• 한국토양비료학회지
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• 제44권1호
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• pp.127-145
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• 2011

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

• 대한환경공학회지
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• 제32권4호
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• pp.369-378
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• 2010

폐기물매립장의 안정화에는 미생물이 중요한 역할을 수행한다. 폐기물매립장에서 미생물군집 변화 모니터링에 말단 제한절편다형성(Terminal Restriction Fragment Length Polymorphism; T-RFLP)법의 활용 가능성을 평가하고자 박테리아의 16S rDNA 서열에 기초한 T-RFLP법으로 4개의 폐기물매립장 내부에서 채취한 침출수의 미생물군집 구조를 조사하였다. T-RFLP법을 사용하여 해석한 침출수 내 우점 미생물군집 구조와 일반적으로 널리 사용되고 있는 16S rDNA 클론 해석법에 의한 우점 미생물군집구조는 유사하였다. 또한, T-RFLP법을 이용하여 폐기물매립장의 구조, 매립 폐기물 종류, 운영기간이 다른 폐기물매립장 침출수의 우점 미생물군집 구조가 서로 다르게 나타나는 것을 확인 할 수 있었다. 따라서 T-RFLP법을 사용하여 폐기물매립장 침출수내 미생물군집 구조를 장기적으로 모니터링 한다면 많은 비용과 시간이 소요되는 클론해석법의 반복적인 수행 없이도 비교적 간단하게 폐기물매립장의 안정화 정도를 평가할 수 있을 것으로 기대한다.

• 미생물학회지
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• 제55권3호
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• pp.220-225
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• 2019

최근 10년간 미생물생태분석 기반의 연구는 차세대염기서열분석법이 개발된 이래로 지속적으로 증가하고 있다. 장내미생물생태와 건강의 연관성은 미생물 생태학 분야에 있어서 중요한 결과로 여겨지고 있다. 미생물 군집 분석은 주로 16S rRNA 유전자 가변 영역의 염기서열을 통해 분석되지만 이는 미생물의 활성 정보를 제공하지 않는다. 본 연구에서는 cDNA 기반의 미생물 생태분석을 수행하고 DNA 및 cDNA기반의 미생물생태분석 결과를 비교하였다. 두 가지의 서로 다른 접근법이 Butyrate producer와 probiotics와 같이 장내 대사과정에서 중요한 미생물의 abundance 뿐만 아니라 비만 지표로 알려진 Firmicutes 와 Bacteroidetes의 비율에 있어서 차이가 있음을 나타내었다. 따라서, cDNA 기반 미생물 군집은 이전에 수행된 DNA 기반 미생물 군집 분석과 비교하여 장내미생물생태의 역할과 관련된 또 다른 분석 방향성을 제공한다.

• 한국토양비료학회지
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• 제46권6호
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• pp.474-481
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• 2013

Understanding the microbial community structure of agricultural soils is important for better soil management in order to improve soil quality. Phospholipid fatty acid analysis has been popularly used in determining the microbial community structure in different ecosystems. The microbial community structure of paddy soil under long-term fertilizer treatments was investigated after 45 years using PLFA analysis. Treatments were control (no fertilization, Con), compost (COM), NPK, NPK+compost (NPKC), PK, NK, and NP. Soil chemical properties were mainly affected by the addition of compost and inorganic P fertilizer. Total nitrogen and organic matter contents were significantly higher in treatments with compost while available $P_2O_5$ and exchangeable calcium were significantly higher in treatments with added inorganic P fertilizer. It was found that microbial communities were responsive to the different fertilizer treatments. PLFA results showed that the soils were dominated by gram-negative bacteria, followed by the actinomycetes, then gram-positive bacteria, and fungi. Principal component analysis of the soil chemical properties and PLFA composition proved to be a more reliable tool because it was more responsive to the changes in soil chemical properties.

• 한국환경농학회지
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• 제38권3호
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• pp.185-196
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• 2019

BACKGROUND: This study investigated the effects of rice genetically modified to be resistant against rice blast and rice bacterial blight on the soil microbial community. A comparative analysis of the effects of rice genetically modified rice choline kinase (OsCK1) gene for disease resistance (GM rice) and the Nakdong parental cultivar (non-GM rice) on the soil microbial community at each stage was conducted using rhizosphere soil of the OsCK1 and Nakdong rice. METHODS AND RESULTS: The soil chemistry at each growth stage and the bacterial and fungal population densities were analyzed. Soil DNA was extracted from the samples, and the microbial community structures of the two soils were analyzed by pyrosequencing. No significant differences were observed in the soil chemistry and microbial population density between the two soils. The taxonomic analysis showed that Chloroflexi, Proteobacteria, Firmicutes, Actinobacteria, and Acidobacteria were present in all soils as the major phyla. Although the source tracking analysis per phylogenetic rank revealed that there were differences in the bacteria between the GM and non-GM soil as well as among the cultivation stages, the GM and non-GM soil were grouped according to the growth stages in the UPGMA dendrogram analysis. CONCLUSION: The difference in bacterial distributions between Nakdong and OsCK1 rice soils at each phylogenetic level detected in microbial community analysis by pyrosequencing may be due to the genetic modification done on GM rice or due to heterogeneity of the soil environment. In order to clarify this, it is necessary to analyze changes in root exudates along with the expression of transgene. A more detailed study involving additional multilateral soil analyses is required.

