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Microbes selected for whole-genome draft sequencing

Two microorganisms nominated by Matthew Fields (microbiology) have been selected by the U.S. Department of Energy’s office of environmental and biological research for whole-genome draft sequencing.

The DOE’s prioritization review panel selected the bacteria Alkaliphilus metalliredigens and Thermoanaerobacter ethanolicus for sequencing at the Joint Genome Institute, through the Microbial Genome Program. The program, a spin-off of the Human Genome Project, aims to completely sequence the genomes of microbes, which make up about 60 percent of Earth’s biomass. Since 1994 the DOE has sequenced the genomes — the blueprint of an organism — of about 100 microbes.

Selection of microbes is competitive and based on their relevance to energy production, waste-remediation and toxic chemical cleanup at hazardous waste sites and the global carbon cycle, among other characteristics.

Field’s nominated bacteria are both capable of metal-reduction and can thrive at extreme environmental conditions. According to Fields, A. metalliredigens – isolated from borate-contaminated leachate ponds in southern California – is the first organism that has been shown to reduce metals under conditions of alkaline pH and high salt.

“This unique biochemical capacity has impacts for bioremediation of heavy metals and radionuclides and also astrobiology,” says Fields. “The Jovian moon, Europa, has been theorized to have a liquid ocean that may be salty and alkaline. A. metalliredigens may be the best example of a metal-reducing microorganism thus observed that could have a lifestyle suitable for this possible environment.”

T. ethanolicus was isolated by a collaborator of Fields from deep subsurface sediments around 200 million years old. Comparison of its genome sequence with that of more recent microbes may give more insight into how genomes evolve.

Draft sequencing of Field’s microbes will be conducted in 2004. “To get the genome sequence determined for a given organism is a huge resource,” says Fields. “It provides insight into the entire metabolism and regulatory pathways present in an organism. However, the determination of a genome sequence is only the beginning. There is much work to be done to understand how a cell’s environment impacts overall physiology and biochemical capacity. ”

Fields joined the Miami faculty this fall from Oak Ridge National Laboratory where he was a research staff scientist.

Date Published: 12/11/2003
Volume: 23   Number: 18

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