Project 4: Meta-Omics of Microbial Communities Involved in Bioremediation

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Project 4: Meta-omics of Microbial Communities Involved in Bioremediation. Trichloroethene (TCE), a common chlorinated solvent, and 1,4-dioxane (dioxane), a solvent stabilizer, both are frequent groundwater contaminants at Superfund sites. Although microbial degradation reactions can effectively transform these contaminants, lack of a holistic and ecologically relevant understanding of the interspecies complexity of subsurface microbial communities impedes the application of robust and effective in situ bioremediation of these compounds. The overall goal of this research is to identify and examine the community-level metabolic interactions that shape the biodegradation capabilities of bioremediating communities. The fundamental understanding of microbial communities from a systems microbiology point of view will be developed by utilizing community-scale tools on two dissimilar model communities that function within different redox environments, i.e. anaerobic and aerobic, to remediate TCE and dioxane, respectively. We hypothesize that important interspecies interactions and keystone functions that regulate multiple community behaviors will be identified by applying an integrated meta-omics based approach, which in turn will provide insights to facilitate engineering efficient bioremediation processes. DNA-based stable isotope probing will be used to distinguish and identify functional organisms and the important interdependent relationships within communities capable of biodegrading TCE or dioxane. Targeted metagenomic analyses will then be employed to reveal the metabolic and functional diversity of interdependent biodegrading organisms and their supporting or inhibiting partners in the communities. Comprehensive metatranscriptomic analyses based on mRNA-targeted microarrays will be employed to investigate the global gene expression in the communities under different environmental perturbations in order to reveal microbial behaviors in response to the changes. In order to design diagnostic tools that can be applied to query environmental samples at TCE and dioxane-contaminated sites, we will identify and validate quantitative biomarkers for key metabolic as well as interacting genes using quantitative expression analyses in conjunction with community metabolite-analyses. Finally, we will apply the diagnostic tools developed throughout the research to examine environmental samples to assess microbial behaviors and interactions in these samples in order to guide and optimize in situ bioremediation strategies.