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Final Progress Reports: University of California-Berkeley: Meta-Omics of Microbial Communities Involved in Bioremediation

Superfund Research Program

Meta-Omics of Microbial Communities Involved in Bioremediation

Project Leader: Lisa Alvarez-Cohen
Grant Number: P42ES004705
Funding Period: 2000-2017
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Final Progress Reports

Year:   2016  2010  2005 

This project is improving the ability to cleanup groundwater contamination using naturally occurring microorganisms with a process called in situ bioremediation. In situ bioremediation is an effective and desirable approach since contaminants are destroyed directly in the ground, rather than transferred to the surface where human exposure may occur. The specific objectives of this study are to develop new tools to reliably monitor the in situ bioremediation of chlorinated solvents and emerging groundwater contaminants. The focus is on advanced molecular tools and isotopic analyses that can be applied quantitatively. Reliable monitoring methods will decrease the uncertainty and cost of bioremediation while enabling the application of more effective risk assessment and risk management techniques.

Over the past year the research teams of Drs. Alvarez-Cohen and Conrad have made significant progress on both molecular biology and stable isotopic approaches. During this year they have developed quantitative polymerase chain reaction (qPCR) techniques to track the specific bacterial strains and their specific proteins involved in in situ bioremediation. The practical application of this work is that a simple, rapid test can be used to determine whether key bacteria and the appropriate enzymes are present at a contaminated groundwater site for in situ bioremediation to be successfully applied. Because this technique is more accurate and faster than previous alternatives, it should greatly facilitate site assessment, application design, and bioremediation monitoring. This year the researchers have also substantially expanded their molecular capabilities to include the use of whole-genome microarrays to apply genomics and transcriptomics to track not only the presence, but also the activities of the bacteria involved in in situ bioremediation.

Beyond their work with chlorinated solvent degrading bacteria, they have also studied the biodegradation of emerging water contaminants N-nitrosodimethylamine, 1,4 dioxane and most recently, polybrominated diphenyl ethers. They have successfully identified naturally-occurring bacteria that are capable of degrading each of these compounds, and are currently working out the biochemical pathways for their degradation. These studies should result in the development of methods for the in situ bioremediation of these compounds in the environment.

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