• Journal of Microbiology and Biotechnology
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• v.22 no.10
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• pp.1330-1335
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• 2012

Foot and mouth disease (FMD) is one of the acute infectious diseases in hoofed and even-toed mammals, including pigs, and it occurs via acute infection by Aphthovirus. When FMD is suspected, animals around the location of origin are typically slaughtered and buried. Other methods such as rendering, composting, and incineration have not been verified in practice in Korea. After the FMD incident, the regular monitoring of the microbial community is required, as microorganisms greatly modify the characteristics of the ecosystem in which they live. This is the result of their metabolic activities causing chemical changes to take place in the surrounding environment. In this study, we investigated changes in the microbial community during a 24 week period with DNA extracts from leachate, formed by the decomposition of buried pigs at a laboratory test site, using denaturing gradient gel electrophoresis (DGGE) with a genomic DNA. Our results revealed that Bacteroides coprosuis, which is common in pig excreta, and Sporanaerobacter acetigenes, which is a sulfur-reduced microbe, were continuously observed. During the early stages (0~2 weeks) of tissue decomposition, Clostridium cochlearium, Fusobacterium ulcerans, and Fusobacterium sp., which are involved in skin decomposition, were also observed. In addition, various microbes such as Turicibacter sanguinis, Clostridium haemolyticum, Bacteroides propionicifaciens, and Comamonas sp. were seen during the later stages (16~24 weeks). In particular, the number of existing microbial species gradually increased during the early stages, including the exponential phase, decreased during the middle stages, and then increased again during the later stages. Therefore, these results indicate that the decomposition of pigs continues for a long period of time and leachate is created continuously during this process. It is known that leachate can easily flow into the neighboring environment, so a long-term management plan is needed in burial locations for FMD-infected animals.

• Journal of Soil and Groundwater Environment
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• v.17 no.5
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• pp.49-55
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• 2012

A 1.28 L-batch reactor and continuous-flow stirred tank reactor (CFSTR) fed with formate and trichloroethene (TCE) were operated for 120 days and 56 days, respectively, to study the effect of formate as electron donor on anaerobic reductive dechlorination (ARD) of TCE to cis-1,2-dichloroethylene (c-DCE), vinyl chloride (VC), and ethylene (ETH). In batch reactor, injected 60 ${\mu}mol$ TCE was completely degraded in the presence of 20% hydrogen gas ($H_2$) in less than 8 days by anaerobic dechlorination mixed-culture (300 mg-soluble protein), Evanite Culture with ability to completely degrade tetrachloroethene (PCE) and -TCE to ETH under anaerobic conditions. Once the formate was used as electron donor instead of hydrogen gas in batch or chemostat system, the TCE-dechlorination rate decreased and acetate production rate increased. It indicates that the concentration of hydrogen produced in both systems is possibly more close to threshold for homoacetogenesis process. Soluble protein concentration of Evanite culture during the batch test increased from 300 mg to 688 mg for 120 days. Through the protein monitoring, we confirmed an increase of microbial population during the reactor operation. In CFSTR test, TCE was fed continuously at 9.9 ppm (75.38 ${\mu}mol/L$) and the influent formate feed concentration increased stepwise from 1.3 mmol/L to 14.3 mmol/L. Injected TCE was accumulated at 18 days of HRT, but TCE was completely degraded at 36 days of HRT without accumulation of the injected-TCE during the left of experiment period, getting $H_2$ from fermentative hydrogen production of injected formate. Although c-DCE was also accumulated for 23 days after beginning of CFSTR operation, it reached steady-state in the presence of excessive formate. We also evaluated microbial dynamic of the culture at different chemical state in the reactor by DGGE (denaturing gradient gel electrophoresis).

