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ORNL leading effort to help harness power of Shewanella
OAK RIDGE, Tenn.,
Nov. 11, 2005
Tremendous amounts of data being generated about a microbe adept at bioremediation will be more efficiently organized and shared through a new $3 million project headed by Oak Ridge National Laboratory.
The award by the Department of Energy's Office of Science builds upon advances made through a three-year consortium whose members have already sequenced the genome - the genetic makeup - of seven strains of the Shewanella, a relatively common microbe with diverse capabilities. Working with the Joint Genome Institute, researchers hope to sequence the remaining eight strains by the end of 2006.
"Our goals are to gain a better understanding of the Shewanella mechanisms for metal contaminants reduction and other bioremediation applications, and develop a system that makes the information readily available to the research community," said Ed Uberbacher, a member of ORNL's Life Sciences Division and leader of the project.
When the work is complete, researchers worldwide will be able to query across the many individual research domains and projects, link to analysis applications, visualize data in a cell systems context and produce new knowledge. This will be accomplished while minimizing the effort, time and complexity to participating laboratories, Uberbacher said.
This effort could have a dramatic impact on the bioremediation mission involving approximately 2 trillion gallons of heavy metal contaminated groundwater and 75 million cubic meters of soil and subsurface sediment at various DOE and other sites around the nation.
"Biological knowledge emerging from genome sequencing efforts and new programs such as Genomics: Genomes to Life have the potential to put microbial cells and communities or cell components to work to meet the challenges of this critical DOE mission," Uberbacher said.
This three-year project, officially known as "An Integrated Knowledge Resource for the Shewanella Federation," will play a key role in helping researchers gain a more complete understanding of the response systems in organisms such as Shewanella and how they respond to changes in their environment. This can be achieved through a combination of many different methods, including sampling of strains present at DOE waste sites, characterization of in situ and mutant physiologies and exploration of conditions conducive to optimal reduction of metals.
This is one of six recently announced DOE projects aimed at increasing knowledge of microbes and microbial communities with potential applications in bioremediation, ethanol and hydrogen production, cleanup of former nuclear weapons production sites and minimizing global warming by controlling the cycling of atmospheric carbon dioxide.
Other ORNL researchers involved in the project are Nagiza Samatova, Andrey Gorin and Denise Schmoyer of the Computer Science and Mathematics Division and Loren Hauser of the Life Sciences Division. Other collaborators are the University of Tennessee, Oak Ridge Institute for Science and Education, Pacific Northwest National Laboratory, Michigan State University, University of Southern California, Marine Biological Laboratory and Boston University. These collaborators form what is known as the Shewanella Federation, a multi-investigator and cross-institutional consortium formed to characterize and model the biology of the Shewanella.
ORNL is managed by UT-Battelle for the Department of Energy.