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The American Society for Microbiology (ASM), the largest single life science organization in the world, with more than 42,000 members, appreciates the opportunity to provide written testimony on the Fiscal Year (FY) 2004 budget for the Department of Energy (DOE) science programs.

The ASM represents scientists working in academic, medical, governmental and industrial institutions worldwide. Microbiological research is focused on human health and the environment and is directly related to DOE programs involving microbial genomics, climate change, bioremediation and basic biological processes important to energy sciences.

The Office of Science supports unique and critical pieces of U.S. research in scientific computation, climate change, geophysics, genomics, and the life sciences. This research is conducted at both the DOE national laboratories and at approximately 250 universities nationwide through peer-reviewed, competitive research. The Office of Science is also an invaluable contributor to the scientific programs of the National Institutes of Health (NIH) and the National Science Foundation (NSF). These partnerships bridge the gap between the physical sciences, the life sciences and computational sciences, allowing science to refine and advance our efforts in deciphering genomes and their critical functions. The Office of Science is a leader in these efforts and promoting multi-disciplinary research that seeks to harness the capabilities of microbes and microbial communities to help us to produce energy, clean up waste, and sequester carbon from the atmosphere. Furthermore, these cross-disciplinary programs contribute enormously to the knowledge base and training of the next generation of scientists while providing worldwide scientific cooperation in physics, chemistry, biology, environmental science, mathematics, and advanced computational sciences.

The Office of Science will play an increasingly important role in the Administration's goal of U.S. energy independence in this decade. Many DOE scientific research programs share the common goal of producing and conserving energy in environmentally responsible ways. Programs include basic research projects in microbiology, as well as, extensive development of biotechnological systems to produce alternative fuels and chemicals, to remediate environmental problems, and to reduce wastes and pollution.

The Administration's proposed budget for FY 2004 requests $3.3 billion for the Office of Science, an increase of $5 million over FY 2003. The ASM would like to submit the following comments and recommendations for funding levels for research in the Biological and Environmental Research (BER) and Basic Energy Sciences (BES) programs for FY 2004. Federal investment in these programs today, will help to ensure fundamental research to find solutions to future environmental and energy problems while maintaining U.S. scientific leadership worldwide.

Microbial Genomics

The Administration has requested $10 million for FY 2004, which is the same level as in FY 2003. In view of the tremendous potential from microbial genomic sequencing, the ASM recommends that Congress provide $15 million for FY 2004. In 1994, the Office of Biological and Environmental Research developed the Microbial Genomics Program as a compliment to the Human Genome Program. This early leadership in microbial genomics has allowed the program to decipher the genomic sequences of many of the non-pathogenic microorganisms available today. This information provides clues into how we can design biotechnological processes that advance research in a number of disciplines and national priorities, such as biogeochemical cycles, global warming, and alternative energy research. Fundamental microbial research will continue to underpin DOE's research capabilities in other BER and BES programs, including: Genomes to Life; bioremediation research; and carbon sequestration. DOE has also developed, at the Joint Genome Institute (JGI), a highly efficient, centralized sequencing facility that is a unique and valuable resource for serving the nation's non-medical microbiological researchers.

Knowing the complete DNA sequence of a microbe provides important keys to the biological capabilities of the organism and is the first step in developing strategies to more efficiently detect, counteract, use, or reengineer that microbe to address an assortment of national issues. The DOE has completed the DNA sequencing of more than 50 microbes with potential uses in energy, waste cleanup, and carbon sequestration. For instance, the JGI has completed the genomic DNA of several algae important in the ocean's photosynthesis process and in soil bacteria that assimilate carbon dioxide, both important biological processes for carbon dioxide capture from the atmosphere.

The ASM applauds DOE's leadership in recognizing this important need in science and endorses expansion of its microbial genome sequencing efforts, particularly in using DNA sequencing to learn more about the functions and roles of the 99% of the microbial world that cannot yet be grown in culture.

Genomes to Life Program

The ASM strongly supports the Administration's funding of the Genomes to Life (GTL) program at $59 million for FY 2004. The GTL program is ushering in a new biological era-the era of systems biology, which will allow us to understand entire living organisms and their interactions with the environment. This new level of exploration (i.e., systems biology) will empower scientists to pursue completely new approaches to discovery and spur the development of new products or services from microbes and other organisms. With a deeper, genetically based understanding of living organisms, the potential to utilize and refine their functions will allow us to address many of today's challenges in carbon sequestration, energy transformation, and environmental clean up.

The Genomes to Life program has just begun to demonstrate the potential application of microorganisms for energy, medicine, agriculture, environment, and national security needs. This research will potentially offer new biotechnology solutions to these challenges and those of tomorrow. Underlying the potential applications of biotechnology for clean energy, mitigating climate change, and environmental cleanup is the need for a solid understanding of the functions, behaviors and interactions of every biological part (the genes and proteins) of a microorganism. If we are to improve the productivity of forests, bioremediation agents, biomass crops and agricultural systems, it is imperative to understand how these biological machines work. This will require a staggering amount of expertise across the sciences (e.g., physical and computational), new computational capabilities, new tools, and new interdisciplinary approaches to genomics research.

