• Molecular & Cellular Toxicology
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• 제2권1호
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• pp.11-14
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• 2006

In this study we attempted to develop a novel genomic method to selectively isolate target functional microbial genomes from environmental samples. For this purpose, stable isotope probing (SIP) was applied in selectively isolating organic pollutant-assimilating populations. When soil microbes were fed with $^{13}C-labeled $ biphenyl, biphenyl-utilizing cells were incorporated with the heavy carbon isotope. The heavy DNA portion was successfully separated by CsCl equilibrium density gradient. And the diversity in the heavy DNA was sufficiently reduced, being suitable for the current DNA microarray techniques to detect biphenyl-utilizing populations in the soil. In addition, we proposed a new way to get more genetic information by combining this SIP method with selective metagenomic approach. The increased selective power of these new DNA isolation methods will be expected to provide a good quality of new genetic information, which, in turn, will result in development of a variety of biomarkers that may be used in assessing ecotoxicology issues including the impacts of organic hazards, and antibiotic-resistant pathogens on human and ecological systems.

• 미생물학회지
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• 제45권1호
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• pp.1-9
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• 2009

미생물 군집 내의 미생물은 순수하게 배양된 미생물과는 다른 생리적 특징을 갖는다. 전통적으로 미생물 연구는 순수배양에 초점을 맞추어 이루어져 왔고 실제 생태계에 존재하는 대부분의 미생물들이 난배양성 미생물로 알려져 있다. 따라서 복잡한 미생물 군집에서 미생물의 기능에 대한 연구는 실질적으로 미진한 실정이다. 그러나 stable isotope probing (SIP), fluorescence in situ hybridization (FISH)와 microautoradiography (MAR)의 조합, isotope micrarray, 메타게노믹스 등의 새로운 분석방법들은 미생물 군집 내에서 난배양성 미생물의 기능 분석을 어느 정도 가능하게 해 주었다. 본 논문에서는 이들 방법 등에 대해 간단히 설명하고 좀 더 정확한 결과를 얻기 위한 최신 연구 동향을 소개하고자 한다.

• Environmental Engineering Research
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• 제12권5호
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• pp.231-237
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• 2007

The microbial eco-physiology has been the vital key of microbial ecological research. Unfortunately, available methods for direct identity of microorganisms and for the investigation of their activity in complicated community dynamics are limited. In this study, metagenomics was considered as a promising functional genomics tool for improving our understanding of microbial eco-physiology. Its potential applications and challenges were also reviewed. Because of tremendous diversity in microbial populations in environment, sequence analysis for whole metagenomic libraries from environmental samples seems to be unrealistic to most of environmental engineering researchers. When a target function is of interest, however, sequence analysis for whole metagenomic libraries would not be necessary. For this case, nucleic acids of active populations of interest can be selectively gained using another cutting-edge functional genomic tool, SIP (stable isotope probing) technique. If functional genomes isolated by SIP can be transferred into metagenomic library, sequence analysis for such selected functional genomes would be feasible because the reduced size of clone library may become adequate for sequencing analysis. Herein, integration of metagenomics with SIP was suggested as a novel functional genomics approach to study microbial eco-physiology in environment.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2005년도 INTERNATIONAL SYMPOSIUM ON SOIL & GROUNDWATER ENVIRONMENT
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• pp.85-86
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• 2005

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2005년도 총회 및 춘계학술발표회
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• pp.28-30
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• 2005

Because of high population diversity in soil microbial communities, it is difficult to accurately assess the capability of biodegradation of toxicant by microbes in soil and sediment. Identifying biodegradative microorganisms is an important step in designing and analyzing soil bioremediation. To remove non-important noise information, it is necessary to selectively enrich genomes of biodegradative microorganisms fromnon-biodegradative populations. For this purpose, a stable isotope probing (SIP) technique was applied in selectively harvesting the genomes of biphenyl-utilizing bacteria from soil microbial communities. Since many biphenyl-using microorganisms are responsible for aerobic PCB degradation In soil and sediments, biphenyl-utilizing bacteria were chosen as the target organisms. In soil microcosms, 13C-biphenyl was added as a selective carbon source for biphenyl users, According to $13C-CO_2$ analysis by GC-MS, 13C-biphenyl mineralization was detected after a 7-day of incubation. The heavy portion of DNA(13C-DNA) was separated from the light portion of DNA (12C-DNA) using equilibrium density gradient ultracentrifuge. Bacterial community structure in the 13C-DNAsample was analyzed by t-RFLP (terminal restriction fragment length polymorphism) method. The t-RFLP result demonstates that the use of SIP efficiently and selectively enriched the genomes of biphenyl degrading bacteria from non-degradative microbes. Furthermore, the bacterial diversity of biphenyl degrading populations was small enough for environmental genomes tools (metagenomics and DNA microarrays) to be used to detect functional (biphenyl degradation) genes from soil microbial communities, which may provide a significant progress in assessing microbial capability of PCB bioremediation in soil and groundwater.