• Journal of Microbiology
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• 제42권1호
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• pp.9-13
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• 2004

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

• Journal of Microbiology and Biotechnology
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• 제23권6호
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• pp.739-749
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• 2013

The seasonal and spatial diversity of picocyanobacteria (Pcy) in lakes of the Great Mazurian Lakes (GLM) system was examined by DGGE analysis of molecular markers derived from the 16S-23S internal transcribed spacer (ITS) of the ribosomal operon and the phycocyanin operon (cpcBA-IGS). The study of nine lakes, ranging from mesotrophy to hypereutrophy, demonstrated seasonal variance of Pcy. The richness and Shannon diversity index calculated on the basis of both markers were higher in spring and lower in early and late summer. No statistically significant relationships were found between the markers and trophic status of the studied lakes or Pcy abundance. There were, however, statistically significant relationships between the diversity indices and sampling time. The analysis pointed to a different distribution of the two markers. The ITS marker exhibited more unique sequences in time and space, whereas a greater role for common and ubiquitous sequences was indicated by the cpcBA-IGS data. Examination of the Pcy community structure demonstrated that communities were grouped in highly similar clusters according to sampling season/time rather than to the trophic status of the lake. Our results suggest that time is more important than trophic status in shaping the diversity and structure of Pcy communities. The seasonal changes in picocyanobacteria and differences in diversity and community structures are discussed in the context of well-established ecological hypotheses: the PEG model, intermediate disturbance hypothesis (IDH), and horizontal gene transfer (HGT).

• 신재생에너지
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• 제18권2호
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• pp.9-17
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• 2022

In this study, we used the Flux Balance Analysis (FBA) program to examine the behavior of hydrogen and organic acids according to seasonal changes in food wastewater collected from D city. The results showed that average hydrogen conversion rates in spring, summer, autumn, and winter were 1.06, 0.71, 1.21, and 1.13 mol H₂/mol of hexose_added, respectively, indicating a significantly lower hydrogen conversion rate in summer than in other seasons. This phenomenon is believed to occur because the carbohydrate concentration of the incoming food wastewater is low. In addition, Lactobacillus, the lactic acid-producing bacterium, was 21.3% in spring, 27.2% in summer, 17.5% in autumn, and 22.6% in winter. The most distinctive feature of the microbial community in summer was that 15.3% of the Ilyobacter was analyzed. It was confirmed that Ilyobacter, which is involved in the production of acetic acid and propionic acid, is closely associated with the tendency of increasing acetic acid and propionic acid and thus contributes to organic acid change. Clostridium, a hydrogen-producing bacterium, was 76.2%, 50.8%, 78.3%, and 74%, in spring, summer, autumn, and winter, respectively. It was confirmed that Clostridium dominates the microbial community by approximately 70% or more in all seasons except summer.

• 대한환경공학회지
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• 제32권3호
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• pp.227-233
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• 2010

각종 오염지역의 오염토양의 시료를 채취해 DGGE를 이용한 미생물군집구조를 서로 비교함으로써 어떤 요인이 영향을 많이 미치는지를 알아보았다. 미생물군집의 유사도 비교에서 TPH 오염 말고는 대부분의 오염정도가 심하지 않아서 오염 특성보다는 토양시료가 채취된 지역에 따라 더 유사함을 보여주었고 TPH 오염도가 가장 높았던 시료에서만 지역적 특성을 넘어 유사도 차이를 보여 주었다. 이와 같이 오염요인이 너무 크지 않은 경우에는 미생물군집구조가 지역특성 즉 여러 다른 환경요인에 의해 더 크게 영향을 받는 것을 이 연구를 통해 알 수가 있었다. 모든 오염토양의 우점종(배양성 세균) 조사에서 firmicutes와 high GC Gram+에 속하는 세균들이 주로 발견되었고 유류오염이 심한 토양에서 이미 보고된 Arthrobacter, Bacillus, Methylobacterium, Clavibacter, Streptomyces, Nocardia와 아직 보고되지 않은 Leifsonia가 발견되었다.

