Superfund Research Program

Meta-Omics of Microbial Communities Involved in Bioremediation

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

Project-Specific Links

Final Progress Reports

Year:   2016  2010  2005 

This project of the UC Berkeley Superfund Research Program, Lisa Alvarez-Cohen, Ph.D. (CEE Dept.) and Jillian Banfield, Ph.D. (EPS Dept.) focuses on advancing the research team’s fundamental understanding of microbial communities involved in bioremediation. To pursue this goal, they have been analyzing a variety of bioremediation communities using systems biology approaches to study metabolite exchanges that support bioremediation. This past year, the team mainly focused on two objectives of the project. In the first objective, the researchers used a set of novel bioinformatics tools developed by the Banfield group to reanalyze existing metagenomic data from three trichloroethylene (TCE)-detoxifying bioreactors. Their analysis focused on bacteriophages (viruses affecting bacteria) and their roles affecting bioreactor efficiency. Bacteriophages (phages) are usually overlooked in engineered environments albeit their important influence on bacterial communities. The team began by identifying the phage DNA in the metagenomes and assembling it into full phage genomes. Next, they aimed to identify the bacterial host (or hosts) of the phages using the bacterial CRISPR-Cas gene groups. These genes are a type of bacterial immunity system containing small phage DNA sequences that were archived by the bacterium after surviving phage attacks. Matching these small phase DNA sequences in bacteria to the phage genomes, the team can better understand the interactions between phages and bacteria during TCE bioremediation.

The second objective dealt with remediation of soil and ground water co-contaminated with arsenic and TCE. The research team’s previous results showed that the TCE-detoxifying bacterium, Dehalococcoides mccartyi is sensitive to water-dissolved forms of arsenic (arsenate and arsenite). The main focus of this current research is identifying the conditions that drive the native bacterial community to remove the dissolved forms of arsenic by precipitation in order to enable D. mccartyi to remediate TCE. The team’s results show that arsenic is precipitated with sulfur by dual reduction of arsenate and sulfate using lactate as the electron donor. They are currently testing the stability of the precipitates under alternating anaerobic and aerobic conditions.