Microbial Genomics
at the U.S. Department of Energy

Programs Complementary to DOE Microbial Genome Research

This section details some governmental research complementary to DOE microbial genome research--especially as it relates to the Genomics:GTL program (GTL)--a follow on program to the MGP. Because of the centrality of genomics to the study of all life, DOE microbial genome research can benefit other life sciences programs, and progress can be accelerated by synergies attained through data and resources from others. Although vastly different in focus, scope, and scale of research, the projects listed here are united by their underlying study of DNA and its corresponding technologies. Breakthroughs in one can lead to innovations in another.

The information below was taken from web resources and may be incomplete. URLs are provided for further information and exploration. Updates to the online version of this list are encouraged (contact: millsmd@ornl.gov).

DOE Office of Science Programs

Office of Science Office of Biological and Environmental Research (BER)

BER supports basic biological and environmental research relevant to DOE missions. Biological discoveries are needed to clean and protect the environment, offer new energy alternatives, and understand the impacts of energy use on climate change. BER consists of four divisions: Climate Change Research Division, Environmental Remediation Sciences Division, Life Sciences Division, and Medical Sciences Division. GTL is a Life Sciences Division program jointly supported by BER and the Advanced Scientific Computing Research program in DOE's Office of Science. GTL is complementary to other BER research programs.

Environmental Remediation Sciences Division (ERSD)

The Environmental Remediation Sciences Division (ERSD) of DOE’s Office of Science seeks to understand microbial function in diverse environments and how these functions can be harnessed for restoration of contaminated DOE sites. Field-scale models for predicting contaminant fate and transport and designing remedial measures in complex heterogeneous environments depend on understanding biogeochemical reactions occurring in the subsurface at much smaller scales. This knowledge must be both spatially and temporally extrapolated. ERSD is positioned to identify microorganisms and processes by taking advantage of the genomic and proteomic systems biology tools offered by GTL. The goal is to use microbial capabilities for improving our understanding of the complex processes operating in the subsurface, placing them in the context of other simultaneous chemical and physical processes, and scaling the results to the field using advanced conceptual and mathematical models.

ERSD funds numerous laboratory- and field-based projects to evaluate the potential for subsurface microorganisms to immobilize or remobilize contaminant metals (including radionuclides) in situ. Significant progress has been made in detecting subsurface microorganisms associated with this process and in describing and modeling biogeochemical reactions mediated by microbes. A more complete understanding of microbial metabolism and community behavior will help determine the impact of microorganisms on contaminant fate and transport.

• Natural and Accelerated Bioremediation Research (NABIR)
  NABIR concentrates on field- and laboratory-based studies of natural microbial communities and their interactions with heavy-metal and radionuclide contaminants. NABIR focuses on understanding and enhancing natural microbial activities that remove contaminants from groundwater and transform them into chemical forms that pose less risk to humans and the environment. Interactions between GTL and NABIR will be important for providing the scientific foundation to develop more effective microbe-based remediation strategies.

Climate Change Research Division (CCRD)

CCRD fosters research on understanding the basic chemical, physical, and biological processes of the earth's atmosphere, land, and oceans and how these processes may be affected by energy production and use, primarily the emission of carbon dioxide from fossil-fuel combustion. CCRD modeling aims to quantify sources and sinks of greenhouse gases, especially carbon dioxide; accurately predict and assess the potential consequences of climate change; and evaluate the benefits and costs of alternative response options. GTL-related programs include:

• Program for Ecosystem Research (PER) PER supports research that aims to understand and predict impacts of energy-related environmental changes on the processes and component organisms of terrestrial ecosystems.
• Ocean Science (OS) OS focuses on understanding ocean-atmosphere carbon exchange and evaluating ocean-based carbon-sequestration strategies.
• Terrestrial Carbon Processes (TCP) TCP's goal is to understand terrestrial carbon cycling and evaluate the potential of long-term carbon sequestration in terrestrial environments.
• Carbon Sequestration Research BER's carbon-sequestration research program includes both CCRD and Life Sciences Division research that could lead to strategies to improve the use of trees within the genus Populus (poplar) or other trees for long-term sequestration of meaningful amounts of atmospheric carbon in terrestrial ecosystems. Research also emphasizes strategies to use the poplar and microbial genomic sequences to enhance partitioning of carbon into quantitatively important recalcitrant components of trees or soil organic matter that could lead to enhanced carbon sequestration.

Office of Science Office of Basic Energy Sciences (BES)

BES supports research that provides a scientific foundation for developing new and improved energy technologies and for understanding and mitigating the environmental impacts of energy use.

