DNA-based molecular techniques permit the comprehensive determination of microbial diversity but generally do not reveal the relationship between the identity and the function of microorganisms. The first direct molecular technique to enable the linkage of phylogeny with function is DNA-based stable isotope probing (DNA-SIP). Applying this method first helped describe the utilization of simple compounds, such as methane, methanol or glucose and has since been used to detect microbial communities active in the utilization of a wide variety of compounds, including various xenobiotics. The principle of the method lies in providing (13)C-labeled substrate to a microbial community and subsequent analyses of the (13)C-DNA isolated from the community. Isopycnic centrifugation permits separating (13)C-labeled DNA of organisms that utilized the substrate from (12)C-DNA of the inactive majority. As the whole metagenome of active populations is isolated, its follow-up analysis provides successful taxonomic identification as well as the potential for functional gene analyses. Because of its power, DNA-SIP has become one of the leading techniques of microbial ecology research. But from other point of view, it is a labor-intensive method that requires careful attention to detail during each experimental step in order to avoid misinterpretation of results.

Institute of Chemical Technology Prague Department of Biochemistry and Microbiology Technicka 3 166 28 Prague 6 Czech Republic

References provided by Crossref.org

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

Identification of bacteria utilizing biphenyl, benzoate, and naphthalene in long-term contaminated soil

Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil

Cloning the bacterial bphC gene into Nicotiana tabacum to improve the efficiency of phytoremediation of polychlorinated biphenyls

Phyto/rhizoremediation studies using long-term PCB-contaminated soil

Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing