Application of Microarrays to Identify Biomarkers of Reductive Dehalogenating-Microbial Communities
(In collaboration with Gary Andersen and Eoin Brodie at Lawrence Berkeley National Laboratory and Stephen Zinder at Cornell University)
Background. Tetrachloroethene (PCE) and trichloroethene (TCE) have been widely used as industrial solvents and, as a result of poor storage and disposal practices, are now common contaminants of groundwater resources. Fortunately, PCE and TCE can be effectively biodegraded in anaerobic environments by reductive dechlorination processes. Recent progress has been made towards exploiting these processes for bioremediation applications. There remains a need, however, for appropriate and cost-effective biomarkers for assessing, monitoring, and optimizing the performance of these processes. Biomarker development has primarily focused on identifying nucleic acid sequences, peptides, proteins, or lipids of organisms that catalyze biodegradation reactions of interest. Although promising, such approaches are limited in that they do not address the roles of organisms that support and/or enhance the activity of dechlorinating organisms. Novel biomarkers that quantify the presence, abundance, and activity of supporting organisms are therefore needed to more effectively assess and optimize dechlorination processes.
Objective. In this research, we will identify 16S-rRNA-based phylogenetic and mRNA-based functional biomarkers diagnostic of microbial communities that support the robust growth and activity of chlorinated ethene-degrading organisms, with particular emphasis on Dehalococcoides species. Members of the Dehalococcoides genus can degrade chlorinated ethenes completely to ethene and also degrade a wide range of other chlorinated aromatic and aliphatic pollutants.
Summary of Process/Technology. We will apply state-of-the-art microarray-based tools to identify relevant biomarkers. A 16S-rRNA microarray that targets 9000 unique microbial phylogenies will be applied to identify key Archaea and Bacteria that are present and active in a range of Dehalococcoides-containing microbial communities, including enrichment cultures, soil microcosms, and groundwater samples. We will then construct defined co- and tri-cultures that contain Dehalococcoides and one or more of the key supportive organisms. Constructed cultures that exhibit enhanced and sustained rates of dechlorination and/or novel metabolic capabilities, such as the ability to use organic acids as electron donors, will be identified and the 16S-rRNA genes of the supporting organisms will be selected as phylogenetic biomarkers. In addition, a genomic expression microarray that targets the Dehalococcoides genus will be applied to the constructed cultures, to robust enrichment cultures, and to environmental samples to identify functional biomarkers indicative of the activity and/or functional role of supporting organisms. Finally, quantitative PCR will be used to derive correlations between the quantitative detection of these biomarkers, chlorinated ethene degrading activity, and the metabolic requirements of the microbial communities. These models will provide novel tools for assessing the structure and total biodegradative potential of Dehalococcoides in uncharacterized microbial communities.
Benefits. The broadest significance of the proposed work is that it will lead to improved strategies for optimizing in situ bioremediation technologies. The biomarkers developed here could shorten the bioremediation process feedback cycle by replacing traditional diagnostics, such as microcosm responses that are monitored over weeks, with appropriate 16S-rRNA- and gene expression-based diagnostics that can be monitored within hours. Furthermore, the insights gained about important ecological interactions within reductive dechlorinating microbial communities will improve our ability to design, construct, and optimize bioaugmentation and biostimulation systems.
Funded by
Strategic Environmental Research and Development Program (SERDP).
Shown in the figures above are preliminary data of bacterial and archaeal populations that exhibit the greatest changes over the course of treatment at Ft. Lewis, Seattle, a TCE-contaminated site that has undergone in-situ bioremediation.
|
Biodegradation of the Flame Retardants Polybrominated Diphenyl Ethers
Oxygenase-Catalyzed
Biodegradation of Emerging Water Contaminants: 1,4-Dioxane and N-Nitrosodimethylamine
Characterizing and Evolving the Propane Monooxygenase for N-Nitrosodimethylamine Biodegradation and Green Chemistry
Quantifying Gene Expression to Predict and Optimize Reductive Dechlorination by Dehalococcoides spp.
Application of Microarrays to Identify Biomarkers of Reductive Dehalogenating-Microbial Communities
|
