• 상하수도학회지
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• 제26권6호
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• pp.767-777
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• 2012

Annular Biofilm Reactor (ABR) equipped with coupons of three different pipe materials (STS 304, PVC, PE) was used to generate drinking water biofilm samples. The level of assimilable organic carbon (AOC) during the sample generation period was $37.3{\mu}g/L$, and this level did not seem to be low enough to limit the formation of biofilm in this study. Terminal-restriction fragment length polymorphism (T-RFLP) analyses determined T-RF profile as early as 3 h of exposure on PVC coupons. Average surface roughness ($R_a$) measured by atomic force microscopic analyses was 125.7 nm for PVC, and this value was higher than for STS (71.6 nm) and PE (74.0 nm). However, biofilm formation was faster on STS (6 h) than on PE (12 h), which indicated that surface roughness might not be the only factor that controlled the initiation of biofilm development. Upon detection of the T-RF peaks, richness (S) and diversity indices such as Shannon (H) and Simpson (1/D) demonstrated a rather slow increase until 48 h followed by rapid increase regardless of the pipe materials. Differences of microbial community structures among the biofilm samples were determined based on the cluster analysis using Jaccard coefficients (Sj). Biofilm communities could be divided into two distinct groups according to the exposure time regardless of the pipe materials. First group contained a young (< 48 h) biofilm samples (10 out of 11) but second group contained a mature (${\geq}$ 48 h) samples (11 out of 14). Results suggested that, due to the complexity of biofilm, the targeting of the first group of cluster was crucial for optimizing the management of drinking water distribution systems and controlling microbial growth.

• 대한환경공학회지
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• 제37권6호
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• pp.332-339
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• 2015

질소화합물은 부영양화 등 수질을 악화시키는 결과를 초래하므로 질소 제거는 수처리에 있어 가장 중요한 문제들 중 하나이다. 본 연구에서는 독립영양탈질 공정인 CANON (Completely Autotrophic Nitrogen-removal Over Nitrite)을 이용하여 암모니아성 질소 제거 효율을 평가하고, 미생물 군집 분석을 수행하였다. AOB (Ammonium Oxidizing Bacteria)와 ANAMMOX(ANaerobic AMMonium OXidation)균을 동시에 식종하고, $37^{\circ}C$에서 유입 암모니아성 질소농도 100 mg-N/L와 아질산성 질소 농도 100 mg-N/L 조건으로 운전한 결과, 성공적인 CANON 반응이 유도되었다. 유입수에서 아질산성 질소를 제외시키고 암모니아성 질소(100 mg-N/L)만을 공급하였을 때, DO농도 0.4 mg/L 이상에서는 CANON의 성능이 악화되었지만, DO농도를 0.3 mg/L으로 낮추자 71.3%의 총 질소제거효율을 나타내었다. 유입 암모니아성 질소 농도를 50 mg-N/L로 낮추었을 때, 질소 제거효율이 급격히 악화되었다. 그러나 유입농도를 다시 100 mg-N/L로 증가시키자 14일 만에 이전의 질소제거성능을 회복하였고, 이후 $76.1{\pm}4.9%$의 총 질소제거효율을 나타냈다. 온도를 상온($20{\pm}1^{\circ}C$) 조건으로 전환하자 초기에는 불안정한 CANON 반응이 일어났지만, 23일 이후에는 안정적인 총 질소제거효율($70.0{\pm}2.6$%)을 유지하였다. PCR-DGGE를 이용한 미생물군집 분석 결과, 식종원과 CANON의 미생물군집은 확연한 차이를 나타냈지만, CANON의 각 조건에 따른 미생물군집은 크게 다르지 않았다. 따라서 질소제거 성능의 악화는 미생물군집을 구성하는 미생물종의 변화에 기인하기 보다는 구성 미생물종들의 질소제거 활성의 저하에 기인하는 것으로 생각된다. 이러한 결과는 AOB와 ANAMMOX균을 식종하여 CANON 반응을 성공적으로 유도한다면, 이후 농도나 온도의 변화에도 안정적인 미생물군집을 유지할 수 있다는 것을 의미한다.