Energy Biosciences (EB) Energy Biosciences is part of the Chemical Sciences, Geosciences, and Biosciences Division at BES. This program supports basic research to understand the processes of plants and microorganisms that could be used to develop future energy-related biotechnologies. EB emphasizes understanding biological principles rather than optimizing biological processes. Research topics include mechanistic studies of photosynthetic solar-energy capture; mechanisms and regulation of carbon fixation and carbon or energy storage; regulation of plant growth and development; and examination of metabolic pathways relevant to the production of useful chemicals and fuels.

DOE Office of Fossil Energy (FE) Programs

FE supports research and development that address technological challenges of the nation's energy and environmental initiatives. GTL scientific insights could spur R&D in the following FE programs:

Bioprocessing and Biotechnology Research

Bioprocessing and biotechnology activities are part of FE's Advanced Research Programs for Coal and Natural Gas Power Systems. Research is directed toward using biology to develop applications for generating clean, efficient electric power and producing clean fuels from coal. Some research topics include biomodification of coal to reduce mercury emissions; bioremediation of waste streams from power plants; use of microbial toxins to reduce fouling of cooling water intake and discharge systems; investigation of marine microalgae for carbon dioxide biofixation potential; and use of biological systems to produce hydrogen from coal and coal-waste products.

Carbon Sequestration

Carbon Sequestration Core R&D is developing technologies that can capture and permanently store greenhouse gases. GTL will be a scientific foundation for technology development in the following areas:

• Ocean Sequestration Research
• Carbon Capture Research
• Terrestrial Sequestration Research
• Novel Carbon Sequestration Concepts

DOE Office of Energy Efficiency and Renewable Energy (EERE)

Biomass Program

The Biomass Program supports the research and development of advanced technologies that transform biomass into biofuels, biopower, and high-value bioproducts. GTL will play an important role in providing a better understanding of current microbial processes and discovering new microbial capabilities relevant to the Sugar Platform and Products research areas.

Hydrogen Production

Hydrogen Production, within EERE's Hydrogen, Fuel Cells, and Infrastructure Technologies Program, aims to research and develop low-cost, highly efficient hydrogen-production technologies from diverse domestic sources. GTL science could benefit two Hydrogen Production research areas: (1) Biological and Biomass-Based Production, for improving efficiencies of anaerobic fermentation systems; and (2) Photolytic Hydrogen, for photobiological production of hydrogen by green algae.

