Browse > Article
http://dx.doi.org/10.4491/eer.2007.12.5.231

Functional Metagenomics using Stable Isotope Probing: a Review  

Vo, Nguyen Xuan Que (Department of Environmental Science and Engineering, Ewha Womans University)
Kang, Ho-Jeong (Department of Civil and Environmental Engineering, Yonsei University)
Park, Joon-Hong (Department of Civil and Environmental Engineering, Yonsei University)
Publication Information
Environmental Engineering Research / v.12, no.5, 2007 , pp. 231-237 More about this Journal
Abstract
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.
Keywords
Eco-physiology; Functional genomics; Microbial ecology; Systems biology;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Bull, I. D., Parekh, N. R., Hall, G. H., Ineson, P., and Evershed, R. P., 'Detection and classification of atmospheric methane oxidizing bacteria in soil,' Nature, 405, 175-178 (2000)   DOI   ScienceOn
2 Schloss, P. D., and Handelsman, J., 'Biotechnological prospects from metagenomics,' Curr. Opin. Biotechnol., 14, 303-310 (2003)   DOI   ScienceOn
3 Jeon, C. O., Park, W., Padmanabhan, P., DeRito, C., Snape, J. R., and Madsen, E. L., 'Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment,' Proc. Natl. Acad. Sci. USA., 100, 13591-13596 (2003)
4 Lin, J. L., Radajewski, S., Eshinimaev, B. T., Trotsenko, Y. A., McDonald, I. R., and Murrell, J. C., 'Molecular diversity of methanotrophs in Transbaikal soda lake sediments and identification of potentially active populations by stable isotope probing,' Environ. Microbiol., 6, 1049-1060 (2004)   DOI   ScienceOn
5 Madsen, E. L., 'The use of stable isotope probing technique in bioreactor and field studies on bioremediation,' Curr. Opin. Biotechnol., 17, 92-97 (2006)   DOI   ScienceOn
6 Friedrich, M. W., 'Stable isotope probing of DNA: insights into the function of uncultivated microorganisms from isotopically labeled metagenomes,' Curr. Opin. Biotechnol., 17, 59-66 (2006)   DOI   ScienceOn
7 Rickwood, D., Centrifugal methods for characterizing macromolecules and their interactions, in Preparative Centrifugation: a Practical Approach, Oxford University Press, pp. 143-186 (1992)
8 Garcia Martin, H., Ivanova, N., Kunin, V., Warnecke, F., Barry, K. W., McHardy, A. C., Yeates, C., He, S., Salamov, A. A., Szeto., E., Dalin, E., Putnam, N. H., Shapiro H. J., Pangilinan, J. L., Rigoutsos, I., Kyrpides, N. C., Blackall, L. L., McMahnon, K. D., and Hugenholtz, P., 'Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities,' Nat. Biotechnol., 24, 1263-1269 (2006)   DOI   ScienceOn
9 Whiteley, A. S., Manefield, M., and Lueders, T., 'Unlocking the 'microbial black box' using RNA-based stable isotope probing technologies,' Curr. Opin. Biotechnol., 17, 67-71 (2006)   DOI   ScienceOn
10 Griffiths, R. I., Whiteley, A. S., O'Donnell, A. G., and Bailey, M. J., 'Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition,' Appl. Environ. Microbiol., 66, 5488-5491 (2000)   DOI
11 Manefield, M., Whiteley, A. S., Griffiths, R. I., and Bailey, M. J., 'RNA stable isotope probing, a novel means of linking microbial community function to phylogeny,' Appl. Environ. Microbiol., 68, 5367-5373 (2002)   DOI
12 Radajewski, S., McDonald, I. R., and Murrell, J. C., 'Stable isotope probing of nucleic acids: a window to the function of uncultured microorganisms,' Curr. Opin. Biotechnol., 14, 296-302 (2003)   DOI   ScienceOn
13 Radajewski, S., Ineson, P., Parekh, N. R., and Murrell, J. C., 'Stable-isotope probing as a tool in microbial ecology,' Nature, 403, 646-649 (2000)   DOI   ScienceOn
14 Radajewski, S., Webster, G., Reay, D. S., Morris, S. A., Ineson, P., Nedwell, D. B., Prosser, J. I., and Murrell, J. C., 'Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing,' Microbiology, 148, 2331-2342 (2002)   DOI
15 Rondon, M. R., August, P. R., Bettermann, A. D., Brady, S. F., Grossman, T. H., Liles, M. R., Loiacono, K. A., Lynch, B. A., MacNeil, I. A., and Minor, C., 'Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms,' Appl. Environ. Microbiol., 66, 2541-2547 (2000)   DOI
16 Park, J., Congeevaram, S., Ki, D. W., and Tiedje, J. M., 'Use of stable isotope probing in selective isolating target microbial community genomes from environmental samples for enhancing resolution in ecotoxicological assessment,' Molecular and Cellular Toxicology, 2(1), 11-14 (2006)
17 Hutchens, E., Radajewski, S., Dumont, M. G., McDonald, I. R., and Murrell, J. C., 'Analysis of methanotrophic bacteria in Movile cave by stable-isotope probing,' Environ. Microbiol., 6, 111-120 (2004)   DOI   ScienceOn
18 Paul, E. A., and Clark, F. E., Soil microbiology and biochemistry, 2nd ed., Academic Press, Elsevier Science, USA, pp. 130-131(1996)
19 Jeon, C. O., and Madsen, E. L., 'Analysis of microbial community responsible for naphthalene degradation using stable isotope probing in contaminated sediment,' Environmental Engineering Research, 25-26 (2004)
20 Shelswell, K. J., 'Metagenomics: Science of biological diversity,' in The Science Creative Quarterly, http://www.scq.ubc.ca/metagenomics-the- science-of-biological-diversity (2004)
21 Amann, R. I., Ludwig, W., and Schleifer, K. H., 'Phylogenetic identification cation and in situ detection of individual microbial cells without cultivation,' Microbiol. Rev., 59, 143-169 (1995)
22 Staley, J. T., and Konopka, A., 'Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats,' Annu. Rev. Microbiol., 39, 321-346 (1985)   DOI   ScienceOn
23 Venter, J. C., Remington, K., Heidelberg, J. F., Halpern, A. L., Rusch, D., Eisen, J. A., Wu, D., Paulsen, I., Nelson, K. E., Nelson, W. et al., 'Environmental genome shotgun sequencing of the Sargasso Sea,' Science, 304, 66-74 (2004)   DOI   ScienceOn
24 Morris, S. A., Radajewski, S., Willison, T. W., and Murrell, J. C., 'Identification of the functionally active methanotroph population in a peat soil microcosm by stable-isotope probing,' Appl. Environ. Microbiol., 68, 1446-1453 (2002)   DOI
25 Boschker, H. T. S., Nold, S. C., Wellsbury, P., Bos, D., de Graaf, W., Pel, R., Parkers, R. J., and Cappenberg, T. E., 'Direct linking of microbial populations to specific biogeochemical processes by $^{13}C$-labelling of biomarkers,' Nature, 392, 801-805 (1998)   DOI   ScienceOn
26 Whitby, C. B., Hall, H., Pickup, R., Saunders, J. R., Ineson, P., Parekh, N. R., and MacCarthy, A., '$^{13}C$ incorporation into DNA as a means of identifying the active components of ammonia-oxidizer populations,' Lett. Appl. Microbiol., 32, 398-401 (2001)   DOI   ScienceOn