Project 4: Application of comparative genomics, transcriptomics, and proteomics to optimize microbial reductive dehalogenation

We will apply advanced molecular tools to understand and optimize how microbes detoxify the common Superfund pollutants perchloroethene (PCE) and trichloroethene (TCE). These compounds are made less toxic by microbes that break them down and remove chlorine atoms in the absence of oxygen in "anaerobic" processes. By studying these fundamental processes, this project seeks to develop improved methods to remediate these contaminants in their original location without relocating them to the surface. This would reduce potential for exposure.
 
This work focuses on the only genus of bacteria, (Dehalococcoides) known to completely reduce PCE and TCE to ethene. Several "omics" and related methods (whole-genome microarrays, proteomic analyses, and quantitative PCR) will be used to characterize the differences between Dehalococcoides strains and to evaluate gene expression and proteomic changes caused by reductive dechlorination of a variety of substrates, growth in simple and complex microbial communities. Genomic and transcriptomic comparison of Dehalococcoides strains with different degradation abilities will identify the pathways responsible for specific and general metabolism as well as reveal the evolutionary relationship between the various isolated strains. Transcriptomic comparison of Dehalococcoides strains in pure and mixed cultures will identify pathways involved in inter-species interactions, reveal the nutritional needs and metabolic roles of Dehalococcoides in consortia, and address the limitation in bioremediation applications presented by the poor growth of isolated Dehalococcoides strains. Data from strain identification, gene expression, and protein production will be complied into kinetic models that can be used to predict rates of reductive dechlorination by poorly characterized microbial communities. This research will limit human exposure and toxicity of chemicals commonly found at Superfund sites by advancing the development of in situ bioremediation of PCE and TCE.

Monitoring In Situ Bioremediation of TCE, September 4, 2002
http://www-apps.niehs.nih.gov/sbrp/

Mahendra S, Alvarez-Cohen L (2005) Pseudonocardia dioxanivorans sp. nov., a novel actinomycete that grows on 1,4-dioxane. Int J Syst Evol Microbiol 55(2):593-8. [PDF]
 
Sharp JO, Wood TK, Alvarez-Cohen L (2005) Aerobic Biodegradation of N-Nitrosodimethylamine (NDMA) by Axenic Bacterial Cultures. Biotechnology and Bioengineering 89(5):608-18. [PDF]
 
Chu KH, Mahendra S, Song DL, Conrad ME, Alvarez-Cohen L (2004) Stable carbon isotope fractionation during aerobic biodegradation of chlorinated ethenes. Environmental Science and Technology 38(11):3126-3130. [PDF]
 
Mitch WA, Sharp JO, Trussel RR, Valentine RL, Alvarez-Cohen L, Sedlak DL (2003) N-Nitrosodimethylamine as a Water Quality Contaminant. Environmental Engineering Science 20(5): 389-404. [PDF]
 
Bhupathiraju VK, Krauter P, Holman HY, Conrad ME, Daley PF, Templeto AS, Hunt JR, Hernandez M, Alvarez-Cohen L (2002) Assessment of in-situ bioremediation at a refinery waste-contaminated site and an aviation gasoline contaminated site. Biodegradation 13(2):79-90. [PDF]