Microbial Communities Help Solve Environmental Contamination

Dehalococcoides bacteria are the only organisms known to completely reduce chlorinated ethenes to the harmless product ethene.

The Science

Metagenomic sequencing analysis is used in this study to examine the Dhc component in the context of the ANAS microbial community. Metagenomic data provide a broad view of the genetic composition of a community, including information about the identity and potential metabolic capabilities of community members. Researchers focused on three categories of functional genes related to dechlorination activity: genes for RDases, genes for cobalamin biosynthesis enzymes and genes for hydrogenases. The widespread presence of genes for hydrogenases emphasizes the importance of hydrogen metabolism in this community.

The Impact

The phylogenetic composition of ANAS described by metagenomic sequencing generally confirms the composition described by PhyloChip and previous 16S clone library studies, with a few discrepancies in the relative abundances of some taxa and possible variability in the methanogen population. More importantly, the analysis of functional genes relevant to dechlorination provides insight into the capabilities of microbial community members. This is the first time that genes for the first part of the cobalamin biosynthesis pathway have been identified in a Dhc strain, further highlighting the unique adaptation of the ANAS strains to reductive dechlorination, but also suggesting that the non-Dhc community members likely have additional important roles beyond cobalamin biosynthesis.


Microbes are very effective at carrying out a wide range of chemical reactions, even ones that involve substances toxic to higher life forms. Many groundwater sites contaminated with compounds such as trichloroethene (TCE), a pervasive groundwater pollutant often used by industry as cleansers or degreasers, are decontaminated by microbes. Dehalococcoides are the only family of bacteria known to break down TCE to ethene, a harmless chemical compound often used to help ripen fruits. A team of researchers has conducted a metagenomic analysis of a stable dechlorinating community derived from sediment collected at the Alameda Naval Air Station (ANAS) in California. The team identified the other members of this microbial community, since microbes such as Dehalococcoides are known to dechlorinate chemicals more effectively in the presence of other microorganisms. This study showed that all of the genes that code for enzymes involved in dechlorination were associated with Dehalococcoides, emphasizing its importance as the dominant dechlorinating microbe in the ANAS microbial community. Understanding the composition and functioning of communities such as this one will contribute to similar remediation efforts on a variety of cleanup challenges that DOE faces, as well as other processes (e.g., plant nutrition, carbon processing) that microbial communities carry out. The research was based on sequencing carried out by the DOE Joint Genome Institute (JGI).

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Brisson, V. L., K. A. West, P. K. H. Lee, S. G. Tringe, E. L. Brodie, and L. Alvarez-Cohen. 2012. “Metagenomic Analysis of a Stable Trichloroethene-Degrading Microbial Community,” The ISME Journal, 1–13. DOI:10.1038/ismej.2012.15.