• Journal of Microbiology and Biotechnology
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• v.22 no.8
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• pp.1101-1106
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• 2012

Market fresh makgeolli was stored at different temperatures of $4^{\circ}C$ and $25^{\circ}C$ to assess the change of the microbial diversity according to the storage temperature and period. Yeast counts increased until day 3 of storage and decreased thereafter. General and lactic acid bacterial counts continuously increased during storage. The data indicated that the control of growth of microorganisms, particularly general bacteria and lactic acid bacteria (LAB), is essential. Total acid levels started to decrease in the makgeolli stored at $4^{\circ}C$, and increased from day 6 of storage in the makgeolli stored at $25^{\circ}C$. The increase of total acid in the non-refrigerated condition greatly affected the quality of makgeolli. In both the fresh makgeolli samples stored at $4^{\circ}C$ and $25^{\circ}C$, yeast (Saccharomyces cerevisiae) and molds (Aspergillus tubingensis, Candida glaebosa, and Aspergillus niger) were noted. Denaturing gradient gel electrophoresis (DGGE) band patterns were almost constant regardless of the storage period. As for bacteria, Lactobacillus crustorum, L. brevis, and Microlaena stipoides were found in the makgeolli stored at $4^{\circ}C$, and L. crustorum, Lactobacillus sp., L. plantarum, L. brevis, L. rhamnosus, and L. similis were found in the makgeolli stored at $25^{\circ}C$. In particular, in the makgeolli stored at $25^{\circ}C$, L. crustorum and L. plantarum presented dark bands and were identified as the primary microorganisms that affected spoilage of fresh makgeolli.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.169-178
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• 2010

The microbial community structure in Thailand soils contaminated with low and high levels of arsenic was determined by denaturing gradient gel electrophoresis. Band pattern analysis indicated that the bacterial community was not significantly different in the two soils. Phylogenetic analysis obtained by excising and sequencing six bands indicated that the soils were dominated by Arthrobacter koreensis and $\beta$-Proteobacteria. Two hundred and sixty-two bacterial isolates were obtained from arsenic-contaminated soils. The majority of the As-resistant isolates were Gramnegative bacteria. MIC studies indicated that all of the tested bacteria had greater resistance to arsenate than arsenite. Some strains were capable of growing in medium containing up to 1,500 mg/l arsenite and arsenate. Correlations analysis of resistance patterns of arsenite resistance indicated that the isolated bacteria could be categorized into 13 groups, with a maximum similarity value of 100%. All strains were also evaluated for resistance to eight antibiotics. The antibiotic resistance patterns divided the strains into 100 unique groups, indicating that the strains were very diverse. Isolates from each antibiotic resistance group were characterized in more detail by using the repetitive extragenic palindromic-PCR (rep-PCR) DNA fingerprinting technique with ERIC primers. The PCR products were analyzed by agarose gel electrophoresis. The genetic relatedness of 100 bacterial fingerprints, determined by using the Pearson product-moment similarity coefficient, showed that the isolates could be divided into four clusters, with similarity values ranging from 5-99%. Although many isolates were genetically diverse, others were clonal in nature. Additionally, the arsenic-resistant isolates were examined for the presence of arsenic resistance (ars) genes by using PCR, and 30% of the isolates were found to carry an arsenate reductase encoded by the arsC gene.

• Journal of Microbiology and Biotechnology
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• v.26 no.4
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• pp.648-658
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• 2016

Preservation of fresh algae plays an important role in algae seed subculture and aquaculture. The determination and examination of the changes of cell viability, composition, and bacterial species during storage would help to take suitable preservation methods to prolong the preservation time of fresh algae. Nostoc flagelliforme is a kind of edible cyanobacterium with important herbal and dietary values. This article investigated the changes of bacterial species and biochemical characteristics of fresh N. flagelliforme concentrate during natural storage. It was found that the viability of cells decreased along with the storage time. Fourteen bacteria strains in the algae concentrate were identified by PCR-DGGE and were grouped into four phyla, including Cyanobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. Among them, Enterococcus viikkiensis may be a concern in the preservation. Eleven volatile organic compounds were identified from N. flagelliforme cells, in which geosmin could be treated as an indicator of the freshness of N. flagelliforme. The occurrence of indole compound may be an indicator of the degradation of cells.

