• Journal of Korean Society of Environmental Engineers
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• v.31 no.12
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• pp.1069-1074
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• 2009

This study investigated soil microbial community and growth of Zea mays to compare the toxicity of nano and micro-sized Cu and Zn oxide particles in microcosm system. In the presence of nanoparticles, biomass of Zea mays reduced by 30% compared with micro-sized particles and inhibited growth. Dehydrogenase activity was inhibited by CuO nano although it was increased by ZnO nano particles. According to the Biolog test, the microbial diversity was decreased after exposed to CuO nanoparticles and ZnO microparticles. Therefore, though it is widely recognized that nanoparticles are more harmful than microparticles, we can conclude that the diversity of microbial community does not always influenced by the size of particles of nano and micro.

• Korean Journal of Environmental Agriculture
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• v.31 no.1
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• pp.52-59
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• 2012

BACKGROUND: Cultivation of genetically modified(GM) crops rapidly has increased in the global agricultural area. Among those, herbicide resistant GM crops are reported to have occupied 89.3 million hectares in 2010. However, cultivation of GM crops in the field evoked the concern of the possibility of gene transfer from transgenic plant into soil microorganisms. In our present study, we have assessed the effects of herbicide-resistant GM Chinese cabbage on the surrounding soil microbial community. METHODS AND RESULTS: The effects of a herbicide-resistant genetically modified (GM) Chinese cabbage on the soil microbial community in its field of growth were assessed using a conventional culture technique and also culture-independent molecular methods. Three replicate field plots were planted with a single GM and four non-GM Chinese cabbages (these included a non-GM counterpart). The soils around these plants were compared using colony counting, denaturing gradient gel electrophoresis and a species diversity index assessment during the growing periods. The bacterial, fungal and actinomycetes population densities of the GM Chinese cabbage soils were found to be within the range of those of the non-GM Chinese cabbage soils. The DGGE banding patterns of the GM and non-GM soils were also similar, suggesting that the bacterial community structures were stable within a given month and were unaffected by the presence of a GM plant. The similarities of the bacterial species diversity indices were consistent with this finding. CONCLUSION: These results indicate that soil microbial communities are unaffected by the cultivation of herbicide-resistant GM Chinese cabbage within the experimental time frame.

• Journal of Photoscience
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• v.9 no.3
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• pp.45-48
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• 2002

Microbial rhodopsins, photoactive 7-transmembrane helix proteins that use retinal as their chromophore, were observed initially in the Archaea and appeared to be restricted to extreme halophilic environments. Our understanding of the abundance and diversity of this family has been radically transformed by findings over the past three years. Genome sequencing of cultivated microbes as well as environmental genomics have unexpectedly revealed archaeal rhodopsin homologs in the other two domains of life as well, namely Bacteria and Eucarya. Organisms containing these homologs inhabit such diverse environments as salt flats, soil, freshwater, and surface and deep ocean waters, and they comprise a broad phylogenetic range of microbial life, including haloarchaea, proteobacteria, cyanobacteria, fungi, and algae. Analysis of the new microbial rhodopsins and their expression and structural and functional characterization reveal that they fulfill both ion transport and sensory functions in various organisms, and use a variety of signaling mechanisms. We have obtained the first crystallographic structure for a photosensory member of this family, the phototaxis receptor sensory rhodopsin II (SRII, also known as phoborhodopsin) that mediates blue-light avoidance by the haloarchaeon Natronobacterium pharaonis. The structure obtained from x-ray diffraction of 3D crystals prepared in a cubic lipid phase reveals key features responsible for its spectral tuning and its sensory function. The mechanism of SRII signaling fits a unified model for transport and signaling in this widespread family of phototransducers.

• Journal of Microbiology and Biotechnology
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• v.33 no.8
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• pp.1013-1022
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• 2023

Arbuscular mycorrhizal fungi (AMF) are widespread soil endophytic fungi, forming mutualistic relationships with the vast majority of land plants. Biochar (BC) has been reported to improve soil fertility and promote plant growth. However, limited studies are available concerning the combined effects of AMF and BC on soil community structure and plant growth. In this work, a pot experiment was designed to investigate the effects of AMF and BC on the rhizosphere microbial community of Allium fistulosum L. Using Illumina high-throughput sequencing, we showed that inoculation of AMF and BC had a significant impact on soil microbial community composition, diversity, and versatility. Increases were observed in both plant growth (the plant height by 8.6%, shoot fresh weight by 12.1%) and root morphological traits (average diameter by 20.5%). The phylogenetic tree also showed differences in the fungal community composition in A. fistulosum. In addition, Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed that 16 biomarkers were detected in the control (CK) and AMF treatment, while only 3 were detected in the AMF + BC treatment. Molecular ecological network analysis showed that the AMF + BC treatment group had a more complex network of fungal communities, as evidenced by higher average connectivity. The functional composition spectrum showed significant differences in the functional distribution of soil microbial communities among different fungal genera. The structural equation model (SEM) confirmed that AMF could improve the microbial multifunctionality by regulating the rhizosphere fungal diversity and soil properties. Our findings provide new information on the effects of AMF and biochar on plants and soil microbial communities.

• Journal of Veterinary Science
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• v.25 no.5
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• pp.65.1-65.11
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• 2024

Importance: Recent developments in genetic analytical techniques have enabled the comprehensive analysis of gastrointestinal symbiotic bacteria as a screening tool for animal health conditions, especially the endangered gibbons at the National Wildlife Rescue Centre (NWRC). Objective: High-throughput sequencing based on 16S ribosomal RNA genes was used to determine the baseline gut bacterial composition and identify potential pathogenic bacteria among three endangered gibbons housed in the NWRC. Methods: Feces were collected from 14 individuals (Hylobates lar, n = 9; Hylobates agilis, n = 4; and Symphalangus syndactylus, n = 1) from March to November 2022. Amplicon sequencing were conducted by targeting V3-V4 region. Results: The fecal microbial community of the study gibbons was dominated by Bacteroidetes and Firmicutes (phylum level), Prevotellaceae and Lachnospiraceae/Muribaculaceae (family level), and Prevotella (and its subgroups) (genera level). This trend suggests that the microbial community composition of the study gibbons differed insignificantly from previously reported conspecific or closely related gibbon species. Conclusions and Relevance: This study showed no serious health problems that require immediate attention. However, relatively low alpha diversity and few potential bacteria related to gastrointestinal diseases and streptococcal infections were detected. Information on microbial composition is essential as a guideline to sustain a healthy gut condition of captive gibbons in NWRC, especially before releasing this primate back into the wild or semi-wild environment. Further enhanced husbandry environments in the NWRC are expected through continuous health monitoring and increase diversity of the gut microbiota through diet diversification.

• Korean Journal of Organic Agriculture
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• v.27 no.4
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• pp.479-499
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• 2019

This study was conducted to investigate the responses of soil properties and microbial communities to different agricultural management and soil types, including organic management in Andisols (Org-A), organic management in Non-andisols (Org-NA), conventional management in Andisols (Con-A) and conventional management in Non-andisols (Con-NA) by using a pyrosequencing approach of 16S rRNA gene amplicon in Radish farms of volcanic ash soil in Jeju island. The results showed that agricultural management systems had a little influence on the soil chemical properties but had significant influence on microbial communities. In addition, soil types had significant influences on both the soil chemical properties and microbial communities. Organic farming increased the microbial density of bacteria and biomass C compared to conventional farming, regardless of soil types. Additionally, Org-NA had the highest dehydrogenase activity among treatments, whereas no difference was found between Org-A, Con-A and Con-NA and had the highest species richness (Chao 1) and diversity (Phyrogenetic diversity). Particularly, Chao 1 and Phyrogenetic diversity were increased in organic plots by 12% and 20%, compared with conventional plots, respectively. Also, regardless of agricultural management and soil types, Proteobacteria was the most abundant bacterial phylum, accounting for 21.9-25.9% of the bacterial 16S rRNAs. The relative abundance of putative copiotroph such as Firmicutes was highest in Org-NA plot by 21.0%, as follows Con-NA (13.1%), Con-A (6.7%) and Org-A (5.1%.), respectively and those of putative oligotrophs such as Acidobacteria and Planctomycetes were higher in Con-A than those in the other plots. Furthermore, LEfSe indicated that organic system enhanced the abundance of Fumicutes, while conventional system increased the abundance of Acidobacteria, especially in Non-andisols. Correlation analysis showed that total organic carbon (TOC) and nutrient levels (e.g. available P and exchangeable K) were significantly correlated to the structure of the microbial community and microbial activity. Overall, our results showed that the continuous organic farming systems without chemical materials, as well as the soil types made by long-term environmental factors might influence on soil properties and increase microbial abundances and diversity.

