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Principal Investigator: Derek Lovley The purpose of this project is to develop experimental and computational tools to predictively model the behavior of complex microbial communities involved in microbial processes of interest to the Department of Energy. The five year goal is to deliver in silico models that can predict the behavior of two microbial communities of direct relevance to Department of Energy interests: 1) the microbial community responsible for in situ bioremediation of uranium in contaminated subsurface environments; and 2) the microbial community capable of harvesting electricity from waste organic matter and renewable biomass. These communities were chosen in order to address DOE needs for: 1) remediation of metals and radionuclides at DOE sites; and 2) the development of cleaner forms of energy and biomass conversion to energy. Previous studies have demonstrated that the microbial communities involved in uranium bioremediation and electricity harvesting are both dominated by microorganisms in the family Geobacteraceae and that these Geobacteraceae are responsible for the uranium bioremediation and electron transfer to electrodes. Thus, studies of these two communities are complementary. Based on our current rate of progress, it is expected that within five years it will be possible to predict the in situ growth and activity of the predominant Geobacteraceae in the environments of interest solely from relevant geochemical data or to describe in detail the in situ metabolic state of the microorganisms from environmental gene expression data. Furthermore, these computational tools will be able to predict the response of the microbial community to environmental manipulations or manipulation of the genome of the relevant organisms, allowing rational optimization of in situ uranium bioremediation or electricity harvesting via environmental or genetic engineering. This renewal will take advantage of the significant progress that was made in the first two years of the project. This not only includes advances in understanding and modeling of Geobacteraceae physiology and in situ gene expression, but also the development of: a highly qualified, well-integrated research team; the Geobacter Project database system (www.geobacter.org); and the construction of the newly built contiguous space at UMASS-Amherst dedicated to Genomics:GTL research. The research plan consists of five subprojects with the following objectives: 1) describe the genome sequences of the Geobacteraceae that predominate in subsurface sediments undergoing uranium bioremediation and on the surface of energy-harvesting electrodes; 2) identify conserved patterns of gene expression within the Geobacteraceae family, including the Geobacteraceae living in the environments of interest, in response to a range of environmental conditions; 3) complete sub-models of central metabolism and respiration via functional analysis of the Geobacteraceae genomes; 4) identify regulatory networks controlling the expression of key genes related to survival, growth, and activity in subsurface environments and on electrodes; and 5) incorporate the results from objectives 1-4 into a computational model that can predict the growth and metabolism of Geobacteraceae in a wide diversity of environments and can predict changes in the behavior of the Geobacteraceae in response to natural or engineered changes in the environment or genetic engineering of the Geobacteraceae. This project will not only produce models that DOE can use to optimize practical processes of interest, but will also define experimental and computational methods that can be used for the genome-based analysis of other environments, providing unprecedented insight into the functioning of microbial communities.
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