such as Southern hybridization and polymerase chain reaction (PCR). When the total DNAs isolated from microbes in GM zoysiagrass and in wild-type zoysiagrass fields were hybridized with probes for bar or hpt gene, no hybridization signal was detected from both field isolates, while the probes were hybridized with DNA from the positive control. Absence of these genes in the FNAs of soil microorganisms as well as microbes in the gut of locust was further confirmed by PCR. Taken together, our data showed that horizontal gene transfer did not occur in this system. These results further indicate that frequencies of transfer of engineered plant DNA to bacteria are likely to be negligible.

• Journal of Ginseng Research
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• v.43 no.1
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• pp.1-9
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• 2019

Background: Korean ginseng is an important cash crop in Asian countries. However, plant yield is reduced by pathogens. Among the Ilyonectria radicicola-species complex, I. mors-panacis is responsible for root-rot and replant failure of ginseng in Asia. The development of new methods to reveal the existence of the pathogen before cultivation is started is essential. Therefore, a quantitative real-time polymerase chain reaction method was developed to detect and quantify the pathogen in ginseng soils. Methods: In this study, a species-specific histone H3 primer set was developed for the quantification of I. mors-panacis. The primer set was used on DNA from other microbes to evaluate its sensitivity and selectivity for I. mors-panacis DNA. Sterilized soil samples artificially infected with the pathogen at different concentrations were used to evaluate the ability of the primer set to detect the pathogen population in the soil DNA. Finally, the pathogen was quantified in many natural soil samples. Results: The designed primer set was found to be sensitive and selective for I. mors-panacis DNA. In artificially infected sterilized soil samples, using quantitative real-time polymerase chain reaction the estimated amount of template was positively correlated with the pathogen concentration in soil samples ($R^2=0.95$), disease severity index ($R^2=0.99$), and colony-forming units ($R^2=0.87$). In natural soils, the pathogen was recorded in most fields producing bad yields at a range of $5.82{\pm}2.35pg/g$ to $892.34{\pm}103.70pg/g$ of soil. Conclusion: According to these results, the proposed primer set is applicable for estimating soil quality before ginseng cultivation. This will contribute to disease management and crop protection in the future.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.4
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• pp.593-601
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• 2012

Heavy metals and metalloids removal can be considered as one of the most important world challenges because of their toxicity and direct impact on human health. Many processes have been introduced but biological processes of remediation seem to offer the most suitable solution in terms of efficiency and low cost. Actinobacteria constitute one of the major microbial populations in soil, and this can be attributed to their adaptive morphological structure as well as their exceptional metabolic power. Among microbes, actinobacteria are morphologic intermediate between fungi and bacteria. Studies on microbial diversities in metal contaminated lands have shown that actinobacteria may constitute a dominantly active microbiota in addition to ${\alpha}$ Proteobacteria. Furthermore, isolation studies have shown metal removal mechanisms which are reminiscent of notable multiresistant strains, such as Cupriavidus metallidurans. Apart from members of genus Streptomyces, which produce more than 90% of commercialized antibiotics, and the nitrogen fixing Frankia, little attention has been given to other members of this phylum. This is because of difficult culture condition requirements and maintenance. In this review, we focused on specific isolation of actinobacteria and their potential applications in metal bioremediation and plant growth promotion.

• Korean Journal of Environmental Agriculture
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• v.39 no.1
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• pp.26-35
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• 2020

BACKGROUND: Microbes that govern a unique biochemical process of oxidizing ammonia into dinitrogen gas, such as anaerobic ammonium oxidation (anammox) have been reported to play a pivotal role in agricultural soils and in oceanic environments. However, limited information for anammox bacterial abundance and distribution in the terrestrial habitats has been known. METHODS AND RESULTS: Phylogenetic and next-generation sequencing analyses of bacterial 16S rRNA gene were performed to examine potential anammox bacteria in paddy soils. Through clone libraries constructed by using the anammox bacteria-specific primers, some clones showed sequence similarities with Planctomycetes (87% to 99%) and anammox bacteria (94% to 95%). Microbial community analysis for the paddy soils by using Illumina Miseq sequencing of 16S rRNA gene at phylum level was dominated by unclassified Bacteria at 33.2 ± 7.6%, followed by Chloroflexi at 20.4 ± 2.0% and Acidobacteria at 17.0 ± 6.5%. Planctomycetes that anammox bacteria are belonged to was 1.5% (± 0.3) on average from the two paddy soils. CONCLUSION: We suggest evidence of anammox bacteria in the paddy soil. In addition to the relatively well-known microbial processes for nitrogen-cycle, anammox can be a potential contributor on the cycle in terrestrial environments such as paddy soils.

