Where are you from, and what is your role in Extreme 2003?
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-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!