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Proteomics May Be the Key to Predicting Bioremediation Rates

The most powerful component of many remediation plans is also the smallest: millions of invisible microbes silently degrading dangerous chemicals into less harmful byproducts. Introducing or stimulating colonies of helpful microbes can accelerate remediation of sites contaminated with a wide range of chemicals. But how do we know they are doing their job?

Next-generation sequencing (NGS) technologies can rapidly sequence the genomes of bacteria present in soil or water samples and tell us which species are present. But genomics can’t tell us if the bacteria are actively working to degrade contaminants. To get a better understanding of microbial activity and degradation rates, scientists at Battelle are developing new techniques based on the science of proteomics.

Proteomics, or the study of the proteins expressed by an organism, can give scientists a better understanding of contaminant biodegradation. The proteome is the complete set of proteins that are produced or modified by an organism. While the genome of an organism stays consistent over time, the proteome changes depending on the organism’s environment and activities. For example, the genome of a bacterium may tell us that it has the capacity to digest petroleum. The proteins that the bacterium expresses can tell us whether or not it is actually doing so.

Battelle is developing new proteomic technologies to make it easier for researchers to monitor microbial activity and estimate biodegradation rates on contaminated sites. The Department of Defense (DoD) has over 26,000 contaminated groundwater sites, with an estimated remediation cost of $12.8 billion. With over 25% of the remedies in place using enhanced in situ bioremediation (ISB) and over 50% of remedies using monitored natural attenuation (MNA), there is a critical need for accurate, cost-effective methods to monitor microbial activity and efficacy over time. A better understanding of the factors that impact bioremediation rates will help the DoD estimate remediation time and make better decisions about when to transition from active cleanup methods to passive MNA.

Current monitoring methods rely on directly measuring the rate of contaminant degradationin situ. However, direct measurement can be challenging in practice. It can be difficult to get accurate measurement of contaminant concentrations for comparison over time. When comparative measures are possible, they do not distinguish between biodegradation and chemical or physical forms of degradation.

Genomic technologies such as quantitative polymerase chain reaction (qPCR) are commonly used to determine whether specific microbes and/or genes are present and in what quantities. This is sometimes used as a proxy measurement to predict the rate of biodegradation. The presence of microbes does not, however, guarantee that biodegradation is taking place. Factors such as site geochemistry, the bioavailability of the contaminant or the absence of necessary metabolic agents such as oxygen can inhibit microbial activity. By looking at the proteome, researchers now have a way to directly measure metabolic activity associated with biodegradation.

Battelle’s patent-pending technology relies on quantitative proteomics (qProteomics) to quantify the proteins directly involved in the biodegradation of specific contaminants. The proteins and peptides that indicate that biodegradation is taking place are specific to the species of microbe involved and the contaminant that is being degraded. Quantifying the proteins and peptides in an environmental sample can tell researchers how fast degradation is taking place. Battelle has analyzed the proteins and peptides associated with biodegradation of chlorinated solvents and created reference standards that correlate protein and peptide concentrations with degradation rates. Battelle is also conducting internal research to refine sample preparation methods and develop reference standards for other types of contaminants.

Battelle’s technology is already being used to support a Department of Defense (DoD) Environmental Security Technology Certification Program (ESTCP) project for the U.S. Navy. Assessment of Post Remediation Performance of a Biobarrier Oxygen Injection System at an MTBE Contaminated Site (ER-201588) will use proteomic tools to evaluate the long-term performance of remediation methods and monitor microbial activity at the site.