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
Zhang, L; Samad, A; Pombo-de-Oliveira, M S et al. (2015) Global characteristics of childhood acute promyelocytic leukemia. Blood Rev 29:101-25
Gaytán, Brandon D; Vulpe, Chris D (2014) Functional toxicology: tools to advance the future of toxicity testing. Front Genet 5:110
McHale, Cliona M; Smith, Martyn T; Zhang, Luoping (2014) Application of toxicogenomic profiling to evaluate effects of benzene and formaldehyde: from yeast to human. Ann N Y Acad Sci 1310:74-83
Ward, Mary H; Colt, Joanne S; Deziel, Nicole C et al. (2014) Residential levels of polybrominated diphenyl ethers and risk of childhood acute lymphoblastic leukemia in California. Environ Health Perspect 122:1110-6
Xiao, Jianqiao; Lee, Seung-Tae; Xiao, Yuanyuan et al. (2014) PTPRG inhibition by DNA methylation and cooperation with RAS gene activation in childhood acute lymphoblastic leukemia. Int J Cancer 135:1101-9
Morris, Patrick J; Medina-Cleghorn, Daniel; Heslin, Ann et al. (2014) Organophosphorus flame retardants inhibit specific liver carboxylesterases and cause serum hypertriglyceridemia. ACS Chem Biol 9:1097-103
Men, Yujie; Seth, Erica C; Yi, Shan et al. (2014) Sustainable growth of Dehalococcoides mccartyi 195 by corrinoid salvaging and remodeling in defined lactate-fermenting consortia. Appl Environ Microbiol 80:2133-41
Mehinto, Alvine C; Prucha, Melinda S; Colli-Dula, Reyna C et al. (2014) Gene networks and toxicity pathways induced by acute cadmium exposure in adult largemouth bass (Micropterus salmoides). Aquat Toxicol 152:186-94
Koster van Groos, Paul G; Esser, Bradley K; Williams, Ross W et al. (2014) Isotope effect of mercury diffusion in air. Environ Sci Technol 48:227-33
Thomas, Reuben; Hubbard, Alan E; McHale, Cliona M et al. (2014) Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure. PLoS One 9:e91828

Showing the most recent 10 out of 482 publications