• Korean Journal of Environmental Agriculture
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• v.40 no.1
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• pp.49-59
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• 2021

BACKGROUND: Soil salinity causes reduction of crop productivity. Rhizosphere microbes have metabolic capabilities and ability to adaptation of plants to biotic and abiotic stresses. Plant growth-promoting bacteria (PGPB) could play a role as elicitors for inducing tolerance to stresses in plants by affecting resident microorganism in soil. This study was conducted to demonstrate the effect of selected strains on rhizosphere microbial community under salinity stress. METHODS AND RESULTS: The experiments were conducted in tomato plants in pots containing field soil. Bacterial suspension was inoculated into three-week-old tomato plants, one week after inoculation, and -1,000 kPa-balanced salinity stress was imposed. The physiological and biochemical attributes of plant under salt stress were monitored by evaluating pigment, malondialdehyde (MDA), proline, soil pH, electrical conductivity (EC) and ion concentrations. To demonstrate the effect of selected Bacillus strains on rhizosphere microbial community, soil microbial diversity and abundance were evaluated with Illumina MiSeq sequencing, and primer sets of 341F/805R and ITS3/ITS4 were used for bacterial and fungal communities, respectively. As a result, when the bacterial strains were inoculated and then salinity stress was imposed, the inoculation decreases the stress susceptibility including reduction in lipid peroxidation, enhanced pigmentation and proline accumulation which subsequently resulted in better plant growth. However, bacterial inoculations did not affect diversity (observed OTUs, ACE, Chao1 and Shannon) and structure (principle coordinate analysis) of microbial communities under salinity stress. Furthermore, relative abundance in microbial communities had no significant difference between bacterial treated- and untreated-soils under salinity stress. CONCLUSION: Inoculation of Bacillus strains could affect plant responses and soil pH of tomato plants under salinity stress, whereas microbial diversity and abundance had no significant difference by the bacterial treatments. These findings demonstrated that Bacillus strains could alleviate plant's salinity damages by regulating pigments, proline, and MDA contents without significant changes of microbial community in tomato plants, and can be used as effective biostimulators against salinity stress for sustainable agriculture.

• Journal of Microbiology and Biotechnology
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• v.30 no.11
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• pp.1688-1696
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• 2020

Soil physical and chemical characteristics, soil potential denitrification rates (PDR), community composition and nirK-, nirS- and nosZ-encoding denitrifiers were studied by using MiSeq sequencing, quantitative polymerase chain reaction (qPCR), and terminal restriction fragment polymorphism (T-RFLP) technologies base on short-term (5-year) tillage field experiment. The experiment included four tillage treatments: conventional tillage with crop residue incorporation (CT), rotary tillage with crop residue incorporation (RT), no-tillage with crop residue retention (NT), and rotary tillage with crop residue removed as control (RTO). The results indicated that soil organic carbon, total nitrogen and NH₄⁺-N contents were increased with CT, RT and NT treatments. Compared with RTO treatment, the copies number of nirK, nirS and nosZ in paddy soil with CT, RT and NT treatments were significantly increased. The principal coordinate analysis indicated that tillage management and crop residue returning management were the most and the second important factors for the change of denitrifying bacteria community, respectively. Meanwhile, this study indicated that activity and community composition of denitrifiers with CT, RT and NT treatments were increased, compared with RTO treatment. This result showed that nirK, nirS and nosZ-type denitrifiers communities in crop residue applied soil had higher species diversity compared with crop residue removed soil, and denitrifying bacteria community composition were dominated by Gammaproteobacteria, Deltaproteobacteria, and Betaproteobacteria. Therefore, it is a beneficial practice to increase soil PDR level, abundance and community composition of nitrogen-functional soil microorganism by combined application of tillage with crop residue management.

• Journal of Microbiology and Biotechnology
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• v.21 no.9
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• pp.885-892
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• 2011

The bacterial communities in the intestinal tracts of earthworm were investigated by culture-dependent and -independent approaches. In total, 72 and 55 pure cultures were isolated from the intestinal tracts of earthworms under aerobic and anaerobic conditions, respectively. Aerobic bacteria were classified as Aeromonas (40%), Bacillus (37%), Photobacterium (10%), Pseudomonas (7%), and Shewanella (6%). Anaerobic bacteria were classified as Aeromonas (52%), Bacillus (27%), Shewanella (12%), Paenibacillus (5%), Clostridium (2%), and Cellulosimicrobium (2%). The dominant microorganisms were Aeromonas and Bacillus species under both aerobic and anaerobic conditions. In all, 39 DNA fragments were identified by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis. Aeromonas sp. was the dominant microorganism in feeds, intestinal tracts, and casts of earthworms. The DGGE band intensity of Aeromonas from feeds, intestinal tracts, and casts of earthworms was 12.8%, 14.7%, and 15.1%, respectively. The other strains identified were Bacillus, Clostridium, Enterobacter, Photobacterium, Pseudomonas, Shewanella, Streptomyces, uncultured Chloroflexi bacterium, and uncultured bacterium. These results suggest that PCR-DGGE analysis was more efficient than the culturedependent approach for the investigation of bacterial diversity and the identification of unculturable microorganisms.

