Molecular biological methods in environmental engineering

The "omics" revolution has enabled the development of tools for studying structural, functional, and informational macromolecules, as well as metabolites produced by cells under specific environmental conditions. Recent advances in molecular biological methods have facilitated their widespread applications in characterizing microbes in engineered and natural environments, exploring production of biofuels, and optimizing biological processes to improve the performance of wastewater treatment or subsurface remediation systems. Real-time quantitative polymerase chain reaction (qPCR) is a rapid and versatile method of choice for the detection and quantification of microorganisms. Techniques such as cloning, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), automated ribosomal intergenic spacer analysis (ARISA), and microarrays continue to be popular tools to profile microbial community population and diversity in various environments over time and space. Gene expression can be linked to microbial functions for incorporation into predictive fate and transport models. This review summarizes new or significantly revised methods, novel applications of existing methods, and a few high impact studies using advanced molecular methods published after August 2010. New nucleic acid-based methods, detection methods and sensors, and data analysis techniques are also highlighted. This review will serve environmental engineering professionals and microbiologists by providing an overview of recent advances in molecular methods, and their advantages and challenges in bioreactors and in-situ applications.