• Journal of Microbiology and Biotechnology
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• v.28 no.11
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• pp.1823-1833
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• 2018

Fluorescence in-situ hybridization (FISH) is a common and popular method used to investigate microbial communities in natural and engineered environments. In this study, two specific 16S rRNA-targeted oligonucleotide probes, CLZ and KCLZ, were designed and verified to quantify the genus Clostridium and the species Clostridium kluyveri. The optimal concentration of hybridization buffer solution for both probes was 30% (w/v). The specificity of the designed probes was high due to the use of pellets from pure reference strains. Feasibility was tested using samples of Chinese liquor from the famed Luzhou manufacturing cellar. The effectiveness of detecting target cells appears to vary widely in different environments. In pit mud, the detection effectiveness of the target cell by probes CLZ and KCLZ was 49.11% and 32.14%, respectively. Quantitative analysis by FISH technique of microbes in pit mud and fermented grains showed consistency with the results detected by qPCR and PCR-DGGE techniques, which showed that the probes CLZ and KCLZ were suitable to analyze the biomass of Clostridium spp. and C. kluyveri during liquor fermentation. Therefore, this study provides a method for quantitative analysis of Clostridium spp. and C. kluyveri and monitoring their community dynamics in microecosystems.

• Journal of Microbiology and Biotechnology
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• v.30 no.7
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• pp.1005-1012
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• 2020

Acid mine drainage (AMD) has been a serious environmental issue that threatens soil and aquatic ecosystems. In this study, an acid-tolerant sulfate-reducing bacterium, strain S4, was isolated from the mud of an AMD storage pond in Vietnam via enrichment in anoxic mineral medium at pH 5. Comparative analyses of sequences of the 16S rRNA gene and dsrB gene involved in sulfate reduction revealed that the isolate belonged to the genus Desulfovibrio, and is most closely related to Desulfovibrio oxamicus (with 99% homology in 16S rDNA sequence and 98% homology in dsrB gene sequence). Denaturing gradient gel electrophoresis (DGGE) analyses of dsrB gene showed that strain S4 represented one of the two most abundant groups developed in the enrichment culture. Notably, strain S4 was capable of reducing sulfate in low pH environments (from 2 and above), and resistance to extremely high concentration of heavy metals (Fe 3,000 mg/l, Zn 100 mg/l, Cu 100 mg/l). In a batch incubation experiment in synthetic AMD with pH 3.5, strain S4 showed strong effects in facilitating growth of a neutrophilic, metal sensitive Desulfovibrio sp. strain SR4H, which was not capable of growing alone in such an environment. Thus, it is postulated that under extreme conditions such as an AMD environment, acid- and metal-tolerant sulfate-reducing bacteria (SRB)-like strain S4 would facilitate the growth of other widely distributed SRB by starting to reduce sulfate at low pH, thus increasing pH and lowering the metal concentration in the environment. Owing to such unique physiological characteristics, strain S4 shows great potential for application in sustainable remediation of AMD.

• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1193-1201
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• 2012

The analysis and quantification of ammonia-oxidizing bacteria (AOB) is crucial, as they initiate the biological removal of ammonia-nitrogen from sewage. Previous methods for analyzing the microbial community structure, which involve the plating of samples or culture media over agar plates, have been inadequate because many microorganisms found in a sewage plant are unculturable. In this study, to exclusively detect AOB, the analysis was carried out via denaturing gradient gel electrophoresis using a primer specific to the amoA gene, which is one of the functional genes known as ammonia monooxygenase. An AOB consortium (S1 sample) that could oxidize an unprecedented 100% of ammonia in 24 h was obtained from sewage sludge. In addition, real-time PCR was used to quantify the AOB. Results of the microbial community analysis in terms of carbon utilization ability of samples showed that the aeration tank water sample (S2), influent water sample (S3), and effluent water sample (S4) used all the 31 substrates considered, whereas the AOB consortium (S1) used only Tween 80, D-galacturonic acid, itaconic acid, D-malic acid, and $_L$-serine after 192 h. The largest concentration of AOB was detected in S1 ($7.6{\times}10^6copies/{\mu}l$), followed by S2 ($3.2{\times}10^6copies/{\mu}l$), S4 ($2.8{\times}10^6copies/{\mu}l$), and S3 ($2.4{\times}10^6copies/{\mu}l$).

