Project 4: Application of Comparative Genomics, Transcriptomics, & Proteomics Opt

University Of California Berkeley, Berkeley CA

Investigators

Linked publications & trials

Abstract

This proposal will apply advanced molecular tools to understand and optimize the microbial[unreadable] detoxification of common Superfund pollutants, perchloroethene (PCE) and trichloroethene (TCE), which[unreadable] pose a significant threat to human and ecological health. By studying the fundamental processes[unreadable] responsible for anaerobic microbial degradation of PCE and TCE, this work will promote improved situ[unreadable] bioremediation processes. Previous NIEHS-funded research sought to identify and understand the[unreadable] microbes within complex communities responsible for dechlorination. This work takes the next logical step[unreadable] by focusing on the only genus of bacteria, Dehalococcoides, known to completely reduce PCE and TCE to[unreadable] ethene. Whole-genome microarrays, proteomic analyses, and quantitative PCR will be used to characterize[unreadable] the genomic differences between a variety of Dehalococcoides strains and to evaluate gene expression[unreadable] and proteomic changes caused by reductive dechlorination of a variety of substrates, growth in simple and[unreadable] complex microbial communities, and other physiological perturbations. Genomic and transcriptomic[unreadable] comparison of Dehalococcoides strains with different degradation abilities will identify the pathways[unreadable] responsible for specific and general metabolism as well as reveal the evolutionary relationship between the[unreadable] various isolated strains. Transcriptomic comparison of Dehalococcoides strains in pure and mixed cultures[unreadable] will identify pathways involved in inter-species interactions, reveal the nutritional needs and metabolic roles[unreadable] of Dehalococcoides in consortia, and address the limitation in bioremediation applications presented by the[unreadable] poor growth of isolated Dehalococcoides strains. Data from strain identification, gene.expression, and[unreadable] protein production will be complied into kinetic models that can be used to predict rates of reductive[unreadable] dechlorination by poorly characterized microbial communities. This research will meet the SBRP goal of[unreadable] limiting the human exposure and toxicity of chemicals commonly found at Superfund sites by advancing the[unreadable] development of in situ bioremediation of PCE and TCE, a technology that destroys contaminants in their[unreadable] subsurface location without extraction to the surface, avoiding potential human and ecological exposure.