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Department of Energy - FY 2011 Testimony

The American Society for Microbiology (ASM) is pleased to submit the following testimony on the Fiscal Year (FY) 2011 appropriation for the Department of Energy (DOE) science programs. The ASM is the largest single life science organization in the world with more than 40,000 members. The ASM mission is to enhance the science of microbiology, to gain a better understanding of life processes, and to promote the application of this knowledge for improved health and environmental well-being.

The ASM supports the Administration’s FY 2011 budget of $5.1 billion  for the DOE Office of Science, a 4.4 percent increase from FY 2010. The ASM endorses the Administration’s pledge to double funding for the DOE Office of Science by FY 2017. The Office of Science funds intramural and extramural research that might not otherwise exist due to its complexity or cutting edge, theoretical nature. Such research exemplifies the path to technological innovations needed to enhance our economy, our workforce, and our environment.

The DOE’s Office of Science is the largest sponsor of basic research for the physical sciences in the United States. It supports more than 7,000 individual research projects at more than 300 academic institutions, and ten DOE national laboratories. It also provides access to leading edge research facilities for extramural investigators, including an estimated 26,000 that will use these facilities in FY 2011. 

Biological and Environmental Research (BER)

The Office of Biological and Environmental Research, within the DOE Office of Science, oversees research and facilities that support DOE’s energy, environment, and basic research missions.  BER sponsored research provides the foundational science underpinning  DOE’s goals for development of clean bioenergy sources, remediation and/or long term stewardship of legacy environmental contamination and understanding the impacts of climate change on Earth’s ecosystems. 

BER programs enable solutions for some of the nation’s most difficult energy-related and environmental challenges by advancing our basic understanding of climate change, biofuels, carbon sequestration, remediation of subsurface contaminants, and interactions of biological and physical systems. Wide ranging studies of microbes are central to all of these efforts and include pioneering studies of the genetic potential of individual organisms and microbial communities in complex environments, as well as with development of new bioinformatics tools for effectively managing and utilizing large datasets to advance genome enabled scientific research.

Genomic Science

The BER Genomic Science program (formerly Genomics: GTL) accelerates the development of practical solutions to energy and environmental problems by understanding the integrated biological systems of microbes and plants that govern their structure and function.  This program uses a combination of high throughput genome sequencing and cutting-edge systems biology research techniques to understand key biological processes, ranging from molecular-scale networks of single cells to community-scale interactions of ecosystems.  In addition to directly supporting DOE mission-driven research efforts at both academic institutions and DOE national laboratories, publically accessible genomic and metagenomic sequence data produced by DOE facilities encourage and support innovation while helping to solve environmental problems and energize commercial biotechnology in the United States.

Addressing complex environmental and energy problems requires innovative, cross-cutting research, and the Genomic Science program supports a wide range of interdisciplinary research efforts with a strong microbiological component.  For example, a recent research topic, ”Biological Systems Research on the Role of Microbial Communities in Carbon Cycling” seeks to develop new integrated research efforts in genome-enabled systems biology, environmental microbiology, and modeling of biogeochemical processes  aimed at understanding how shifts in environmental variables impact microbially mediated carbon cycling processes. Gaining better quantitative knowledge of these processes is critical to predict the storage or release of carbon from ecosystems and potential levels of CO2, methane, and other greenhouse gasses in the atmosphere.

Joint Genome Institute (JGI)

BER funding supports the DOE-Joint Genome Institute (JGI), which has sequenced over 450 microbial genomes, more than 200 “metagenomes” of microbial communities, as well as 25 plant genomes with energy and environmental significance. The JGI provides access for external researchers to its state of the art sequencing and bioinformatic capabilities. Current sequencing capacity is about four Tera-base pairs per year, and this capacity is continually expanding with advances in sequencing technology and computing. JGI researchers generate results that push the boundaries of 21st century genomics, sequencing organisms that degrade cellulose, capture carbon, and transform environmental contaminants. Their discoveries help stakeholders make decisions about the selection of new bioenergy crops and cost effective bioenergy production. Examples of JGI-supported research reported in 2009 included:

  • Descriptions of genomes of two ocean algae with a focus on the genes that enable carbon capture by fixing CO2; these results may lead to improved production of algae-derived biofuels
  • Comparisons of genomes and proteins expressed from ten strains of Shewanella bacteria; these microbes play important roles in environmental remediation due to their ability to absorb and detoxify certain metals and organic compounds
  • The sequencing of 56 microbes (the “Genomic Encyclopedia of the Bacteria and Archaea” project) from less-explored branches of the microbial taxonomic tree (microbial “dark matter”) to widen the set of reference sequences for comparisons of metagenomic sequencing data and for continued “prospecting” for genes with novel catalytic or enzymatic activities relevant to DOE needs in Bioenergy, carbon cycling, or contaminant remediation.
  • Using a bioreactor to incubate a compost microbial community with switchgrass, it was possible to select for microbes that degraded switchgrass and thus identify new glycoside hydrolases that may have utility in grass cell wall deconstruction, critical to exploiting plants for biofuels

Bioenergy Research Centers

BER supports three DOE Bioenergy Research Centers (BRCs), established in 2007, tasked with developing innovative new strategies for biofuels production.  When created, the multidisciplinary Centers brought together teams of researchers from 18 of the nation’s leading universities, seven DOE national laboratories, at least one nonprofit organization, and a range of private companies. The collective mission is to perform fundamental research addressing barriers to economic production of energy from cellulosic biomass and drastically reduce the nation’s consumption of fossil fuels. Goals include identification of next generation bioenergy crops, discovery of enzymes and microbes that degrade biomass, and creation of microbe-mediated models of fuel production of bioethanol and other next generation biofuels. Each center  applies cutting-edge technologies and research methods, working with a wide range of biomass source materials and managing massive data sets in the search for tomorrow’s clean energy.

Headquartered at DOE’s Oak Ridge National Laboratory, the University of Wisconsin-Madison, and DOE’s Lawrence Berkeley National Laboratory, the three BRCs are investigating microbial processes that can convert diverse crops, such as switchgrass and poplar, into usable fuels. Specific examples include the BioEnergy Science Center’s approaches for screening of samples from natural thermal springs to identify enzymes and microbes that effectively break down and convert biomass at high temperatures and genetically engineering a lignocellulose-degrading microbe for ethanol production. Researchers at the Great Lakes Bioenergy Research Center are developing more refined metabolic models of in microbes to enable rational design of metabolic engineering strategies for enhanced biofuels production.  The Joint BioEnergy Institute is pursuing synthetic biology research on microbial synthesis of a variety of hydrocarbon compounds with higher energy content than ethanol and better compatibility with existing fuel distribution infrastructure.

Basic Energy Sciences (BES)

The Office of BES, administered within the Office of Science, supports fundamental research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, providing the foundations for new energy technologies and supporting DOE missions in energy, environment, and national security.  The portfolio supports work in the natural sciences, emphasizing fundamental research in materials sciences, chemistry, geosciences, and aspects of biosciences. BES also operates sophisticated, state-of-the-art equipment and facilities open to extramural investigators from private institutions, universities, and national laboratories. Research highlights include determination of the structure and organization of the highly efficient light-harvesting chlorosome antenna complex in green sulfur photosynthetic bacteria, elucidation of the methanogenic archaeal translational machinery that allows incorporation of the 22nd amino acid pyrrolysine into proteins, characterization of critical components of the algal light-harvesting complex, and determination of the biosynthetic pathway for methane production from CO2 and molecular hydrogen.

In 2009, BES Energy Biosciences evolved into two complementary and synergistic programs, Photosynthetic Systems and Physical Biosciences.  Both programs support unique areas of fundamental research on plant and non-medical microbial systems.

Photosynthetic Systems

The BES Photosynthetic Systems program supports fundamental research on the biological conversion of solar energy to chemically stored forms of energy, bringing together biology, biochemistry, chemistry, and biophysics approaches to study natural photosynthesis and related processes including carbon fixation and metabolism.  Advances in genomics technologies such as metabolomics along with increased availability of plant genomic sequences are also providing new opportunities to leverage the strengths of the Photosynthetic Systems program in molecular biology and biochemistry with powerful capabilities in imaging and computation.  Example topics of study include light harvesting, exciton transfer, charge separation, transfer of reductant to carbon dioxide, and the biochemistry of carbon fixation and carbon storage. Emphasized areas are those involving strong intersection between biological sciences and energy relevant chemical sciences and physics, such as in self assembly of nanoscale components, efficient photon capture and charge separation, predictive design of catalysts, and self-regulating/repairing systems.  The program aims to provide a critical scientific knowledge base that can inspire the roadmap for artificial photosynthesis and enable new strategies and technologies for more efficient generation of biomass as a renewal energy source.

Physical Biosciences

The BES Physical Biosciences program combines experimental and computational tools from the physical sciences with biochemistry and molecular biology.  The goal is increased fundamental understanding of the complex processes that convert and store energy in plants and non-medical microbes, including archaea.  Examples of research supported by this program include studies that investigate the mechanisms by which energy transduction systems are assembled and maintained, the processes that regulate energy relevant chemical reactions within the cell, the underlying biochemical and biophysical principles determining the architecture of biopolymers and the plant cell wall, and active site protein chemistry that provides a basis for highly selective and efficient bioinspired catalysts.  Combined with efforts in molecular biology and biochemistry, increased use of physical science and computational tools (ultrafast laser spectroscopy, current and future x-ray light sources, quantum chemistry) to probe spatial and temporal properties will give us an unprecedented architectural and mechanistic understanding of biological systems and allow the incorporation of identified principles into the design of bio-inspired synthetic or semi-synthetic energy systems.


The BES administered Experimental Program to Stimulate Competitive Research (EPSCoR) also supports a significant sector of the nation’s energy research, distributing university grants in a number of states across the country. EPSCoR’s interdisciplinary program areas include, among many others: biological and environmental science, advanced computer science, renewable energy science, climate change, genomics, and science education. EPSCoR has traditionally provided academic incubators for innovation and economic recovery.

Research Infrastructure and the Nation’s Workforce

More than 30,000 scientists and engineers work at DOE laboratories and technology centers, but many more are supported through grants and fellowships, or the use of cutting edge facilities and equipment that often are one of a kind. An example was last September’s announcement of up to $12.5 million in Recovery Act funding for at least 80 graduate fellowships to US students pursuing advanced STEM related degrees, through the Office of Science’s new Graduate Fellowship program.

DOE’s Office of Science has also initiated an Early Career Research Program, designed to bolster the nation’s scientific workforce by providing support to exceptional researchers during the crucial early career years, when many scientists do their most formative work.

Another Office of Science program, Workforce Development for Teachers and Scientists, specifically targets workforce shortages and provides college undergraduates and K-12 teachers with DOE laboratory experiences, designed to attract more young Americans into the STEM workforce.

The Office oversees ten world class facilities: the Ames, Argonne, Brookhaven, Lawrence Berkeley, Oak Ridge, Pacific Northwest, and Princeton Plasma Physics national laboratories, plus the Fermi, Thomas Jefferson, and SLAC accelerator facilities. These institutions encourage use by outside researchers and students, typically without cost, if results are posted for public knowledge. Each SC facility is an invaluable resource of unique research tools for scientific specialists. The Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory has hosted more than 10,000 scientists from all 50 states and more than 60 countries since its opening in 1997.  This year, the DOE will permit extramural use of roughly 1.3 billion supercomputer processor hours at its Argonne and Oak Ridge facilities, awarded to researchers whose projects would be impossible without petascale (quadrillion calculations per second) computing.


The ASM supports increased funding for the DOE Office of Science in FY 2011 and urges Congress to fund the Office of science with at least $5.1 billion.  The diverse Office of Science programs and their successes advance the DOE’s strategic mission to sustain the pace of scientific discovery and to educate and train the vital scientific workforce. Global climate change, clean energy, and pristine environments are challenges that demand unflinching responses from the United States’ science and technology sectors. DOE funded science and engineering are integral to our nation’s search for solutions. The Office of Science leads this effort with notable basic and applied energy research, which often is unique in its complexity, technical requirements, or high risk, high impact design. 

The ASM appreciates the opportunity to provide written testimony and would be pleased to assist the Subcommittee as it considers the FY 2011 appropriation for the DOE.