• Journal of Microbiology and Biotechnology
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• 제24권3호
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• pp.313-323
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• 2014

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coal-mining reclamation areas was suggested.

• Journal of Microbiology and Biotechnology
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• 제11권6호
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• pp.994-1001
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• 2001

An easier way of understanding the BNR system was proposed from the study on substrate, nutrient removal tendency, microbial community and its metabolic function by applying the municipal settled sewage. During the anaerobic period, the phosphorus release rate per VFACOD we varied depending on the phosphorus content in the sludge. When the phosphorus content in the sludge was $6\%$ VSS, according to influent VFACOD, the phosphorus release rate and PHA production were $0.35 gPO_4P/gVFACOD$ and 1.0 gPHA/gVFACOD, respectively. The $NO_3N$ requirement for the phosphorus uptake as an electron acceptor was about $0.5 gNO_3N/gPO_4P_{uptake}$ based on the proposed equation with PHA, biomass, production, and the concentration of phosphorus release/uptake. Bacterial-community analysis of the sludge, as determined by FISH and 16SrDNA characterization FISH, revealed that the beta-subclass proteobacteria were the most abundant group ($27.9\%$ of the proteobacteria-specific probe EUB338), and it was likely that representative of the beta-subclass played key roles in activated sludge. The next dominant group found was the gamma-protebacteria ($15.4\%$ of probe EUB338). 16S rDNA clone library analysis showed that the members of${\beta}$- and ${\gamma}$-proteobacteria were also the most abundant groups, and $21.5\%$ (PN2 and PN4) and $15.4\%$ (PN1 and PN5) of total clones were the genera of denitrifying bacteria and PAO, respectively. Prediction of the microbial community composition was made with phosphorus content (Pv, $\%$ P/VSS) in wasted sludge and profiles of COD, PHA, $PO_4P,\;and\;NO_3N$ in an anaerobic-anoxic SBR unit. Generally, the predicted microbial composition based upon metabolic function, i.e., as measured by stoichiometry, is fairly similar to that measure by the unculturable dependent method. In this study, a proposal was made on he microbial community composition that was more easily approached to analyze the reactor behavior.

• Journal of Applied Biological Chemistry
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• 제56권2호
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• pp.95-100
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• 2013

현재 토양 생태에서 토양미생물은 유기물 분해, 질소 순환, 식물의 질소 이용 등 중요한 역할을 하고 있어, 토양 내 미생물 다양성을 분석하기 위한 연구는 지속적으로 진행되어 오고 있다. 본 연구에서는 논 토양의 미생물 생태 다양성을 조사하기 위한 효과적인 방법으로 denaturing gradient gel electrophoresis (DGGE)를 적용하고자 본 연구를 수행하였다. 논 토양 미생물의 DNA를 분리하기 위하여 lysis buffer method, skim milk bead method, sodium phosphate buffer method, Epicentre SoilMaster DNA extraction kit (Epicentre, USA), Mo Bio PowerSoil kit (Mo Bio, USA)를 이용하여 토양 내 gDNA 최적 추출방법을 확인하였다. 그 결과 Mo Bio PowerSoil kit를 사용하였을 때 Shannon 다양성지수가 세균 3.3870, 진균 3.6254으로 미생물 다양성 분석시에 가장 효과적이었다. DGGE 분석을 위한 조건은 세균의 경우 6% polyacylamide gel, 45-60% denaturing gradient였고, 진균의 경우 6% polyacrylamide gel, 45-80% denaturing gradient에서 최적 분석조건을 보였다. 위의 분석법을 적용하여 논 토양내의 미생물 군집의 변화를 살펴보면 시간의 변화 요인에 의해 미생물 변화가 일어나는 것을 알 수 있었다. 본 연구에서 사용된 DGGE 분석법을 통해 논토양 미생물의 분석 가능성을 제시 할 수 있었다.

