We recommend that you upgrade your browser. The following is a list of popular options:
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.
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.
The blowout of the Macondo 252 well following the explosion of the Deepwater Horizon drilling unit resulted in the release to the environment of approximately 4.2 million barrels of oil and 1.7 x 107 g natural gases into the Gulf of Mexico over an 83 day time period from April to July 2010. This complex mixture of hydrocarbons was released at a depth of 1500m and subject to physical and chemical partitioning as it moved through the water column. We identified subsurface hydrocarbon intrusions forming at around 1000-1300m below the surface. This has been referred to as a deep-sea oil plume and consisted of dissolved gases and soluble components of oil such as mono-aromatics and monocyclic alkanes. These intrusions also reportedly contained small, neutrally buoyant oil droplets that retained some insoluble hydrocarbon fractions at depth. Using a systems biology approach we tracked the microbial community composition to determine the relationships between microbial dynamics, and hydrocarbon and dissolved-oxygen concentrations. A shift in microbial community structure corresponded with a succession of dominant hydrocarbon degrading bacteria consuming distinctive fractions of the released oil. Ongoing work seeks to identify the distribution of specific classes of hydrocarbon degrading organisms over a wider scale.
A fundamental understanding of microbial community structure and function, and its linkage to biogeochemistry in petroleum reservoirs, may enable control of reservoir souring, the release of highly toxic and corrosive hydrogen sulfide through the reduction of sulfate. Recent studies suggest that most petroleum reservoirs have well-established microbial communities and that these communities have had a major long-term impact on the evolution of petroleum . Perturbations to this community would not only alter community structure and function, but reservoir geochemistry as well, impacting reservoir quality and oil recovery. The objective of the MEHR Ecogenomics Project is to develop a systems biology approach utilizing high-resolution, molecular methods that will enable monitoring, characterization, and ultimately lead to the control of MEHR environments to limit reservoir souring.
Human impact, in the form of increased urbanization, agricultural practices, wildlife management and decaying infrastructure has resulted in a marked decrease in water quality in California. This impacts anyone who would kneel down and take a drink from a cool stream or a lake as they hike or otherwise take advantage of California’s abundant outdoor recreational activities. Significant increases in illnesses have been reported for those who swim in our beaches compared to those that never venture into the water. The surfing community has been aware of this phenomenon for years and organizations such as the Surfrider Foundation have created reporting tools to identify how and where they get sick to help identify pollution hotspots. My laboratory is interested in identifying sources of fecal pollution as a first step towards control and mitigation. We are far more at risk of getting sick from water contaminated with sewage, septic wastes and other human sources compared to non-human fecal sources such as birds or grazing animals. To accurately differentiate sources we have developed a technology to comprehensively identify the total microbial community composition in water samples including the hundreds of source-specific microbes from each fecal source. We are using this method to assess risks at contaminated beaches, develop Total Maximum Daily Load (TMDL) to calculate the maximum amount of pollution that a recreational beach can receive and still meet water quality standards and, finaly, determine how the fecal-specific species signals change over time in water.
In this age of drought and weather uncertainty, using high quality water sources at a rate faster than the environment can replenish them for the transportation of sanitary waste is becoming an increasingly unsustainable practice. There is growing recognition that source control sanitation methods, as opposed to “end-of-pipe” treatment will be the only sustainable method for bringing proper sanitation to emerging economies while at the same time, bringing environmentally sustainable practices to developed areas. Our current thermophilic composting project examines how the microbial community in the source material changes in the lifecycle of the composting process. While there have been several attempts to develop various sanitary waste composting technologies, there is little understanding of the microbial process itself, which will be essential to optimize not only the process, but the overall safety of such practices. Assuring complete pathogen destruction in fully processed compost will increase the acceptance of this process as an alternative to water transport methods for waste disposal.