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ESD Ecology Department
Earth Sciences Division Home
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Molecular Microbial Ecology (MME)
Our
research group uses molecular approaches
for the study of a variety of natural
microbial communities. 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,
bioinformatics and metagenomics) to provide
insight into the survival of environmental
microorganisms under stressful conditions. Current
research in the lab focuses on the microbial
ecology of a number of environments including
the air, water, soil, and deep subsurface
with an emphasis on the natural distribution
of pathogens in the environment. By
understanding processes that allow specific
bacteria to exploit unique environments
we hope to better understand critical
mechanisms for survival.
Our
laboratory is a center for microarray
research at LBNL. We are working
on advanced technologies to measure microbial
species composition, whole-genome transcriptional
analysis, and SNP discovery for epidemiology
studies. We use Affymetrix high-density
microarrays for much of our work. The
combinatorial power of at least 500,000
oligonucleotide probes has greatly increased
precision and reproducibility in our measurements. We
have designed arrays for the broad characterization
of species in a microbial community using
the 16S rRNA gene, pathogen specific diagnostics
using unique signatures, bacterial gene
expression using whole genome sequence,
and SNP discovery for genotyping of bacterial
strains.
Current
projects in our lab include understanding
mechanisms of bacterial diversity using
16S rRNA gene sequence to measure relative
abundance of individual members of microbial
communities. We have developed novel
microarray systems to measure dynamic changes
and we are working with the Joint Genome
Institute in Walnut Creek, CA to develop
a rapid system for classifying the thousands
of individual sequences from clone libraries
that we a constructing. We are also
measuring whole genome transcriptional
expression of bacteria subjected to different
environmental stresses. With collaborators
at Stanford University and the University
of California at Berkeley, we are developing
systems for Caulobacter crescentus,
Dehalococcoides ethenogenes, and Thiobacillus
ferrooxidans.
We
are also interested in the survival and spread
of pathogens in the environment. We
are studying two related pathogens with very
distinctive disease lifecycles, Salmonella
enterica serovar Enteritidis and Yersinia
pestis. We have completed a 10X
draft genome sequence of a phage type 4 strain
of Salmonella enteritidis and have
recently finished two strains of Yersinia
pestis, Nepal516, and Antiqua. To
better understand the epidemiology of these
pathogens, we are identifying novel SNPs
for high accuracy genotyping in a partnership
with Perlegen Sciences from Mountain View,
CA. We are also assisting Callida Genomics
in a project to develop a diagnostic system
for the identification of plague (Yersinia
pestis) and anthrax (Bacillus anthracis)
using a revolutionary SBH system. Details
of individual projects may be seen by selecting
the Research Projects link on the left.
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