Molecular biological methods offer flexible and powerful tools to environmental practitioners and researchers interested in studying environmental challenges in natural and engineered systems. In recent years, these techniques have allowed investigators to connect the fate, transport, and transformation of environmental chemical contaminants and pathogens with biological processes of functionally diverse microorganisms or microbial communities. Indeed, the boundaries of microbial ecosystems are constantly refined as researchers discover new links that extend beyond Bacteria to include Archaea and unicellular Eukarya.

Quantitative polymerase chain reaction (qPCR) provides a rapid and sensitive approach to determine gene abundance and expression from a wide range of microorganisms from complex environments. Whole genome arrays (WGA) and functional gene arrays (FGA) are being used to elucidate transcriptional changes in response to environmental parameters. Antibiotic resistance profiling and microbial source tracking studies continue to benefit from the information provided by a molecular-based experimental design. Quantitative fluorescent in situ hybridization (qFISH) and next generation sequencing technologies are changing the way we view suspended solids in wastewater treatment. Innovative sensors are being developed that couple molecular biological, chemical, or physical properties to improve the sensitivity and specificity for intended targets. Thus, advanced molecular analysis complements conventional approaches to provide a more comprehensive understanding of microbes and microbial processes in the environment. The purpose of this review is to summarize high impact studies and novel applications of molecular methods for environmental engineering professionals and scientists.