• 한국토양비료학회지
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• 제45권5호
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• pp.829-835
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• 2012

경제적 및 농업적 장점은 유전자 변형 작물 재배면적의 증가를 가져왔다. 그러나 유전자 변형 작물의 상업적 재배전에 유전자 변형 작물의 인간건강 및 환경에 미칠 잠재적 위해성에 대한 면밀한 검토가 필수적이다. 본 연구에서는 Bt벼의 토양미생물 군집에 미치는 영향을 조사하였다. 토양화학성분을 분석한 결과, Bt벼와 낙동벼 근권토양 간 화학성분의 유의성 있는 차이는 없는 것으로 조사되었다. 재배전, 재배초기, 최고분얼기의 토양미생물 군집밀도를 조사했을 때 Bt벼 근권토양의 세균, 방선균, 진균 군집밀도는 낙동벼와 유사한 수준으로 나타났다. 시기별 DGGE 분석결과 Bt 벼 근권토양 전체미생물상은 낙동벼와 차이가 없는 것으로 조사되었다. Pyrosequencing을 통한 Bt벼와 낙동벼의 미생물 군집조성을 조사한 결과 주요 미생물상 분포에 있어서도 매우 유사한 양상을 나타내었다. 위의 결과들을 종합해볼때 Bt 재배에 따른 토양미생물상에 미치는 영향은 미미한 것으로 사료된다. 수확 후 벼 잔존물이 토양환경에 미치는 영향에 대해서는 좀 더 연구가 진행되어야 할 것이다.

• The Plant Pathology Journal
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• 제37권6호
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• pp.521-532
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• 2021

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

• Journal of Microbiology and Biotechnology
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• 제29권10호
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• pp.1624-1628
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• 2019

Banana planting altered microbial communities and induced the enrichment of Fusarium oxysporum in rhizosphere compared with that of forest soil. Diseased plant rhizosphere soil (WR) harbored increased pathogen abundance and showed distinct microbial structures from healthy plant rhizosphere soil (HR). The enriched taxon of Bordetella and key taxon of Chaetomium together with some other taxa showed negative associations with pathogen in HR, indicating their importance in pathogen inhibition. Furthermore, a more stable microbiota was observed in HR than in WR. Taken together, the lower pathogen abundance, specific beneficial microbial taxa and stable microbiota contributed to disease suppression.

• 한국지하수토양환경학회지:지하수토양환경
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• 제29권3호
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• pp.1-13
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• 2024

This study investigated the hydrogeochemical and microbiological characteristics of freshwater on Ulleung Island, a volcanic island in the Ulleung Basin on the East Coast of Korea. The shallow groundwater (CSW, NRGW) and the surface water (SISW) samples are classified as Na-HCO₃ type, reflecting an alkaline rock type and an oxidizing environment due to the influence of a highly permeable pyroclastic rock layer. In contrast, the deep groundwater sample (DMW) is classified as Ca-HCO₃ type, suggesting the influence of deep-sourced carbon dioxide and reducing conditions. Microbial communities in the water samples are generally dominated by Proteobacteria, with the relative abundance of major genera varying depending on water quality and environmental conditions. Network analysis reveals the ecological characteristics of microbial communities adapted to specific environments. The presence of pathogenic genera in the shallow groundwater suggests potential groundwater contamination, necessitating appropriate management to ensure its use as drinking water or domestic water. The findings of this study provide valuable insights into the ecological characteristics of Ulleung Island's groundwater resources and can inform future groundwater management strategies.

