Scientists decipher genome of bacterium that helps clean up major groundwater pollutants

Chemical byproducts of dry cleaning and silicon chip production are dechlorinated by the microbe dehalococcoides ethenogenes

Scientists have deciphered the genome sequence of a microbe that can be used to clean up pollution by chlorinated solvents – a major category of groundwater contaminants that are often left as byproducts of dry cleaning or industrial production.

The study of the DNA sequence of Dehalococcoides ethenogenes, which appears in the January 7 issue of Science, found evidence that the soil bacterium may have developed the metabolic capability to consume chlorinated solvents fairly recently – possibly by acquiring genes in an adaptation related to the increasing prevalence of the pollutants. “The genome sequence contributes greatly to the understanding of what makes this microbe tick and why it’s metabolic diet is so unusual,” says TIGR scientist Rekha Seshadri, the primary author of the Science paper.

D. ethenogenes, which was discovered by Cornell University scientists at a sewage treatment plant in Ithaca, NY, is the only known microbe that is known to reductively dechlorinate the pervasive groundwater pollutants tetrachloroethelene (PCE) and trichloroethylene (TCE). That dechlorination produces a nontoxic byproduct, ethene.

A collaborator on the sequencing project is Cornell microbiologist Stephen Zinder, whose lab was the first to isolate the bacterium. Another major collaborator was Lorenz Adrian of the Institute for Biotechnology at the Technical University of Berlin, Germany. The D. ethenogenes project was sponsored by the U.S. Department of Energy’s Office of Biological Energy Research.

Studies by Zinder and others have shown that members of the genus Dehalococcoides are necessary for complete dechlorination of PCE and TCE at contaminated sites. “When I first looked at a purified PCE-degrading culture under a microscope, the tiny organism looked like junk to me,” says Zinder. “I never dreamed I’d some day we’d know the genome sequence of that ’junk.’ ” Today, environmental consulting companies are using Dehaloccocoides cultures to assure remediation at numerous sites contaminated by PCE or TCE – by one count, there are at least 17 Dehaloccocoides bioremediation sites in ten states, including Texas, Delaware and New Jersey.

“Because chlorinated solvents have polluted so many water sources, there is a pressing need for new techniques to clean up such pollutants,” says TIGR Associate Investigator John Heidelberg, the senior author of the Science paper. Heidelberg, who has led several projects to sequence microbes with bioremediation potential, says the sequence information on D. ethenogenes is likely to boost such efforts.

There are several reasons why deciphering a microbe’s DNA sequence can help scientists find better ways to use it. For one, the analysis of that sequence helps researchers learn about how the organism functions on a metabolic level. In the case of D. ethenogenes, scientists found 19 different reductive dehalogenases (RDs) – which allow the microbe to “breathe” chlorinated solvents. Those RDs, in combination with the bacterium’s five hydrogenase complexes and its severely limited repertoire of other metabolic modes, show that D. ethenogenes is highly specialized for respiratory reductive dechlorination using hydrogen as the electron donor.

By comparing the genomic sequence of D. ethenogenes with that of other Dehalococcoides spp. and related organisms that have different capabilities and spectra for dehalogenation, scientists should be able to deepen the understanding of the chemical process and the best ways to use microbes in the bioremediation of sites that are contaminated with halogenated organic compounds.

If scientists can capitalize on what they have learned about the RDs and their regulation, they could design enhanced or more effective approaches for removing TCE and toxic metabolites such as vinyl chloride from the environment. Seshadri says that capability to remove such chlorinated solvents “is important to both the ecology and the economy.”

In the long-term, genome data could serve as a foundation for development of phylogenetic and functional marker probes, for detection and monitoring of D. ethenogenes in the environment and for studies of the genetics of microbial populations. The project also will help scientists study the evolution of catabolic pathways.

The study suggests that the microbe may have developed the metabolic capability to consume chlorinated solvents fairly recently – possibly by acquiring genes in an adaptation related to the increasing prevalence of the pollutants. As evidence, they point out that about 13.6 percent of the D. ethenogenes genome consists of integrated elements and four of the RD genes are located in such regions suggesting that they may have been relatively recently added to the microbe’s repertoire.

The genome of D. ethenogenes is the first complete sequence from the green nonsulfur group of bacteria. By comparing its genome sequence with that of the more than 50 other species sequenced at TIGR, scientists have learned more about the phylogenetic diversity of microbes.

As the leading center for microbial genomics, TIGR has now deciphered the genome sequences of numerous microbes that have potential for use in bioremediation. Those include:

• Geobacter sulfurreducens, which can help mop up uranium pollution and produce energy in the process.
• Desulfovibrio vulgaris, which can help remediate metallic pollutants such as uranium and chromium.
• Shewanella oneidensis, which can remove metals such as chromium and uranium from water.
• Pseudomonas putida, a soil bacterium that breaks down organic pollutants.
• Deinococcus radiodurans, a radiation-resistant bacterium that can be used to help bioremediate radionucleotides at radioactive waste sites.
• Caulobacter crescentus, which could be used for bioremediation in low-nutrient aquatic environments.

“These talented microbes are providing us with important tools to help clean up pollutants,” says TIGR President Claire M. Fraser, a coauthor of the Science paper. “By revealing the secrets of microbial metabolism, genomics can be a boon to the environment.”