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Research Interests

  • Microbial Ecology
  • Genomics
  • Diversity in Extreme Environments

Research Description

Research focus is in the area of microbial ecology and includes the examination of phylogenetic diversity in natural environments.  The laboratory uses molecular approaches to study the dynamics of microbial community structure under changing environmental conditions. This includes the development of new techniques to dissect the microbial diversity of complex ecosystems.  The long-term goal of this research is to integrate different fields of biology (i.e., genomics, ecology, molecular biology, proteomics and bioinformatics) to provide insight into the interactions of environmental microorganisms under stressful conditions.  We hope to harness the existing capabilities of beneficial microbes to improve water quality, reduce contamination and limit the amount of carbon released into the atmosphere. The current research focuses on the remediation of oil spills, limiting sulfate reduction in oil reservoirs, tracking sources of fecal pollution in marine and freshwater systems and using thermophilic composting to reduce the impact of wastes on watersheds and to improve land use productivity. The laboratory has developed Greengenes, a 16S rRNA gene sequence repository and online toolset, for aligning/annotating novel sequences, interpreting microarray results and developing phylogenetically specific probes.  We have been part of the Data Analysis and Coordination Center for the Human Microbiome Project and have examined the tremendous diversity of human-associated microbes. We have developed numerous microarray systems, including the third-generation (G3) PhyloChip, for the measurement of microbial diversity and the identification of bacterial communities by 16S rRNA gene sequences.  We have also developed additional microarray systems, including microarrays for whole-genome expression profiling in response to various environmental stimuli.