Advancements in molecular techniques and applications in environmental engineering

Molecular biological tools continue to be well suited to the challenges and complexity of research focused on the natural and engineered environments. These methods are being applied to an increasing range of efforts in environmental engineering research and practice for an improved understanding of important biological processes. While real-time quantitative PCR (qPCR) has become a staple analytical technique in the molecular toolbox, other nucleic acid-based techniques are gaining popularity. Microbial community analysis has seen an increasing impact in the literature in part due to the diverse array of analytical techniques that are able to provide information on structural changes including catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), microarrays, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP) and next generation sequencing technologies. Novel biosensors that integrate molecular analysis are being developed to rapidly detect and quantify microorganisms, estrogenic compounds and other targets of interest. The advent of advanced molecular analyses has resulted in an exponential rise in genomic, transcriptomic, and metabolomic data. Hence, methods involving quality control are gaining popularity as the concern for rigorous standards in molecular data collection and analysis keeps pace with demand. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments.