WALNUT CREEK, Calif. — The U.S. Department of Energy’s investment in large-scale genome sequencing is paying dividends, with powerful implications for the nation’s energy and environmental cleanup needs, according to a report just released by the DOE Joint Genome Institute.
As the leading national user facility targeting microbes and microbial communities, plants, and aquatic organisms, DOE JGI is serving to close a critical gap of knowledge while unlocking the potential of this largely unexplored cache of the planet’s living matter.
Highlights from the scores of significant projects tackled by DOE JGI between 2002 and 2005 include:
- The poplar, the first tree to be sequenced, provides a resource to fully exploit the possibilities of trees – to grow faster, to convert biomass to fuel more effectively, to sequester more carbon from the atmosphere, and to clean up waste sites.
- The diatom, a single-celled organism from the ocean, absorbs the major greenhouse gas carbon dioxide in amounts comparable to all the world’s tropical rain forests combined.
- Sequencing of sulfate-reducing bacteria, a DOE Genomics:GTL program undertaking, has helped chart the previously unseen metabolic processes of Desulfovibrio desulfuricans G20, a microbe that has a robust appetite for such toxic metals as uranium and chromium.
- White rot fungus, a major player in the carbon cycle, is capable of efficiently degrading the tough plant polymer lignin, one of the most abundant natural materials on earth, and can remediate explosive contaminants, pesticides and toxic waste.
“By marshalling the resources of now five national laboratories, DOE JGI has driven down the cost of sequencing while generating world-class science for developing effective strategies for clean energy, environmental remediation, and carbon management,” said Dr. Raymond L. Orbach, Director of DOE’s Office of Science.
“During this extraordinarily productive period, DOE JGI’s powerful engine of innovation has contributed to the sequencing of over 300 organisms, amounting to over 100 billion letters of DNA logged into the public databases.”
“DOE JGI sequence data and computational tools have enabled well over 250 peer-reviewed publications during this remarkable phase,” said Dr. Aristides Patrinos, DOE’s Associate Director of Science for the Office of Biological and Environmental Research. “The market for DOE JGI genomics is steadily growing and diversifying as the contributions to the scientific literature testify.”
“Sequencing’s role in biology has extended to fields far beyond what was contemplated when the Human Genome Project was launched fifteen years ago,” said DOE JGI‘s Director, Dr. Eddy Rubin. “DNA sequence has now become a vital commodity for informing scientific disciplines ranging from climatology to geochemistry and beyond. DOE JGI is empowering the science of numerous researchers around the world carrying out sequence-based investigations to better understand the natural sciences.”
DOE JGI scientists are also blazing new trails in the emerging field of metagenomics – isolating, sequencing, and characterizing DNA extracted directly from environmental samples – to obtain a profile of the microbial community residing in a particular environment. DOE JGI and its collaborators used a metagenomic strategy to characterize the microbial community responsible for the production of sulfuric acid deep inside an abandoned mine. For decades this toxic stream has seeped out to pollute a prominent river system, costing millions of dollars annually to remediate the situation. With the help of DNA sequencing, cheaper, more effective strategies to combat this problem are coming to light.
“In the same way the human genetic code is advancing biomedicine, we see metagenomics, fueled by GTL, the DOE Microbial Genome Program and the Community Sequencing Program, yielding revolutionary insights into the complexities of the biosphere and reaffirming the need for DOE JGI contributions.” Rubin said.
The 50-page DOE JGI Progress Report 2002-2005 can be downloaded from http://www.jgi.doe.gov/whoweare/JGI_Progress.pdf . A hard copy can be requested from gilbert21 [at] llnl.gov ( . )
The DOE Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories – Lawrence Livermore, Lawrence Berkeley, Los Alamos, Oak Ridge, and Pacific Northwest – along with the Stanford Human Genome Center to advance genomics in support of the DOE mission related to clean energy and environmental characterization and clean-up.
Additional information about DOE JGI can be found at: http://www.jgi.doe.gov/