I received my undergraduate training at Northwestern University where I majored in Biology. While at Northwestern, I worked for Dr. James A. Lippincott on Agrobacterium tumefaciens Ti plasmid transfer and integration. It was here that I first developed an interest in molecular biology and plant pathology. I then went to the University of California at Berkeley were I eventually ended up working the laboratory of Dr. Steven Lindow as a staff research associate for almost eight years. I was rapidly educated in the workings of the news media and public perceptions of scientific research with the lab’s release of Ice Minus Pseudomonas syringae into the environment. I went to graduate school in the Department of Plant Pathology at UC Berkeley with Dr. Lindow as my advisor and Dr. Andy O. Jackson as my mentor in molecular biology. My interest was in the bacterium’s response to stress in the environment and received my Ph.D. under Steve Lindow in the characterization of epiphytic fitness mutants of P. syringae subjected to UV and desiccation stresses. The mid-90s was not the best time for agricultural research funding, so for my post-doc I changed fields, still keeping my interest in bacterial interactions in the environment. I joined Dr. Ken Wilson’s lab in the Infectious Diseases Division of Duke University Medical Center where I studied culture-resistant human pathogens and the epidemiology of the anthrax pathogen, Bacillus anthracis. While at Duke University I was fortunate enough to be the first to discover sequence-based differences for the differentiation of strains of B. anthracis. The variable number tandem repeats (VNTR) that I discovered became the basis for a strain identification system for B. anthracis that is still in use today. I joined Lawrence Livermore National Laboratory as a Principle Investigator in the Biology and Biotechnology Research Program. While at LLNL, I set up a research program in bacterial diagnostics and environmental monitoring of pathogens. I joined Lawrence Berkeley National Laboratory in 2003 as a Scientist in the Earth Sciences Division. I have set up a laboratory to study bacterial responses to selected environments. I have been very excited to be at a place where I am exposed to the latest technological breakthroughs and to be right next door to the UC Berkeley campus where I am able to interact with the leaders in the field of microbiology. I am currently Head of the Ecology Department at LBNL.
Keywords: Microbial ecology, genomics
My research focus is in the area of microbial ecology and includes the examination of phylogenetic diversity in natural environments. My 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. My 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. My 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.