Use of Stable Isotope Probing in Selectively Isolating Target Microbial Community Genomes from Environmental Samples for Enhancing Resolution in Ecotoxicological Assessment

  • Park, Joonhong (School of Civil and Environmental Engineering, Yonsei University) ;
  • Congeevaram, Shankar (School of Civil and Environmental Engineering, Yonsei University) ;
  • Ki, Dong-Won (School of Civil and Environmental Engineering, Yonsei University) ;
  • Tiedje, James M. (Center for Microbial Ecology, Michigan State University)
  • 발행 : 2006.03.31

초록

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.

키워드

참고문헌

  1. Stahl, D.A. High-throughput techniques for analyzing complex bacterial communities. Adv Exp Med Biol. 517-547 (2004)
  2. Loy, A., Kusel, K., Lehner, A., Drake, H.L. & Wagner, M. Microarray and functional gene analyses of sulfate-reducing prokaryotes in low-sulfate, acidic fens reveal cooccurrence of recognized genera and novel lineages. Appl Environ Microbiol. 70, 6998-7009 (2004) https://doi.org/10.1128/AEM.70.12.6998-7009.2004
  3. Denef, V. et al. Validation of a more sensitive method for using spotted oligonucleotide DNA microarrays for functional genomics studies on bacterial communities. Environ Microbiol. 5. 933-943 (2003) https://doi.org/10.1046/j.1462-2920.2003.00490.x
  4. Zhou, J., Xia, B., Huang, H., Palumbo, A.V. & Tiedje, J.M. Microbial diversity and heterogeneity in sandy subsurface soils. Appl Environ Microbiol. 70, 1723- 1734 (2004) https://doi.org/10.1128/AEM.70.3.1723-1734.2004
  5. Venter, J.C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66-74 (2004) https://doi.org/10.1126/science.1093857
  6. Zhou, J., Bruns, M.A. & Tiedje. J.M. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 62, 316-322 (1999)
  7. Radajewski, S. et al. Identification of active methylotroph populations in an acidic forest soil by stableisotope probing. Microbiology 148, 2331-2342 (2002) https://doi.org/10.1099/00221287-148-8-2331