DNA Sequencing
The DOE Office of Biological and Environmental Research (BER) supports fundamental research in a variety of missions. DNA sequencing has contributed to the science of a number of BER programs, including the Genomics:GTL Program, the Terrestrial Carbon Processes Program, the Natural and Accelerated Bioremediation Research (NABIR) Program, the Environmental Management Science Program (EMSP), the Ocean Science Program, and carbon sequestration research, part of the Administration’s Climate Change Technology Program.
The Genomics:GTL Program, a partnership with the DOE Office of Advanced Scientific Computing Research, supports research into systems microbiology towards the comprehensive understanding of proteins and protein machines, gene regulatory networks, and microbial communities, and the development of computing and information infrastructure to enable a predictive understanding of biological systems.
The NABIR Program supports research on microbial biotransformations and/or immobilization of metal and radionuclide wastes. The EMSP supports research into microbially mediated biotransformations of DOE-relevant organic wastes such as chlorinated solvents. The Ocean Sciences and Terrestrial Carbon Processes Programs support research to understand the global carbon cycle including strategies for carbon sequestration.
Genome sequencing supports these programs by generating and providing initial analyses of microbial DNA sequence information to further the understanding and application of microbiology relating to energy production, chemical and materials production, environmental carbon management, and environmental remediation.
For more than 10 years, genomic sequencing of a range of microorganisms that live in a wide diversity of environments has provided a considerable information base for scientific research related not only to DOE missions, but also to other Federal agency missions and U.S. industry. (http://www.tigr.org/tdb/mdb/mdbcomplete.html); (http://microbialgenome.org/organisms.shtml); and (http://genome.jgi-psf.org/microbial/). Nonetheless, most of our current knowledge of microbiology still is derived from individual species that either cause disease or grow easily and readily as monocultures under laboratory conditions and are thus easy to study. The preponderance of species in the environment falls in neither of these categories and remains largely unknown to science. Many are thought to grow as part of interdependent consortia in which one species supplies a nutrient necessary for the growth of another. Little is known of the organization, membership, or functioning of these consortia, including those involved in environmental processes of DOE interest. In addition, genomic analyses of microbes suggests that processes such as lateral gene transfers at various times in the evolutionary history of some microbial lineages may have blurred the understanding we thought we had of their phylogenetic relationships.
BER publishes an annual invitation for suggestions of microbial targets for genomic sequencing to address mission needs in carbon sequestration, energy production, and bioremediation. Projects for sequencing are selected following scientific peer review and evaluation for mission relevance. Information on selections made for FY 2004 and FY 2005 can be found at http://www.jgi.doe.gov/sequencing/seqplans.html. A complete list of microbes sequenced by DOE can be found at http://microbialgenome.org/brochure.pdf, http://www.tigr.org, and http://www.genomesonline.org/. In addition, the DOE Joint Genome Institute (JGI) runs a Community Sequencing Program (CSP). This program was created to provide the scientific community at large with access to high-throughput sequencing. Sequencing projects are chosen based on scientific merit, judged through independent peer review. Criteria for participation in this program, the review process, and interactions between JGI and participants are outlined at http://www.jgi.doe.gov/CSP/overview.html. Through this program, the Department of Energy aims to assist and further sequence-based scientific research from a broad range of disciplines. The CSP consists of two programs: Information on organisms selected for sequencing in the CSP in FY 2004 and FY 2005 can be found at the JGI's Sequencing Plans & Progress website.