National Science Foundation (NSF) Programs

• Biochemical Engineering and Biotechnology (BEB). BEB supports basic engineering research that aims to understand and achieve quantitative assessments of biomolecular processes (in vivo, in vitro, and ex vivo) that can be used to develop practical biotechnological applications. BEB projects cover a wide range of biotechnological research areas: Fermentation, enzyme studies, recombinant DNA technology, bioprocess control and optimization, metabolic-pathway engineering, cell culturing, tissue engineering, food processing, and relevant information-technology development.
• Biocomplexity in the Environment (BE): Integrated Research and Education in Environmental Systems. BE promotes new approaches to studying the dynamic nature of biological systems and their impact on physical and chemical processes of the environment. All environments (including natural ecosystems and agricultural and urban lands) and organisms from microbes to humans fall within the BE framework.
• Biological Databases and Informatics (BD&I) Program. BD&I supports new approaches to the management, analysis, and dissemination of biological knowledge that will benefit the scientific community and the general public. BD&I will explore theoretical research on data structures; develop new types of databases with architectures better suited to the complexity of biology; and design easy-to-use interfaces and tools for data analysis and use.
• Biological Oceanography Program. This program supports the study of marine organisms and their interactions with each other and with elements in their environment. Subfields in this program include ecosystem and biogeochemical processes; community and population ecology; behavioral, reproductive, and life-history ecology; physiological and chemical ecology; and evolutionary ecology.
• Biomolecular Systems Cluster. The Biomolecular Systems Cluster supports research to develop technologies and computational and experimental approaches for the study of biomolecular complexes, mechanistic studies of biomolecular activity, and characterization of higher-order biochemical processes by which organisms acquire and use energy.
• Catalysis and Biocatalysis. This program fosters fundamental and applied research in the following areas: Kinetics and mechanisms of chemical reactions important to the production of fuels, chemicals, and specialized materials; characterization of chemical reactions at or near solid surfaces; electrocatalytic processes with industrial or commercial importance; green chemistry or use of biorenewable resources; kinetic modeling and theory of biocatalysis; reactive deposition and processing for thin-film materials; and the use of chemical reaction or transport knowledge to design or control chemical reactors.
• Cellular Systems Cluster. This program focuses on the structure, function, and regulation of plant, animal, and microbial cells and their interactions with the environment and with one another. Microbial Observatories (MO) and Microbial Interactions and Processes (MIP) are included in this cluster. MO's goal is to establish a network of sites for observing and understanding microbial diversity in different habitats over long time periods. MIP supports shorter-term, smaller-scale microbial-diversity research that is not site based.
• Ecological Biology Cluster (EBC). EBC supports experimental, observational, theoretical, and modeling studies on the structure and function of complex biological associations in natural and managed ecological systems. This program includes the National Center for Ecological Analysis and Synthesis, which analyzes ecological information, tests ecological theories, examines sociological issues relevant to ecology, supports education and outreach, and informs science policy and management decisions.
• Ecosystem Science Cluster (ESC). ESC supports investigations of terrestrial, aquatic, and wetland ecosystems. Projects that use new or existing quantitative or conceptual models to synthesize and integrate knowledge are encouraged. ESC research includes Ecosystem Studies, which concentrate on whole-system processes and relationships in ecosystems, spanning a wide range of spatial and temporal scales; and Long-Term Ecological Research (LTER), which involves studies at a network of more than a dozen field sites.
• Environmental Engineering and Technology. The Environmental Engineering and Technology program supports research on the use of innovative biological, chemical, and physical processes to remediate polluted land, water, and air resources and the development of principles for pollution avoidance.
• Frontiers in Integrative Biological Research (FIBR). FIBR supports large interdisciplinary research to seek answers to important, understudied, nondisease-related biological questions. By encouraging research that creatively applies science concepts and strategies with research tools that span a broad range of disciplinary and intellectual boundaries, FIBR supports collaborative projects that may not fit readily into existing programs.
• Genes and Genome Systems Cluster (GGSC). GGSC supports research on the genetic mechanisms and genome organization, expression, and regulation of all organisms (prokaryote, eukaryote, phage, and virus).
• Geobiology and Environmental Geochemistry (GEG). GEG fosters research on (1) biological factors in geophysical and geochemical processes; (2) rates and mechanisms of inorganic and organic geochemical processes; (3) natural and anthropogenic impacts on biogeochemical cycles; (4) geochemical phenomena, widely ranging spatially from planetary and regional to mineral surface and supramolecular; and (5) development of tools, methods, and models for low-temperature geochemistry and geobiological research. GEG encourages the use of new bioanalytical tools to study terrestrial environments.
• Instrument Development for Biological Research (IDBR). IDBR supports research that will develop new and improved instrumentation, software for operating instrumentation, and data-analysis methods to advance the study of biological systems at any level. Proof-of-concept development for entirely novel instrumentation is encouraged.
• Mathematical Biology. This program supports research on mathematics important to the biological sciences that does not involve statistics or probability. NSF programs in statistics and probability may include research specific to other areas of science and engineering.
• Research in Biogeosciences 2005 (BioGeo). BioGeo fosters research that explores the interactions of microbes with earth materials (including minerals, rocks, hydrates, soils, and dust). Research should elucidate past and present roles of microbial communities in earth processes, microbial strategies for deriving energy and nutrients, and how these strategies alter earth materials and the environment.

National Institutes of Health (NIH)