• Korean Journal of Environmental Biology
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• v.37 no.3
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• pp.317-334
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• 2019

The present study was conducted to investigate the differences in managed farming practices, including low-intensive farming, duck farming, and golden apple snail farming, in a rice ecosystem by comparing terrestrial arthropod communities. A total of 75 species from 70 genera belonging to 43 families in 11 orders were identified from 9,622 collected arthropods. Araneae, Hemiptera, and Coleoptera were the richest taxa. Collembola was the most abundant, followed by Diptera, Hemiptera, and Araneae. Bray-Curtis similarity among the farming practices was very high (76.7%). The biodiversity of each farming practice showed a similar seasonality pattern. The richest species group was the predators, followed by the herbivores. The species richness and diversity of ecologically functional groups among the farming practices were not statistically significant, except for the abundance of predators in golden apple snail farming. The biodiversity seasonality of ecological functional groups in each farming practice showed similar patterns. The biomass of Araneae, Hemiptera, Coleoptera, and Diptera was greater than the other taxa, in general. The biomass of each ecological functional group showed little difference and the biomass fluctuation patterns in each farming practice were almost the same. Collectively, the community structures and biodiversity of terrestrial arthropods among the farming practices in the present study were not different. The present study may contribute to sustain rich biodiversity in irrigated rice fields and to advanced studies of food webs or energy flow structures in rice fields for ecological and sustainable agriculture.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.232-239
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• 2006

The microbial activity and bacterial community structure of activated sludge reactors, which treated free cyanide (FC), zinc-complexed cyanide (ZC), or nickel-complexed cyanide (NC), were studied. The three reactors (designated as re-FC, re-ZC, and re-NC) were operated for 50 days with a stepwise decrease of hydraulic retention time. In the re-FC and re-ZC reactors, FC or ZC was almost completely removed, whereas approximately 80-87% of NC was removed in re-NC. This result might be attributed to the high toxicity of nickel released after degradation of NC. In the batch test, the sludges taken from re-FC and re-ZC completely degraded FC, ZC, and NC, whereas the sludge from re-NC degraded only NC. Although re-FC and re-ZC showed similar properties in regard to cyanide degradation, denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene of the bacterial communities in the three reactors showed that bacterial community was specifically acclimated to each reactor. We found several bacterial sequences in DGGE bands that showed high similarity to known cyanide-degrading bacteria such as Klebsiella spp., Acidovorax spp., and Achromobacter xylosoxidans. Flocforming microorganism might also be one of the major microorganisms, since many sequences related to Zoogloea, Microbacterium, and phylum TM7 were detected in all the reactors.

• Environmental Engineering Research
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• v.25 no.1
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• pp.29-35
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• 2020

The aim of this study was to estimate the microbial metabolic activity of indigenous soil microbes under the radon exposure with different intensity and times in the secured laboratory radon chamber. For this purpose, the soil microbes were collected from radon-contaminated site located in the G county, Korea. Thereafter, their metabolic activity was determined after the radon exposure of varying radon concentrations of 185, 1,400 and 14,000 Bq/㎥. The average depth variable concentrations of soil radon in the radon-contaminated site were 707, 860 and 1,185 Bq/㎥ from 0, 15, and 30 cm in deep, respectively. Simultaneously, the soil microbial culture was mainly composed of Bacillus sp., Brevibacillus sp., Lysinibacillus sp., and Paenibacillus sp. From the radon exposure test, higher or lower radiation intensities compared to the threshold level attributed the metabolic activity of mixed microbial consortium to be reduced, whereas the moderate radiation intensity (i.e. threshold level) induced it to the pinnacle point. It was decided that radon radiation could instigate the microbial metabolic activity depending on the radon levels while they were exposed, which could consequently address that the certain extent of threshold concentration present in the ecosystem relevant to microbial diversity and population density to be more proliferated.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.350-350
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• 2017

