DNA Stable Isotope Probing to Examine Organisms Involved in Biodegradation

In situ applications of molecular biology to terrestrial and aquatic ecosystems have advanced the study of activities of microorganisms without the need for cultivation. DNA-based fingerprinting tools, such as 16S-TTGE, T-RFLP, DGGE, or pyrosequencing, facilitate in assessing pesticide impacts on microbial community composition. Quantitative PCR or functional gene microarrays help us understand effects of pesticides on genes of interest. Such tools improve our understanding of environmental impacts on microbial phylogeny or function, though few can link a specific organism to its function in situ. Stable isotope probing (SIP) emerged specifically to provide this linkage. SIP approaches vary in sensitivity, specificity, and inference space, depending on biomolecules targeted to obtain phylogenetic information. Combining SIP with “omics” tools further characterizes responses of microbial communities to environmental events. Herein we have reviewed strengths and weaknesses of common SIP techniques, with emphasis on the ecology of pesticide degradation.