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My current research has two goals. 1) Determine the controls of microbial community structure in natural systems. 2) Assess the significance of microbial community structure in controlling the rate of microbial processes. My thesis research focused on determining the rate and ecological importance of the microbial process, denitrification, in coastal sediments. To determine if microbial community structure could control denitrification, I developed nucleic acid probes to detect a key gene in denitrification, nitrite reductase. I have continued to develop techniques to assess the distribution of microbes in a variety of systems and, through expression vectors, the activity of these microbes. Currently I work with Dr. Patricia Holden at the Bren School on understanding the distribution of bacteria in soils and coastal waters. We utilize terminal restriction fragment length polymorphisms (TRFLPs) of PCR-amplified 16S rDNA to quantify bacterial diversity and community structure. In soils, we examined the vertical distribution of bacteria and determined that ecological theories, such as the intermediate disturbance hypothesis, can predict patterns of bacterial diversity (LaMontagne et al. 2001). In coastal systems, we are comparing bacterial diversity and community structure in salt marshes that face various levels of nutrient and toxin pollution to determine if bacterial diversity and community structure indicate ecosystem health. The EPA funds this research as part of a multidisciplinary approach entitled the Pacific Estuarine Ecosystem Indicator Research (PEEIR) Consortium (http://www.bml.ucdavis.edu/peeir/). In related projects, we have demonstrated that bacterial diversity decreases with oil content in marine sediments (Bergmann et al. 2002) and urbanization of coastal watersheds (Holden and LaMontagne 2002). The relationship between urbanization and bacterial community structure led us to examine if microbial community structure indicates the source of fecal contamination of coastal waters (LaMontagne and Holden 2002). To test this hypothesis we are comparing bacterial communities, as assessed by PCR-TRFLP, in fecal samples from four sources: human, bovine, canine and avine. This project is organized by the Southern California Coastal Water Resource Project.
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