• Journal of Microbiology and Biotechnology
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• v.20 no.2
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• pp.254-264
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• 2010

To obtain an efficient natural lignocellulolytic complex enzyme, we screened an efficient lignocellulose-degrading composite microbial system (XDC-2) from composted agricultural and animal wastes amended soil following a long-term directed acclimation. Not only could the XDC-2 degrade natural lignocelluloses, but it could also secrete extracellular xylanase efficiently in liquid culture under static conditions at room temperature. The XDC-2 degraded rice straw by 60.3% after fermentation for 15 days. Hemicelluloses were decomposed effectively, whereas the extracellular xylanase activity was dominant with an activity of 8.357 U/ml on day 6 of the fermentation period. The extracellular crude enzyme noticeably hydrolyzed natural lignocelluloses. The optimum temperature and pH for the xylanase activity were $40^{\circ}C$ and 6.0. However, the xylanase was activated in a wide pH range of 3.0-10.0, and retained more than 80% of its activity at $25-35^{\circ}C$ and pH 5.0-8.0 after three days of incubation in liquid culture under static conditions. PCR-DGGE analysis of successive subcultures indicated that the XDC-2 was structurally stable over long-term restricted and directed cultivation. Analysis of the 168 rRNA gene clone library showed that the XDC-2 was mainly composed of mesophilic bacteria related to the genera Clostridium, Bacteroides, Alcaligenes, Pseudomonas, etc. Our results offer a new approach to exploring efficient lignocellulolytic enzymes by constructing a high-performance composite microbial system with synergistic complex enzymes.

• Journal of Hydrogen and New Energy
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• v.19 no.5
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• pp.410-416
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• 2008

합성 및 두부 제조 폐수로부터 혐기 세균 복합체를 이용하여 수소를 생산하였다. 수소생산 혐기 세균 복합체는 하수처리장 농축 소화조에서 발생하는 슬러지를 $90^{\circ}C$에서 20분간 열처리하여 얻었다. 혐기 세균 복합체는 $37^{\circ}C$ 회분식 운전조건에서 1% (w/v) 포도당 함유 PYG (peptone-yeast extract-glucose) 배지로부터 1.15 L-$H_2$/g-균체건조량의 수소를 생산할 수 있었고, 이때 주요 유기산으로 15 mM acetate와 32 mM butyrate가 생성되었다. 같은 발효조건에서 1.4% 전분과 0.07% 환원당을 포함하는 두부 제조 폐수로부터 1.76 L $H_2$/L-두부제조폐수의 수소를 발생하였다. 이와 같은 결과로 부터 포도당과 두부 제조 폐수로부터 혐기세균 복합체에 의한 수소생산 효율은 각각 1.9과 0.9 mol $H_2$/mol 포도당을 나타내었다. 반연속운전(HRT, 12 시간)시 합성폐수를 이용하여 60일 이상 안정적으로 수소를 생산할 수 있었고, 이 때 혐기 세균 복합체는 1.3-2.0 L $H_2$/L-배양액을 발생하였다. PCR-DGGE(polymer chain reaction-denaturing gradient gel electrophoresis) 분석결과, 반응기 내 세균 복합체의 주요 미생물은 Clostridium 종이었다. 본 연구는 적절한 열처리를 통해 혐기 소화조 슬러지로부터 고활성 수소생산 세균 복합체를 얻을 수 있으며, 이들 세균 복합체를 이용하여 합성 및 두부제조 폐수로부터 효율적인 수소생산이 가능하다는 것을 나타내고 있다.