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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 

Professor Alvarez-Cohen is a leader in understanding how microbes break down contaminants and what can be done to make bioremediation work for contaminants found at hazardous waste sites. She was elected to the National Academy of Engineering because of her discoveries of new organisms that can contribute to bioremediation. She has been involved for many years in providing advice through service on many committees at the National Academy of Sciences.

Overall goals

Investigators are working with microbes that can break down compounds that are common contaminants of groundwater at Superfund sites (and other hazardous sites). They are focusing on chlorinated compounds that are difficult to break down to non-toxic forms. Microbes that can break down these contaminants tend to act very slowly, so such bioremediation takes a long time. Based on their research on the biology and ecology of the microorganisms, investigators are trying to determine how to speed up this process. They are looking at adding other organisms to the mix and making changes in conditions. They hope to find better ways to remediate sites contaminated with TCE, the most common Superfund groundwater contaminant, which was formerly used as a solvent in everything from dry cleaning to white out.

The microorganisms they are using are bacteria of the genus Dehalococcoides (Deha). These bacteria degrade chloroethenes like TCE into a nontoxic form. Using these methods, the water stays within the contaminated aquifer during bioremediation, without pump-and-treat technologies. This is cost-effective and minimizes human and ecological exposure. The project uses cutting-edge molecular biological techniques to identify the bioprocesses responsible for efficient degradation of chloroethene compounds. The goal is to engineer the conditions to optimize dechlorination activities during bioremediation and to develop the tools needed to monitor conditions throughout this process.

Important discoveries so far

Investigators have developed molecular tools that allow them to study both the fundamental and applied aspects of Dehalococcoides, a bacterium capable of bioremediating chloroethenes. These tools have led to new discoveries about the growth of this organism, leading to optimization strategies that promote more successful bioremediation.

Accomplishments for the last year

One specific strategy of this research is to identify the enzymes of the Deha bacteria that contribute to robust growth and to degradation of TCE. Previous studies demonstrated that when Deha is grown with another kind of bacteria, the Deha grows to higher densities more rapidly, and TCE is broken down to ethene more quickly. (The other bacteria were a type that ferments lactate, known as Desulfovibrio vulgaris Hildenborough (DVH).)

Over the past year, investigators compared the proteins produced when the two bacteria were grown together to the proteins produced when Deha was grown by itself. This was to find out what biological pathways were contributing to the greater growth of the bacteria and greater remediation of the TCE when the two bacteria were grown together.

When the two bacteria were grown together, proteins that were significantly regulated were involved in functions such as electron transfer and coenzyme acquisition for TCE degradation. This indicates that the greater growth for the two bacteria occurred because DVH produces compounds that help to meet metabolic requirements of Deha, known as syntrophy. This is an application of proteomics methods.

Work last year also dealt with the RNA responses of Deha to environmentally relevant parameters. The investigators applied a custom-designed genus-wide microarray to a Dehalococcoides-containing microbial community (referred to as ANAS) that was enriched from a local Superfund site. Characterization of Deha DNA in ANAS revealed a unique collection of functional genes that differ from any currently sequenced Dehalococcoides strains. RNA was collected and analyzed at three time points throughout the ANAS growth cycle in order to study Dehalococcoides under feast and famine growth conditions. Microarray analysis revealed that under feast conditions, the dominant functions represented by abundant RNA are associated with protein synthesis. On the other hand, under the famine condition, abundant RNA is dominantly related to stress response genes, such as chaperones, heat shock proteins, antioxidant genes and transcriptional regulation genes. These insights into the transcriptomes of Dehalococcoides under different environmental parameters will improve the understanding of the physiology of these bacteria in the environment. This is essential in the development of more effective strategies for in situ bioremediation of chloroethenes. Ongoing studies are also being conducted to compare the RNA profiles of unknown Dehalococcoides strains in other Superfund site enrichments grown under environmental conditions favoring methanogenesis and/or vitamin B12 availability.

What the investigators plan to do next

This work has far-reaching significance because the investigators have developed molecular tools that allow them to study both the fundamental and the applied aspects of Dehalococcoides, a bacterium capable of bioremediating chloroethenes. These tools have allowed them to make new discoveries about the growth of this organism, leading to optimization strategies that promote more successful in situ bioremediation.

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