• Journal of Life Science
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• v.33 no.6
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• pp.481-489
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• 2023

The taste and quality of soy sauce, a fermented liquid condiment, is greatly influenced by microbial metabolism during fermentation. To investigate the microbiological characteristics of ganjang during the initial fermentation process, we prepared meju (fermented soybean) blocks fermented with starter cultures and solar salts and analyzed the microbial community quantitively using 16S rRNA gene profiling from ganjang that had been fermented over a five-week period. The ganjang samples were collected and analyzed after soaking for week one (1W), three (3W), and five (5W) weeks. We found that Halomonadaceae was significantly higher in the 1W group (89.83%) than the 3W and 5W groups (14.46%, and 13.78%, respectively). At a species level, Chromohalobacter beijerinckii and Chromohalobacter canadensis were the dominant species in the 1W group but several taxa such as Bacillus subtilis, Pediococcus acidilactici, and Enterococcus faecalis were more abundant in the 3W and 5W groups. Pearson correlation analysis of the relative abundance of the bacteria showed a negative correlation between Chromohalobacter and two bacterial genera Bacillus and Enterococcus. Beta-diversity showed a statistical distinction between the 1W and the 3W and 5W groups, while no significance was evident between the 3W and 5W groups. Linear discriminant effect size analysis was used to identify biomarkers and significant differences in the relative abundance of several halophilic bacteria, Bacillus sp. and lactic acid bacteria at 1W, 3W, and 5W, recpectively, which indicates the important role of the bacterial community at these time points.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.90-93
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• 2002

The revolution in molecular biology has given us greatly increased ability to obtain and to modify biological resources and to use them for the benefit of all humankind. The sequencing and the associated analysis of gene functions for a growing number of genomes will have an unprecedented effect on the uses of biological resources and the need for access to them. To investigate the diversity of microbial community in swamp, molecular systematic methods were applied. By amplified rDNA restriction analysis (ARDRA) and rDNA partial sequence analysis, $75\%$ of the isolates were known species. In case of uncultured analysis, almost all the selected clones were new species candidate. Especially archea and uncultured bacterial analyses, all clones were new taxon candidates. As for the eukaryotic diversity, several yeast form cultures were isolated from various samples of swamp. Among them, about $60\%$ of the isolates were easily identified. In case of a new species candidate, most strain were included in hymenomycetal yeasts.

• Journal of Conservation Science
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• v.37 no.4
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• pp.357-361
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• 2021

In order to determine the changes in microbial community due to termites, soil microorganisms surrounding the termites were investigated. First, bacterial communities from soil with termites collected at Seonamsa temple, Suncheon city, Korea were compared by next-generation sequencing (NGS, Illumina Miseq). The bacterial composition of soil from Daeungjeon without termites and the soil from Josadang, Palsangjeon, and Samjeon with termites were compared. Next, the bacterial composition of these soils was also compared with that of humus soil cultured with termites. A total high-quality sequences of 71,942 and 72,429 reads were identified in Seonamsa temple's soil and humus soil, respectively. The dominant phyla in the collected Seonamsa temple's soil were Proteobacteria (27%), Firmicutes (24%) and Actinobacteria (21%), whereas those in the humus soil were Bacteriodetes (56%) and Proteobacteria (37%). Using a two-dimensional plot to explain the principal coordinate analysis of operational taxonomic unit compositions of the soil samples, it was confirmed that the samples were divided into soil with and without termites, and it was especially confirmed that the Proteobacteria phylum was increased in humus soil with termites than in humus soil without termites.

• Journal of Life Science
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• v.27 no.9
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• pp.1086-1095
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• 2017

There is growing interest in groundwater resources to overcome the loss of surface water resources due to climate change. An understanding of the microbial community of aquifers is essential for monitoring and evaluating groundwater contamination, as well as groundwater management. Most microorganisms that inhabit aquifer ecosystems are attached to sediment particles rather than planktonic, as is the case in groundwater. Since sampling aquifer sediment is not easy, groundwater, which contains planktonic microorganisms, is generally sampled in microbial community research. Although many studies have investigated microbial communities in contaminated aquifers, there are only a few reports of microbial communities in uncontaminated or pristine aquifers, resulting in limited information on aquifer microbial diversity. Such information is needed for groundwater quality improvement. This paper describes the ecology and community structure of groundwater bacteria in uncontaminated aquifers. The diversity and structures of microbial communities in these aquifers were affected by the concentration or distribution of substrates (e.g., minerals, organic matter, etc), in addition to groundwater characteristics and human activities. Most of the microbial communities in these uncontaminated aquifers were dominated by Proteobacteria. Studies of microbial communities in uncontaminated aquifers are important to better understand the biogeochemical processes associated with groundwater quality improvement. In addition, information on the microbial communities of aquifers can be used as a basis to monitor changes in community structure due to contamination.