• 한국환경농학회지
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• 제27권2호
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• pp.133-138
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• 2008

Fire can affect microbial community structure of soil through altered environmental conditions, nutrient availability, and biotic source for microbial re-colonization. We examined the influence of fire on chemical properties and soil enzyme activities of soil for 10 months. We also characterized the soil microbial community structure through ester-linked fatty acid analysis(EL-FAME). For this study, we established five burned plots(1*1 m) and 5 unburned plots outside the margin of fire. Soil was sampled three soil cores in a each plots and composited for analysis at 1, 3, 5, 8, and 10 month after fire. The fire caused an increase in soil pH, exchangeable Ca, and Mg, organic matter, available $P_2O_5$ compared to unburned sites. The content of $NH_4-N$ in burned site was significantly higher than that of unburned site and this effect continued for 8 months after fire. There was no difference of $NO_3-N$ content in soil between burned and unburned site. Fire caused no change in acid phosphatase and arylsulfatase activities but $\beta$-glucosidase and alkaline phosphatase activities in burned site were increased compared to unburned site. Microbial biomass as estimated by total concentration of EL-FAMEs in burned sites was significantly higher than that of unburned sites at one month after fire. Burned site decreased the EL-FAMEs indicative of gram-positive bacteria and tended to increase the fatty acid associated with gram-negative bacteria at one and three months after fire. The sum of EL-FAME compound $18:2{\omega}6,9c$ and $18:1{\omega}9c$ as served fungal biomarkers was decreased in burned site compared to unburned site.

• 한국토양비료학회지
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• 제47권2호
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• pp.100-106
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• 2014

The present study investigated variations in soil microbial communities by fatty acid methyl ester (FAME) and the chemical properties at 24 sites of upland soils in Gyeongnam Province. The electrical conductivity of the soil under potato cultivation was significantly higher than those of the red pepper and soybean soils (p < 0.05). The gram-negative bacteria community in potato soil was significantly lower than those in the garlic and soybean soils (p < 0.05). The communities of actinomycetes and arbuscular mycorrhizal fungi in the red pepper soil were significantly higher than those in the potato soil (p < 0.05). In addition, the cy17:0 to 16:$1{\omega}7c$ ratio was significantly lower in red pepper, soybean, and garlic soils compared with potato soil, indicating that microbial stress decreased. Consequently, differences in soil microbial community were highly associated with cultivated crop species, and this might be resulted from the difference in soil chemical properties.

• Advances in environmental research
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• 제2권1호
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• pp.61-80
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• 2013

Quantification of viable forms of microbial community (bacteria and fungi) using culture-dependent methods was done in order to characterize the indoor air quality (IAQ). Role of those factors, which may influence the concentration of viable counts of bacteria and fungi, like ventilation, occupancy, outdoor concentration and environmental parameters (temperature and relative humidity) were also determined. Volumetric-infiltration sampling technique was employed to collect air samples both inside and outside the schools. As regard of measurements of airborne viable culturable microflora of schools during one academic year, the level of TVMCs in school buildings was ranged between 803-5368 cfu/$m^3$. Viable counts of bacteria (VBCs) were constituted 63.7% of the mean total viable microbial counts where as viable counts of fungi (VFCs) formed 36.3% of the total. Mean a total viable microbial count (TVMCs) in three schools was 2491 cfu/$m^3$. Outdoor level of TVMCs was varied from 736-5855 cfu/$m^3$. Maximum and minimum VBCs were 3678-286 cfu/m3 respectively. Culturable fungal counts were ranged from 268-2089 cfu/$m^3$ in three schools. Significant positive correlation (p < 0.01) was indicated that indoor concentration of viable community reliant upon outdoor concentration. Temperature seemed to have a large effect (p < 0.05, p < 0.01) on the concentration of viable culturable microbial community rather than relative humidity. Consistent with the analysis and findings, the concentration of viable cultural counts of bacteria and fungi found indoors, were of several orders of magnitude, depending upon the potential of local, spatial and temporal factors, IO ratio appeared as a crucial indicator to identify the source of microbial contaminants.