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.

Public Health Relevance

TCE and dioxane, suspected human carcinogens, are common groundwater contaminants at Superfund sites. This research focuses on gaining a holistic understanding and developing novel biomarkers of the community-level metabolism and interactions that shape the bioremediation capabilities of subsurface microbial communities. Results from this research will meet SRP research goals by facilitating the assessment, design and optimization of in situ bioremediation of TCE and dioxane-contaminated sites.

Agency
National Institute of Health (NIH)
Type
Hazardous Substances Basic Research Grants Program (NIEHS) (P42)
Project #
5P42ES004705-27
Application #
8659376
Study Section
Special Emphasis Panel (ZES1)
Project Start
Project End
Budget Start
Budget End
Support Year
27
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California Berkeley
Department
Type
DUNS #
City
Berkeley
State
CA
Country
United States
Zip Code
94704
Counihan, Jessica L; Ford, Breanna; Nomura, Daniel K (2016) Mapping proteome-wide interactions of reactive chemicals using chemoproteomic platforms. Curr Opin Chem Biol 30:68-76
Shen, Hua; McHale, Cliona M; Haider, Syed I et al. (2016) Identification of Genes That Modulate Susceptibility to Formaldehyde and Imatinib by Functional Genomic Screening in Human Haploid KBM7 Cells. Toxicol Sci 154:194
Smith, Martyn T; Guyton, Kathryn Z; Gibbons, Catherine F et al. (2016) Key Characteristics of Carcinogens as a Basis for Organizing Data on Mechanisms of Carcinogenesis. Environ Health Perspect 124:713-21
Hsu, Ling-I; Briggs, Farren; Shao, Xiaorong et al. (2016) Pathway Analysis of Genome-wide Association Study in Childhood Leukemia among Hispanics. Cancer Epidemiol Biomarkers Prev 25:815-22
Carlos-Wallace, Frolayne M; Zhang, Luoping; Smith, Martyn T et al. (2016) Parental, In Utero, and Early-Life Exposure to Benzene and the Risk of Childhood Leukemia: A Meta-Analysis. Am J Epidemiol 183:1-14
Liu, Haizhou; Bruton, Thomas A; Li, Wei et al. (2016) Oxidation of Benzene by Persulfate in the Presence of Fe(III)- and Mn(IV)-Containing Oxides: Stoichiometric Efficiency and Transformation Products. Environ Sci Technol 50:890-8
Barazesh, James M; Prasse, Carsten; Sedlak, David L (2016) Electrochemical Transformation of Trace Organic Contaminants in the Presence of Halide and Carbonate Ions. Environ Sci Technol 50:10143-52
Shen, Hua; McHale, Cliona M; Haider, Syed I et al. (2016) Identification of Genes That Modulate Susceptibility to Formaldehyde and Imatinib by Functional Genomic Screening in Human Haploid KBM7 Cells. Toxicol Sci 151:10-22
Hu, Xindi C; Andrews, David Q; Lindstrom, Andrew B et al. (2016) Detection of Poly- and Perfluoroalkyl Substances (PFASs) in U.S. Drinking Water Linked to Industrial Sites, Military Fire Training Areas, and Wastewater Treatment Plants. Environ Sci Technol Lett 3:344-350
Bailey, Kathryn A; Smith, Allan H; Tokar, Erik J et al. (2016) Mechanisms Underlying Latent Disease Risk Associated with Early-Life Arsenic Exposure: Current Research Trends and Scientific Gaps. Environ Health Perspect 124:170-5

Showing the most recent 10 out of 573 publications