• Bioinformatics and Computational Biology (BCB) Roadmap Initiatives. Four National Centers for Biomedical Computing (NCBC) established in 2004 are the key programmatic initiatives of the NIH BCB Roadmap. These centers aim to develop and implement the core of a universal computing infrastructure urgently needed to speed progress in biomedical research. The centers will create innovative software programs and other tools that will enable the biomedical community to integrate, analyze, model, simulate, and share data on human health and disease.
• Biomedical Information Science and Technology Initiative (BISTI). Launched in 2000, BISTI's goal is to make optimal use of computer science and technology to address problems in biology and medicine. A BISTI consortium serves as the focus of biomedical computing issues at NIH and facilitates implementation of BISTI recommendations. The consortium is composed of representatives from NIH centers and institutes and other federal agencies concerned with bioinformatics and computational applications. The consortium's mission is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and initiatives between the disciplines of computational and biomedical sciences.
• Complex Biological Systems Initiative. This National Institute for General Medical Sciences (NIGMS) program promotes quantitative, interdisciplinary approaches to problems of biomedical significance, particularly those that involve the complex, interactive behavior of many components. Three classes of initiatives are supported: Interdisciplinary research to attract investigators trained in mathematically based disciplines to the study of biomedical problems; mechanisms to train biomedical scientists in quantitative approaches and to acquaint nonbiologists with biological problems; and interdisciplinary training for scientists at the pre- and postdoctoral levels.
• National Institute of Allergy and Infectious Diseases (NIAID) Microbial Sequencing Centers. NIAID's Microbial Sequencing Centers (MSCs) sequence microorganisms and invertebrate vectors of disease that are considered agents of bioterrorism or responsible for emerging and reemerging diseases.
• National Technology Centers for Networks and Pathways. As part of the NIH Roadmap for Medical Research, two National Technology Centers for Networks and Pathways were established and several more are planned. The primary goal of these centers is to develop new technologies to study the dynamics of molecular interactions within cells. Such capabilities are crucial for expanding the identification of biological pathways and developing treatments for diseases involving such pathways. The awards are administered by the National Center for Research Resources, an NIH component that supports primary research to create and develop critical resources, models, and technologies.
• Protein Structure Initiative (PSI). PSI is a 10-year project funded largely by NIGMS to determine the three-dimensional (3D) shapes of a wide range of proteins. These structures are expected to shed light on protein function in many life processes and could lead to the development of new medicines. The long-range goal of PSI is to make 3D atomic-level structures of most proteins easily obtainable from knowledge of their corresponding DNA sequences. The first half of this project-a pilot phase that started in 2000-has centered on developing new tools and processes that enable researchers to determine quickly, cheaply, and reliably the shapes of many proteins found in nature. PSI projects are in federal, university, and industry laboratories.
• Systems Biology Initiative (SBI). This NIGMS program supports systems biology research for areas central to its mission of supporting basic biomedical research and developing new computational approaches to biomedical complexity. SBI's goal is to establish national centers for systems biology that develop pioneering research, training, and outreach programs focused on quantitative, systems-level analysis of biomedically important phenomena within the NIGMS mission. High priority is given to projects that integrate multi-investigator, multi­disciplinary approaches with a high degree of interplay between computational and experimental approaches. Innovation is critical for design of both research projects and infrastructure with the mission of serving communities beyond participating investigators, institutions, and collaborators.

Department of Agriculture (USDA): Cooperative State Research, Education, and Extension Service (CSREES)

• Agricultural Plant Biochemistry. The aim is to characterize the biochemical processes and pathways in the cell and the genes and proteins involved in them.
• Biobased Products and Bioenergy Production Research Program. This program supports the tripling of U.S. use of biobased products by 2010 and more research on biomass processing and conversion.
• Biology of Plant-Microbe Associations. This program supports fundamental and mission-linked research on interactions among plants and their associated microbes, including fungi and fungal-like microbes, bacteria, viruses, viroids, and mycoplasma-like organisms.

Department of Defense (DoD): Defense Advanced Research Projects Agency (DARPA)

• BioCOMP Program. BioCOMP develops a computational framework to enable construction of sophisticated models of intracellular processes that can be used to predict and control the behavior of living cells. In addition, BioCOMP generates new computational paradigms and engineering applications that use biomolecules as information-processing, sensing, or structural components.
• Biological Input/Output Systems Program (BIOS). BIOS will develop robust technologies for designing DNA-encoded "plug-and-play" modules that will enable use of organisms (e.g., plants, microbes, lower eukaryotes) as remote sentinels for reporting the presence of chemical or biological analytes.
• BioSPICE. BioSPICE is a set of open-source software tools that can be used by biological researchers to model the processes of living cells. It is being used to study several different biological systems: Bacterial systems to investigate such phenomena as sporulation, chemotaxis, and bacterial metabolism; viral systems to understand Lambda-phage, HIV-1, and host-pathogen interactions; eukaryotic systems to model cell cycles, cellular differentiation, immunological function, and cell signaling; and synthetic systems such as minimal cells. Some mathematical models developed using BioSPICE include pathway and interaction networks, models of gene expression, and probabilistic modeling for sequence analysis. BioSPICE is the product of a collaboration involving DARPA, NSF, academic institutions, and other federal agencies.

