18. Molecular Technologies for Assessment of Bioremediation and Characterization of Microbial Communities at Pollutant-Contaminated Sites

Among the various microbial biodegradation techniques, molecular microbiology methods have revolutionized microbial biotechnology, thus leading to rapid and high-throughput methods for culture-independent assessment and exploitation of microbes present in polluted environments. Whether organic or inorganic, pollutants present in contaminated sites can cause an imbalance in the ecosystem by affecting the flora and fauna. The efficiency of naturally occurring microorganisms for field bioremediation could be significantly improved by the microbial molecular biology approach for its comparatively high efficiency and safety. Many techniques, including polymerase chain reaction (PCR), fluorescent in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), amplified ribosomal DNA restriction analysis (ARDRA), terminal-restriction fragment length polymorphism (TRFLP), single-strand conformation polymorphism (SSCP), and ribosomal intergenic spacer analysis (RISA) can be selectively employed in microbial flora and ecology research. Recent methods such as genotypic profiling, metagenomics, ultrafast genome pyrosequencing, metatranscriptomics, metaproteomics, and metabolomics have provided exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants.

Only 1% of the microbial diversity can be cultured by traditional techniques. Thus, the application of molecular techniques in studying microbial populations in polluted sites without the need for culturing has led to the discovery of novel and previously unrecognized microorganisms. Such complex microbial diversity and dynamics in contaminated soil offer a clear opportunity for bioremediation strategies. These techniques not only prove the existence of microbes in polluted sites but also reveal the undetectable complex relationships among them.

This book chapter presents an overview of the different applications of molecular methods in bioremediation of hydrocarbons and other pollutants in environmental matrices and an outline of recent advances in the applications of such techniques.