Genomic analysis of microbial communities in contaminated sites can confirm the presence or absence of microorganism with the potential to break down contaminants. But how do you know if they are actually doing the job? The emerging science of proteomics provides insights into the metabolic activity of microbial communities that can help researchers better predict natural degradation of contaminants and determine whether sites are good candidates for monitored natural attenuation (MNA).
Battelle has validated proteomic methods that can be applied to a variety of contaminants, including emerging contaminants of interest like PCBs and munitions constituents. Just like DNA, proteins act as unique biological markers for a species. While genomic sequencing uses sequencing of DNA, proteomics uses nanoLC coupled with high-resolution mass spectrometry for identification and quantification of peptides of interest. The presence of protein shows not only the presence of a species but also indicates the metabolic activity. Protein analysis can, therefore, be used to determine whether or not a microbial species with the capacity to biodegrade a contaminant is actually doing so, and at what rate.
Proteomics can thus provide better insight into how quickly contaminants can be expected to biodegrade naturally. This information can be used to inform decisions on whether or not a site should be moved to MNA, which is significantly less expensive than active remediation. It could also be used to evaluate and monitor the success of remediation activities including bioaugmentation (in which microbial species with the capacity to biodegrade a contaminant are directly added to a site) or biostimulation (in which substrates are added to promote the growth of naturally occurring microbial communities). Battelle is researching these and other applications that could benefit from proteomic assessment methods.
We are currently working with the U.S. Army Corps of Engineers (USACE) to apply proteomics methods to chlorinated solvents such as tetrachloroethene (PCE) and trichloroethene (TCE). We are also finishing project work with the Navy where proteomics was applied to assess degradation of methyl tertiary-butyl ether (MTBE), a gasoline additive, at contaminated sites.
There are approximately 26,000 military sites known to have groundwater contaminated with chlorinated solvents. Chlorinated solvents are a family of chemicals used for a wide variety of commercial and industrial purposes, including degreasers, cleaning solutions, paint thinners, pesticides, resins and glues. They have been linked to long-term health effects that include damage to the nervous system, kidneys, or liver, chronic skin conditions and cancer.
Active cleanup of U.S. Army sites contaminated with chlorinated solvents is estimated to cost nearly $13 billion. Moving some of these sites to less active measures or MNA could save billions of dollars.
Battelle is applying proteomics to the problem through a project funded through the Department of Defense’s (DoD’s) Environmental Security Technology Certification Program (ESTCP) program. The objective of the study is to clearly define and validate correlations between in situ degradation rates of TCE and other chlorinated volatile organic compounds (cVOCs) and quantities of biomarker genes, transcripts, and key proteins. Initial studies by our research team have correlated the abundance of specific proteins with cVOC degradation. These correlations will be confirmed in microcosm tests and verified at a DoD field site. This study expects to demonstrate that (1) proteomics provides additional information and enhances the value of currently accepted environmental molecular biological tools (MBTs) for contaminant biodegradation monitoring, and (2) integrated quantitative nucleic acid- and protein-based biomarker analyses can inform in situ degradation rates.
For this project, Battelle is working closely with collaborators at USACE, The University of Tennessee, Scissortail Environmental Solutions, LLC, Oregon State University and CB&I Federal Services. The project team includes internationally recognized remediation experts who are working together to advance the methodology.
Moving forward, Battelle is continuing research into the use of proteomics for other types of contaminants and refining methods for proteomic analysis. Our combination of analytical and field expertise, specialized equipment and trained technical staff allow us to provide integrated solutions for proteomic analysis that can be applied to a broad range of environmental challenges.