US EPA

1043774 

Journal Article 

Review 

DNA-based stable isotope probing: a link between community structure and function 

Uhlík, O; Jecná, K; Leigh, MB; Macková, M; Macek, T 

2009 

1 

Science of the Total Environment
ISSN: 0048-9697
EISSN: 1879-1026 

407 

12 

3611-3619 

English 

18573518 

10.1016/j.scitotenv.2008.05.012 

WOS:000266446400001 

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. 

DNA-based stable isotope probing (SIP); C-13; Microbial diversity; Bioremediation; 16S rRNA genes; Functional genes