In FY 2004, the GTL program will increase its emphasis on DNA sequencing of microbes and microbial communities. This sequencing will serve as the core biological data needed to further understand the control and function of molecular machines and microbial communities. The ASM applauds the programs continued focus on microbial communities and notes that this represents the kind of interdisciplinary science that DOE has done successfully in the past, making use of advanced technologies, specialized facilities, teams of scientists, and computational power. The ASM also sees this program as the basis for an expanded effort to understand more broadly how genomic information can be used to understand life at the cellular level and urges Congress to fully support this exciting program.

Climate Change Research

The ASM is pleased to see the Administration's support of Climate Change Research continue in its FY 2004 budget. The ASM endorses the President's proposed $143 million budget, an increase of $6 million over FY 2003. The Society is also supportive of the proposed $19 million budget for the Ecological Processes section for FY 2004, a $5 million increase over FY 2003.

In FY 2003, the Administration launched the Climate Change Research Initiative (CCRI), to study the potential effects of greenhouse gases and aerosol emissions on the climate and the environment. The Climate Change Research Subprogram is DOE's contribution to the cross-agency CCRI and applies DOE's expertise in genomics and computational climate modeling to determine the effects of greenhouse emissions on the global climate. The Climate Change Research subprogram supports four areas of research: Climate and Hydrology, Atmospheric Chemistry and Carbon Cycle, Ecological Processes, and Human Interactions. This research is focused on understanding the physical, chemical, and biological processes affecting the Earth's atmosphere, land, and oceans and how these processes may be changing because of greenhouse emissions.

The Ecological Processes portion of the subprogram is focused on understanding and simulating the effects of climate and atmospheric changes on the biological structure and functioning of planetary ecosystems. Research in 2004, will focus on understanding the responses of a simplified terrestrial ecosystem (e.g., higher plants, consumers of plant production, and soil microorganisms) to changes in a key environmental factor, such as, temperature. This research is critical if we are to better understand the changes occurring in our ecosystems from increasing levels of atmospheric radiation absorptive gases.

The ASM urges Congress to support this important research within the Office of Science budget. The Climate Change Research subprogram is a key component in developing more accurate climate modeling and ecosystem data, and promises to yield new technologies to address future climate changes.

Basic Energy Science

The Administration's requested funding for the Office of Basic Energy Sciences (BES) is $1 billion for FY 2004. This program is a principal sponsor of fundamental research for the nation in the areas of materials sciences, chemistry, geosciences, and biosciences as it relates to energy. Biosciences funds an array of microbiological and plant research focused on harvesting and converting energy from cellulose and other products of photosynthesis into renewable resources.

The ASM is supportive of DOE's continued emphasis upon biobased energy research as a key component of the nation's energy portfolio. In 2004, biosciences will continue to focus on recent successes in its cellulose biosynthesis program, which is funding research into the synthesis of cellulose, the most abundant biomolecule, as a potential biofuel. Other microbiological research (e.g., Molecular Mechanisms of Natural Solar Energy Conversion, $12 million in FY 2004) supported by the program includes fundamental research into the characterization of molecular mechanisms involved in the conversion of solar energy into biomass, biofuels, bioproducts, and other renewable energy resources. Furthermore, the ASM believes continued research into energy-rich plants and microbes be a DOE priority as genomic technologies have given this research area a tremendous new resource for advancing the Agency's bioenergy goals.

The ASM is also supportive of new activities, such as, the Metabolic Regulation of Energy Production program ($19 million for FY 2004), which supports the biological advances needed to complement the chemical nanoscale program within the Office of Science.


DOE's bioremediation research is contained in the Natural and Accelerated Bioremediation Program (NABIR). The Administration's proposed budget for the NABIR program is $24.1 million. The ASM supports the Administration's request for bioremediation research. However, the ASM believes that greater benefits will be achieved if the NABIR program is increased to $30 million.

In FY 2004, the NABIR program will focus on a number of efforts: Biotransformation (microbiology to elucidate the mechanisms of biotransformation of metals and radionuclides), Community Dynamics and Microbial Ecology (structure and activity of subsurface microbial communities), and Biogeochemical Dynamics (the dynamic relationships among geochemical, geological, hydrological, and microbial processes).

Bioremediation scientists are searching for cost-effective technologies to improve current remediation methods to clean up DOE's contaminated sites. This research has the potential to lead to new discoveries into reliable methods of bioremediation of metals and radionuclides in soils and groundwater. The NABIR program supports the basic research that is needed to understand this technology to more reliably develop the practical applications for cost-effective cleanup of pollutants at DOE sites. The ASM strongly recommends that additional funding be allocated to balance the program elements and pollutants studied as originally envisioned when the NABIR Program was designed.

New Technologies and Unique Facilities

New technologies and advanced instrumentation derived from DOE's expertise in the physical sciences and engineering have become increasingly valuable to biologists. The beam lines and other advanced technologies for determining molecular structures of cell components are at the heart of current advances to understand cell function and have practical applications for new drug design. DOE's advances in high throughput, low cost DNA sequencing; protein mass spectrometry, cell imaging and computational analyses of biological molecules and processes are other unique contributions of DOE to the nation's biological research enterprise. Furthermore, DOE has unique field research facilities for environmental research important to understanding biogeochemical cycles, global change and cost-effective environmental restoration. In short, DOE's ability to conduct large-scale science projects and draw on its unique capabilities in physics, computation and engineering is critical for future biological research.

The ASM strongly supports the basic science agenda across the scientific disciplines and encourages Congress to maintain its commitment to the Department of Energy research programs to maintain U.S. leadership in science and technology.