Molecular Biological Tools Used in Assessment and Remediation of Petroleum Hydrocarbons in Soil and Groundwater

Molecular biological tools (MBTs) are used to assess and characterize the microbiology and associated biological processes at contaminated sites, including ecological roles, phylogenetic diversity, and metabolic and co-metabolic capabilities related to contaminant biodegradation and biotransformation. MBTs have changed our approach to the assessment and remediation of petroleum hydrocarbons in the environment. In contaminated-site management, several MBTs and stable isotope analysis methods can be used to measure the presence, abundance, and activity of petroleum hydrocarbon-degrading microorganisms and transformation pathways: (1) quantitative polymerase chain reaction (qPCR) to quantify microorganisms and genes encoding enzymes for biodegradation or biotransformation, (2) DNA sequencing to comprehensively identify the microorganisms presence and microbial community structure, (3) stable isotope probing (SIP) provides conclusive evidence of biodegradation through the use of 13C-labeled surrogate compounds of petroleum hydrocarbons that microbes use as carbon and/or energy sources, and (4) compound-specific isotope analysis (CSIA) measures the ratio of naturally occurring stable isotopes within a contaminant to indicate (bio)degradation. This chapter discusses the use, benefits, and limitations of MBTs. Several real-world case studies are provided to demonstrate how to investigate the biodegradation of petroleum hydrocarbon constituents under varying field conditions to better characterize governing biogeochemical processes and to better inform remedial decisions.