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Where are you from, and what is your role in Extreme 2004?
I
am an Assistant Research Professor at the Desert Research Institute
in Reno, Nevada, where I have a Molecular Microbial Ecology and Genomics
Lab. I am a co-principal
investigator (PI)
with Craig Cary on
a National Science Foundation-funded Biocomplexity project, "A Metagenome
Analysis of an Extreme Microbial Symbiosis." My role in our project
is leading the development of DNA microarray technologies to study
gene expression in the bacterial community that lives in close association
with the Pompeii worm (Alvinella pompejana).
This cruise is
my first opportunity to collect samples of the Alvinella bacterial
epibionts, along with environmental data that describes the geochemical
and physical habitat that they live in. We will use this information
and the epibiont genetic information (RNA and DNA) to understand what
genes they use to meet the daily life requirements at the hydrothermal
vents.
What questions are you trying to answer and why?
The Alvinella epibiont metagenome project is aimed at studying
how the bacterial epibionts living on the dorsal (back) surface of the
Alvinella pompejana polychaete worms, respond at the level of
gene expression to changes in the chemical (inorganic and organic compounds
that provide carbon and energy), and the physical (temperature and pressure)
conditions at the hydrothermal vent. This consortia has been the subject
of a number of previous studies, though there are still many unanswered
questions as to what role they play in the symbiosis with the worm, how
they adapt to rapid changes in temperature, what their basic metabolic
strategy is, etc., mainly because the microorganisms have evaded cultivation,
making it difficult to address these key questions in biology. Thus, in
our project, we have adopted a genomics approach in which we are sequencing
a large part of the DNA of the microbial consortia living with Alvinella
pompejana.
Following sequence annotation (identification of genes
in the sequence), my group will develop DNA microarrays with nearly
all of the unique genes found in the metagenome so that we can assess
which genes are turned on (or off) when we collect at the vents. We are interested in genes that are involved in how the epibionts make
their living (do they use inorganic or organic carbon?), what compounds
they can use as electron acceptors since oxygen is very low in the local
vent habitat (do they use sulfate, sulfur, nitrate, iron oxides, or other
metal oxides?). This will provide us with the information that is required
to model their metabolism and better understand the requirements for life
of these organisms at the vents.We're also interested in genes that are involved in survival through
the variations in temperature that the epibionts endure on a daily basis
(they could experience temperatures from 20° – 80° C!). This
will help us understand how microorganisms withstand big shifts in
temperature quickly, while maintaining the integrity of their cells
and cellular constituents (i.e. membranes, transporters, and proteins).
Why is this research important? What are the benefits?
Our
efforts should have direct benefits to improving the understanding of
the basic biology of the Alvinella epibionts, including metabolic
pathways they utilize, how they contribute to detoxification of the local
environment that the worm inhabits, how they contribute to the mutualistic
relationship with the worm, whether their proteins are specially adapted
to function over large temperatures (eurythermal adaptation), and if the
epibiont cells communicate with each other using small molecules called
homoserine lactones. The metagenome approach being used to access the
genomes and describe the metabolic capabilities in the Alvinella
epibionts marks a significant step in modern biology. If we can use this
approach to study organisms that are either difficult to sample, difficult
to cultivate, or both (such is the case in this study), we are only limited
then by our imaginations and funding to get access to the samples of interest
to develop a comprehensive understanding of microbial diversity and function
in environments worldwide.
What's your background, and what lured you into marine science/education?
My interest in marine science dates back to my youth. I was fortunate
to grow up on the Monterey Peninsula, California, where there is a most
amazing intertidal zone, inhabited by a diverse and beautiful group of
marine invertebrates and algae. In high school I found my calling in science,
and after taking a year-long marine science course, I was hooked! In college,
I majored in biochemistry, which provided a broad background in chemistry
and an introduction to molecular biology, giving a solid foundation to
build my interests in marine science upon.
Following my undergraduate education, I worked at the Bermuda Biological
Station for Research. I gained a wealth of information during the two
years I spent in Bermuda, and a desire to go back to school to earn
a graduate degree. I had become quite interested in biogeochemistry,
and at the same time really had a desire to use molecular sciences to
address questions in marine sciences. I embarked on a master's program
in cell and molecular biology, then a Ph.D. program in ecology, evolution,
and marine biology, in both cases using molecular tools to describe
marine microbial assemblages, their diversity, and the patterns of that
diversity in nature on environmental gradients or over time. I then
gained experience during a postdoctoral research position at the Center
for Microbial Ecology in microbial functional genomics, a rapidly evolving
and fascinating field, which is in its infancy with regard to environmental
applications, but a field that I feel I am very lucky to be exploring!
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