• Journal of Microbiology and Biotechnology
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• 제25권6호
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• pp.765-770
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• 2015

Recent sequencing technology development has revolutionized fields of microbial ecology. MiSeq-based microbial community analysis allows us to sequence more than a few hundred samples at a time, which is far more cost-effective than pyrosequencing. The approach, however, has not been preferably used owing to computational difficulties of processing huge amounts of data as well as known Illumina-derived artefact problems with amplicon sequencing. The choice of assembly software to take advantage of paired-end sequencing and methods to remove Illumina artefacts sequences are discussed. The protocol we suggest not only removed erroneous reads, but also dramatically reduced computational workload, which allows even a typical desktop computer to process a huge amount of sequence data generated with Illumina sequencers. We also developed a Web interface (http://biotech.jejunu.ac.kr/ ~abl/16s/) that allows users to conduct fastq-merging and mothur batch creation. The study presented here should provide technical advantages and supports in applying MiSeq-based microbial community analysis.

• Environmental Engineering Research
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• 제14권1호
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• pp.3-9
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• 2009

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

• KSBB Journal
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• 제28권5호
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• pp.275-281
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• 2013

Soil microbial community analysis of farmland soil sprayed with lye in order to use fertilizer in Nigeria was performed. As a control, two kinds of soils not sprayed with lye, located in Eungo and Lagos with general practice in agriculture was selected. Soil sprayed with lye was pH 8.25 through alkalization reaction, while the other soil samples were pH 6.22 and 5.94. Substrate utilization and species diversity index of soil sprayed with lye were low than that of the other soils with the analysis of Biolog ecoplate. As a result of principal component analysis, the relationship between three samples was low. Microbial community analysis was performed by DGGE and most of them were soil uncultured bacterium. Especially, Uncultured Acidobacteria and Uncultured Methylocystis sp., which had been isolated from the rhizosphere of soybean grown in that site were discovered in the soil sprayed with lye.

• Korean Chemical Engineering Research
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• 제48권2호
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• pp.147-156
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• 2010

폐가스 처리용 바이오필터의 핵심 요소 기술은 생촉매(미생물), 담체, 설계 운전 기술 및 진단 관리 기술이다. 특히, 바이오필터의 성능은 부하 조건과 바이오필터 내 미생물 군집 구조에 의해 영향을 받는다. 지금까지 바이오필터의 미생물 연구는 대부분 배양법을 기초로 하여 수행되어 왔으나, 최근에 보다 신속하고 정확하게 미생물 군집을 분석할 수 있는 방법들이 제시되고 있다. 본 논문에서는 생리적, 생화학적 및 분자생물학적 미생물 군집 분석 방법과 이를 활용한 바이오필터의 미생물 군집 특성을 조사한 연구사례를 소개하고, 미생물 군집 분석법의 바이오필터에 적용 가능성에 대해 고찰하였다. Community-level physiological profile 방법은 시료 중에 포함된 종속영양미생물의 탄소기질 이용능력을 기반으로 군집 특성을 조사하는 것이며, Phospholipid fatty acid analysis는 미생물 세포막 지방산을 분석하여 군집 특성을 조사하는 방법이다. 환경시료로부터 직접 추출한 DNA를 활용하는 분자생물학적 분석법에는 "partial community DNA analysis"와 "whole community DNA analysis"가 있다. 전자의 방법은 PCR 과정에 의해 증폭시킨 염기서열을 분석하는 것으로 ribosomal operon 유전자가 가장 많이 활용되었다. 이 방법은 다시 PCR fragment cloning 및 genetic fingerprinting으로 구분되며, genetic fingerprinting 방법으로는 denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism, ribosomal intergenic spacer analysis 및 random amplified polymorphic DNA 방법으로 세분화된다. 추출된 전체 군집의 DNA를 분석하는 방법에는 total genomic cross-DNA hybridization, 총 추출 DNA의 열 변성/재결합 방법 및 밀도구배를 이용하여 추출한 DNA를 분획화하는 방법 등이 있다.

• 상하수도학회지
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• 제20권5호
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• pp.685-690
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• 2006

The differences in microbial community structures between planktonic microorganism and biofilm in rivers were investigated using respiratory quinone profiles. The compositions of microbial quinone for 4 tributaries of the Kyongan Stream located in/flowing through Yongin City, Gyeonggi-Do were analyzed. Ubiquinone(UQ)-8, UQ-9, menaquinone(MK)-6 and Plastoquinone(PQ)-9 were observed in all samples of planktonic microorganism and biofilm for the sites investigated, Most planktonic microorganism and biofilm had UQ-8(15 to 30%) and PQ-9(over 30%) as the dominant quinone type. These results indicated that oxygenic phototrophic microbes(cyanobacteria and/or eukaryotic phytoplankton) and UQ-8 containing proteobacteria constituted major microbial populations in the river. The quinone concentration in the river waters tested, which reflects the concentration of planktonic microorganisms, increases with increasing DOC. Further research into this is required. The microbial diversities of planktonic microorganism and biofilm calculated based on the composition of all quinones were in the range from 4.2 to 7.5, which was lower than those for activated sludge(ranging from 11 to 14.8) and soils(ranging from 13.4 to 16.8). The use of quinone profile appears to be a useful tool for the analysis of microbial community structure in river.