The study was conducted to evaluate differences of growth characteristics of rice cultivated in two different regions (Cheonan and Jeonju). It focused on nutritional composition and anti-nutritional factors of rice straw produced from 21 rice varieties including GM rice (Iksan 483). The range of general nutrition ingredient is that crude was 0.97 ~ 3.2 %, carbohydrate was 67.45 ~ 80.01 %, crude protein was 1.46 ~ 4.81 %, crude ash was 6.52 ~ 18.96 %, crude fiber was 25.77 ~ 40.02 %, NDF was 51.84 ~ 67.77 %, ADF was 27.11 ~ 40.44 %, calcium was 0.49 ~ 5.18 mg/g and phosphorous was 0.26 ~ 2.77 mg/g. The general nutritional contents of GM rice were included above range. The range of phytic acid of rice straws cultivated in Cheonan and Jeonju was 0 ~ 0.056 mg/ml and 0 ~ 0.059 mg/ml, respectively. The phytic acid content of GM was 0.033 mg/ml, which was in the range of the content of rice straw in Cheonan and Jeonju. The range of trypsin inhibitor of rice straws cultivated in Cheonan and Jeonju was 0.061 ~ 0.461 TIU/mg and 0 ~ 1.278 TIU/mg, respectively. The trypsin acid content of GM was 0.461 TIU/mg, which was in the range of the content of rice straw in Cheonan and Jeonju. In addition, we investigated microbial community from each soil sample by using metagenomics sequencing based on rRNA microbial diversity in order to inspect indirect changes of soil environment with cultivation of GM rice. Metagenomics analysis was carried out using soil samples cultivated with GM and non-GM rice for before transplanting, young panicle differentiation stage, heading stage, and ripening stage. Beta diversity of microbial community in both soil environments were calculated by using Bray-Curtis distance method and showed low value with an average of 0.24 (dissimilarity = 1). As a result, it was confirmed that the cultivation of GM does not give a significant effect on the change of microbial composition in soil. Therefore, Our study demonstrates that there is no difference in the composition of soil microorganism due to GM and non-GM rice.

• Journal of Life Science
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• v.29 no.2
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• pp.248-255
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• 2019

This research confirmed the diversity and characterization of gut microorganisms isolated from the intestinal organs of Muraenesox cinereus, collected on the Samcheonpo Coast and Seocheon Coast in South Korea. To isolate strains, Marine agar medium was basically used and cultivated at $37^{\circ}C$ and pH7 for several days aerobically. After single colony isolation, totally 49 pure single-colonies were isolated and phylogenetic analysis was carried out based on the result of 16S rRNA gene DNA sequencing, indicating that isolated strains were divided into 3 phyla, 13 families, 15 genera, 34 species and 49 strains. Proteobacteria phylum, the main phyletic group, comprised 83.7% with 8 families, 8 genera and 26 species of Aeromonadaceae, Pseudoalteromonadaceae, Shewanellaceae, Enterobacteriaceae, Morganellaceae, Moraxellaceae, Pseudomonadaceae, and Vibrionaceae. To confirm whether isolated strain can produce industrially useful enzyme or not, amylase, lipase, and protease enzyme assays were performed individually, showing that 39 strains possessed at least one enzyme activity. Especially the Aeromonas sp. strains showed all enzyme activity tested. This result indicated that isolated strains have shown the possibility of the industrial application. Therefore, this study has contributed for securing domestic genetic resources and the expansion of scientific knowledge of the gut microbial community in Muraenesox cinereus of South Korea.

• Economic and Environmental Geology
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• v.57 no.3
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• pp.305-317
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• 2024

To investigate the effect of changes in microbial communities on arsenic release in soil, experiments were conducted on arsenic-contaminated soils (F1, G7, and G10). The experiments involved three groups of the experimental sets; ① BAC: sterilized soil + Bacillus fungorum, ② IND: indigenous bacteria, and ③ MIX: indigenous bacteria + B. fungorum, and incubated them for seven weeks using lactate as a carbon source under anaerobic conditions. The experimental results showed that higher concentrations of arsenic were released from the IND and MIX soils, where indigenous bacterial communities existed, compared to BAC. Significantly higher levels of arsenic were released from the G10 soil, which showed higher pH, compared to the F1 and G7 soils. In the G10 soil, unlike other soils, the proportion of As(III) among the released arsenic was also low. These results may be attributed to differences in microbial community composition that vary depending on the soil. By the seventh week, the diversity of microbial species in the IND and MIX soils had significantly decreased, with dominant orders such as Eubacteriales and Bacillales thriving. Bacteroidales in the seventh week of the MIX in the F1 soil, Rummeliibacillus in the seventh week of the IND and MIX of the G7 soil, and Enterobacterales in the IND and MIX of the G10 soil were dominant. At present, it is not known which mechanisms of microbial community changes affect the geochemical behavior of arsenic; however, these results indicate that microbiome in the soil may function as one of the factors regulating arsenic release.

• Microbiology and Biotechnology Letters
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• v.45 no.1
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• pp.71-80
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• 2017

Tea is the most popular beverage in the world. The three main types are green, black, and post-fermented. Post-fermented teas are produced by the microbial fermentation of sun-dried green tea leaves (Camellia sinensis). In this study, the composition of the bacterial communities involved in the production of traditional oriental post-fermented teas (Korean algacha, dancha, and Chinese pu-erh) were investigated using 16S rRNA gene analysis. The dominant microorganisms present in the post-fermented teas included the ${\alpha}$-proteobacteria Rhodobacteraceae and Sphingomonas, and the ${\gamma}$-proteobacteria Pantoea. Cluster analysis confirmed that the microbial populations present in both Korean and Chinese post-fermented teas grouped into the same class. Interestingly, the dominant microorganism present in the Korean post-fermented teas was a bacterium, while for the Chinese post-fermented tea, it was a fungus.