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Microbiologist's research selected for DNA sequencing

11/02/2004

Research by a Miami University microbiologist--and state-of-the-art DNA sequencing--may one day result in cleanup of contaminated waste sites by microorganisms.

Matthew Fields’ project is one of the first 23 selected for a new Community Sequencing Program of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI).

The JGI awarded Fields and co-principal investigator Jizhong Zhou of the Oak Ridge National Laboratory 600 MB of DNA sequencing. DNA sequences will be determined for microorganisms in groundwater community samples from contaminated sites at the Natural and Accelerated Bioremediation Research Field Research Center. The site contains high-concentration plumes of mobile uranium, along with volatile organic mercury and other heavy metals.

The whole community sequence data will provide baseline information for understanding how the microbial community adapts to extreme toxic, mixed waste environments, according to Fields. “This study will be the first to examine at the genome level how contaminants will affect microbial community structure.” That information will provide the basis for development of strategies for in situ waste remediation of contaminated sites.

Microbes, the oldest form of life on earth, represent the vast majority of life on the planet, but fewer than one percent have been cultured, according to the JGI. Fields’ project will characterize some of the as-yet uncultured organisms in the groundwater microbial community. The project site contains about 20 different bacterial groups, both “known” and novel. It will also provide an opportunity to test ecological and evolutionary theories about the relationship between phylogenetic (evolutionary development of a species) diversity and the functional properties of ecosystems.

“The primary goal of the CSP is to provide a world-class sequencing resource for expanding the diversity of disciplines-geology, oceanography, and ecology, among others-that can benefit from the application of genomics,” says JGI director Eddy Rubin. “Just as physicists and climatologists submit proposals to get time on accelerators and supercomputers to address fundamental questions, we are inviting investigators to bring to the JGI important scientific challenges.”

Last year two microbes nominated by Fields were selected for whole-genome draft sequencing by the JGI. Work on sequencing Alkaliphilus metalliredigens and Thermoanaerobacter ethanolicus -both of which are capable of metal-reduction and can thrive at extreme temperatures-is in progress.

Miami’s recent acquisition of state-of-the-art DNA sequencing instrumentation, made possible by a National Science Foundation major research instrumentation grant, will also facilitate Fields’ research.

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