• 한국환경농학회지
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• 제38권3호
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• pp.197-204
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• 2019

BACKGROUND: Living modified microorganisms (LMMs) have been focused in two very different aspects of positive and negative effects on ecology and human health. As a model experiment, wild type and a foreign origin gene-harboring modified E. coli strains were subjected to comparison of their metabolomes and potential effects on soil microbiota in the laboratory sets. This study assumes the unintentional release of LMMs and tries to suggest potential effects on the soil microbiota even at minimal settings. METHODS AND RESULTS: Metabolomes from the wild type and LM E. coli were analyzed by NMR and the profiles were compared. In the laboratory soil experiments, the two types of E. coli were added to the soils and monitored for the bacterial community compositions. Those metabolomic profiles did not show significant differences. The microbial community structures from the time series soil DNAs for both the sets using wild type and LMO also did not indicate significant changes, but minor by the addition of foreign organisms regardless of wild or LMO. CONCLUSION: Even if the recombinant microorganism (LMO) is released into the soil environment, the survival of microorganisms in the environment would be one of the major factors for the transfers of foreign genes to other organisms and diffusion into the soil environment.

• Journal of Microbiology and Biotechnology
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• 제26권7호
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• pp.1320-1332
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• 2016

Light hydrocarbons accumulated in subsurface soil by long-term microseepage could favor the anomalous growth of indigenous hydrocarbon-oxidizing microorganisms, which could be crucial indicators of underlying petroleum reservoirs. Here, Illumina MiSeq sequencing of the 16S rRNA gene was conducted to determine the bacterial community structures in soil samples collected from three typical oil and gas fields at different locations in China. Incubation with n-butane at the laboratory scale was performed to confirm the presence of "universal microbes" in light-hydrocarbon microseepage ecosystems. The results indicated significantly higher bacterial diversity in next-to-well samples compared with background samples at two of the three sites, which were notably different to oil-contaminated environments. Variation partitioning analysis showed that the bacterial community structures above the oil and gas fields at the scale of the present study were shaped mainly by environmental parameters, and geographic location was able to explain only 7.05% of the variation independently. The linear discriminant analysis effect size method revealed that the oil and gas fields significantly favored the growth of Mycobacterium, Flavobacterium, and Pseudomonas, as well as other related bacteria. The relative abundance of Mycobacterium and Pseudomonas increased notably after n-butane cultivation, which highlighted their potential as biomarkers of underlying oil deposits. This work contributes to a broader perspective on the bacterial community structures shaped by long-term light-hydrocarbon microseepage and proposes relatively universal indicators, providing an additional resource for the improvement of microbial prospecting of oil and gas.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• The Plant Pathology Journal
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• 제39권4호
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• pp.397-408
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• 2023

Fire blight disease, caused by Erwinia amylovora, is a devastating affliction in apple cultivation worldwide. Chemical pesticides have exhibited limited effectiveness in controlling the disease, and biological control options for treating fruit trees are limited. Therefore, a relatively large-scale survey is necessary to develop microbial agents for apple trees. Here we collected healthy apple trees from across the country to identify common and core bacterial taxa. We analyzed the endophytic bacterial communities in leaves and twigs and discovered that the twig bacterial communities were more conserved than those in the leaves, regardless of the origin of the sample. This finding indicates that specific endophytic taxa are consistently present in healthy apple trees and may be involved in vital functions such as disease prevention and growth. Furthermore, we compared the community metabolite pathway expression rates of these endophyte communities with those of E. amylovora infected apple trees and discovered that the endophyte communities in healthy apple trees not only had similar community structures but also similar metabolite pathway expression rates. Additionally, Pseudomonas and Methylobacterium-Methylorobrum were the dominant taxa in all healthy apple trees. Our findings provide valuable insights into the potential roles of endophytes in healthy apple trees and inform the development of strategies for enhancing apple growth and resilience. Moreover, the similarity in cluster structure and pathway analysis between healthy orchards was mutually reinforcing, demonstrating the power of microbiome analysis as a tool for identifying factors that contribute to plant health.