Contamination at DoD sites is susceptible to multiple natural and enhanced biological degradation processes. The potential for biodegradation has been well documented in the scientific literature. Still, acceptance of this process by regulatory and public stakeholders entails a significant burden of proof that requires the proponent to provide compelling evidence of ongoing treatment efficacy. Converging lines of evidence are often required, which include contaminant flux and concentrations and degradation activity (geochemical and microbial). Furthermore, the field practitioner must have the knowledge and tools necessary to determine if natural or enhanced bioremediation will meet specified remedial action objectives and to design efficient and cost effective treatment systems.

Rapid advances in molecular biology have affected practices in many fields, including bioremediation. Such advances have had a profound impact on the understanding of biological remedial processes, and they are, used extensively in the research community. Despite these developments, the use of these advances in the operational cleanup community is still limited. There is, however, tremendous potential for molecular biological tools to improve the design, implementation, field performance, and monitoring of remediation technologies.

Molecular biological tools are technologies that target biomarkers (e.g., specific nucleic acid sequences, peptides, proteins, or lipids) to provide information about organisms and processes relevant to the assessment and/or remediation of contaminants in the environment or other engineered systems. In the context of bioremediation, molecular biological tools also include other modern technologies that measure microbial populations and activity in situ.

In 2005, SERDP and ESTCP sponsored an Expert Panel Workshop on Research and Development Needs for the Environmental Remediation Application of Molecular Biological Tools, which identified high priority research topics in this area.

Identifying relevant biomarkers and tools to measure them in the field is critical to developing effective methods for managing bioremediation of contaminated groundwater. Biomarkers that help assess the degradative potential of a microbial population can improve remediation design for contaminants such as chlorinated solvents and explosives found on DoD sites. SERDP and ESTCP are supporting work to achieve the following:

• Identify and develop biomarkers for organisms and their associated microbial communities that are involved in degrading groundwater contaminants of concern to DoD
• Identify and develop biomarkers to evaluate community structure and to assess the total degradative potential of a microbial population
• Develop the relationship between biomarker measurements and functional activity or in situ contaminant degradation rates
• Improve methods to support identification and development of key biomarkers and their relationship to functional activity

A key step in translating these laboratory technologies into field use is developing a better understanding of the effects of the sampling process on the accuracy and efficacy of molecular biological tools. Also needed are improved sampling techniques for their efficient use in groundwater and associated saturated soils environments. Ongoing research goals include the following:

• Develop a better understanding of the effects of all steps in the sampling process
• Develop improved sampling and processing techniques for groundwater and associated saturated soil samples
• Develop a quantitative understanding of the relationship between biomarkers measurements in samples and conditions in situ

Efforts are focused on developing practical knowledge and guidance on how to use molecular biological tools to improve bioremediation systems in the field.