• Research in Plant Disease
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• v.29 no.4
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• pp.399-404
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• 2023

Agricultural activities and the number of farms in the subarctic regions have been increasing annually after the coronavirus disease 2019 pandemic to achieve food self-sufficiency. Potatoes are vulnerable to soft rot bacteria at all stages of production, storage, and transportation. A novel bacterium, Pseudomonas sp. N3-W, isolated from Alaska tundra soil, grows at 5-25℃ and produces extracellular protease(s). N3-W caused necrotic spots (hypersensitivity) in hot pepper leaves and soft rot disease (pathogenicity) in potato tubers. The psychrotolerant N3-W caused significant soft rot symptoms on potatoes at a broad temperature range (5℃, 15℃, and 25℃). In contrast, mesophilic Pectobacterium carotovorum KACC 16999 induced severe rotting symptoms in potatoes at their optimal growth temperature of 15℃ and 25℃. However, it barely produced symptoms at 5℃, which is the appropriate storage and transportation temperature for potatoes. The results of pathogenicity testing imply that psychrotolerant soft rot pathogens from polar regions may cause severe soft rot not only during the crop growing season but also during storage and transportation. Our study indicates the possibility of new plant pathogen emergence and transmission due to the expansion of crop cultivation areas caused by permafrost thawing in response to recent polar warming.

• Applied Biological Chemistry
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• v.33 no.2
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• pp.138-142
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• 1990

The effects of heavy metals Cd, Cu, Cr, Ni, and Zn on the degradation of the insecticide fenitrothion (O, O-dimethyl O-4-nitro-m-tolyl phosphorothioate), the fungicide IBP (5-benzyl O, O-diisopropyl phosphorothioate), and the herbicide butachlor (N-butoxymetyl-2-chloro-2', 6'-diethylacetanilide) in flooded soils were examined in the laboratory. The degradation of the 3 pesticides in soil was greatly inhibited by the amendment of the 5 heavy metals. The inhibition rate was high in the order of butachlor>IBP>fenitrothion. Populations of fenitrothion-and butachlor-degrading microbes, which were counted by the MPN method, were lower in heavy metals added soil than in the control soil. The effect of heavy metals on the degradation of the 3 pesticides in soil varied with the kind and concentration of heavy metals and the kind of pesticides.

• Journal of Microbiology and Biotechnology
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• v.25 no.5
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• pp.569-578
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• 2015

Cold water paddy field soils are relatively unproductive, but can be ameliorated by supplementing with inorganic fertilizer from animal waste-based composts. The yield of two rice cultivars was significantly raised by providing either chicken manure or cow dung-based compost. The application of these composts raised the soil pH as well as both the total nitrogen and ammonium nitrogen content, which improved the soil's fertility and raised its nitrification potential. The composts had a measurable effect on the abundance of nitrogencycling-related soil microbes, as measured by estimating the copy number of various bacterial and archaeal genes using quantitative real-time PCR. The abundance of ammonia oxidizing archaea and bacteria was markedly encouraged by the application of chicken manure-based compost. Supplementation with the composts helped promote the availability of soil nitrogen in the cold water paddy field, thereby improving the soil's productivity and increasing the yield of the rice crop.

• Journal of Microbiology and Biotechnology
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• v.26 no.2
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• pp.248-254
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• 2016

A soil metagenome contains the genomes of all microbes included in a soil sample, including those that cannot be cultured. In this study, soil metagenome libraries were searched for microbial genes exhibiting lipolytic activity and those involved in potential lipid metabolism that could yield valuable products in microorganisms. One of the subclones derived from the original fosmid clone, pELP120, was selected for further analysis. A subclone spanning a 3.3 kb DNA fragment was found to encode for lipase/esterase and contained an additional partial open reading frame encoding a wax ester synthase (WES) motif. Consequently, both pELP120 and the full length of the gene potentially encoding WES were sequenced. To determine if the wes gene encoded a functioning WES protein that produced wax esters, gas chromatography-mass spectroscopy was conducted using ethyl acetate extract from an Escherichia coli strain that expressed the wes gene and was grown with hexadecanol. The ethyl acetate extract from this E. coli strain did indeed produce wax ester compounds of various carbon-chain lengths. DNA sequence analysis of the full-length gene revealed that the gene cluster may be derived from a member of Proteobacteria, whereas the clone does not contain any clear phylogenetic markers. These results suggest that the wes gene discovered in this study encodes a functional protein in E. coli and produces wax esters through a heterologous expression system.