Other Programs

• HUPO Proteomics Standards Initiative
• National Aeronautics and Space Administration (NASA) Ames Genome Research Facility. Research at the facility includes the Nanopore Project and functional genomics.
• NASA Fundamental Space Biology Program (FSB). FSB has increased emphasis on cell and molecular biology and developmental biology, as well as on the growing disciplines of evolutionary biology and genomics. Part of the program's purpose is to increase visibility and funding for molecular biology research.
• National Institute of Standards and Technology (NIST) Biotechnology Division. The mission of the NIST Biotechnology program is to advance the commercialization of biotechnology by developing the scientific and engineering technical base, reliable measurements, standards, data, and models to enable U.S. industry to quickly and economically produce biochemical products with appropriate quality control. The division is organized into four groups: DNA Technologies; Bioprocess Measurements; Structural Biology; and Cell and Tissue Measurements.
• National Oceanic and Atmospheric Administration (NOAA) Office of Global Programs (OGP) Climate and Global Change Program. OGP assists NOAA by sponsoring scientific research aimed at understanding climate variability and predictability. Through studies in these areas, researchers coordinate activities that jointly contribute to improved predictions and assessments of climate change over a continuum of time scales from season to season, year to year, and throughout a decade and beyond.
• United Nations Educational, Scientific and Cultural Organization (UNESCO) Microbial Resources Centres (MIRCEN). MIRCEN comprises 34 academic and research institutes in developed and developing countries involved in a global collaborative effort to harness microbiological research and biotechnological applications for the benefit of humankind. The global MIRCEN network's research and training activities aim to (1) provide a global infrastructure incorporating national, regional, and international cooperating laboratories geared to the management, distribution, and use of the microbial gene pool; (2) reinforce use of the rhizobial gene pool in developing countries with an agrarian base; (3) foster development of new inexpensive technologies native to specific regions; (4) promote economic and environmental applications of microbiology; and (5) serve as the network's focal centers for training.
• U.S. Geological Survey (USGS) Biological Resource Division. The USGS Biological Resource Division works with others to provide the scientific understanding and technologies needed to support the sound management and conservation of U.S. biological resources. USGS is committed to data and information sharing and has established the National Biological Information Infrastructure, a network of distributed databases and information sources on biological resources.

Interagency Cooperation

For more information on the following programs, see the web site for current and archived solicitations after each entry.

• Environmental Molecular Science Institutes (EMSI). EMSI is a partnership between NSF and DOE for collaborative, interdisciplinary research to attain a fundamental, molecular-level understanding of natural and anthropogenic processes in the environment. An institute typically supports a group of six or more investigators from academic institutions, nonprofit organizations, industry, or national laboratories with complementary research interests.
• Interagency Microbial Genome Sequencing Program (USDA with NSF). This program supports high-throughput sequencing of the genomes of a wide range of microorganisms (including viruses, bacteria, archaea, fungi, oomycetes, protists, and agriculturally important nematodes).
• Interagency Modeling and Analysis Group (No web site available; see last call for proposals.) This group is a collaboration among NSF, NIH, NASA, and DOE to encourage the integrative systems engineering approach to multiscale modeling, combining theoretical and computational approaches. This collaboration aims to formulate and validate novel computational and statistical methods and relationships for spanning multiple scales, broaden and expand currently established levels of modeling expertise and multiscale modeling activities, and produce models of practical utility to the community at large. The group also plans to form a consortium of investigators for information exchange on critical issues including model intraoperability and evaluation and open-source software sharing.
• Joint DMS/BIO/NIGMS Initiative to Support Research in the Area of Mathematical Biology. This initiative supports research on mathematical and statistical problems related to the biological sciences, including conferences, educational research experiences, postdoctoral research fellowships, and acquisition of computational equipment. It involves the NSF Directorate for Mathematical and Physical Sciences' Division of Mathematical Sciences, the NSF Directorate for Biological Sciences, and NIH NGMIS.
• Mathematical Sciences: Innovations at the Interface of the Sciences and Engineering. The Mathematical Sciences Priority Area (MSPA) cuts across multiple NSF directorates and supports the integration of mathematical and statistical research with a wide range of science disciplines. Initially, MPSA interdisciplinary projects are focusing on mathematical challenges associated with handling large data sets, managing and modeling uncertainty, and modeling complex nonlinear systems.
• Metabolic Engineering Working Group (MEWG). MEWG is a collaboration among eight agencies and departments to provide research funding and agency in-kind support (e.g., equipment, lab space, and materials) to gain a better understanding of metabolic pathways and metabolic engineering in living systems. Conceptual and technical approaches necessary to understand the integration and control of genetic, catalytic, and transport processes will be valuable as fundamental research and also will provide the underpinning for many applications of immediate value. Participating institutions include the Department of Commerce, Environmental Protection Agency, DoD, DOE, NASA, NIH, NIGMS, NSF, and USDA.
• Microbial Genome Sequencing Program. This program is a collaboration between NSF and USDA CSREES. It supports high-throughput genome sequencing of microorganisms (e.g., viruses, bacteria, archaea, fungi, oomycetes, protists, and agriculturally important nematodes) that have fundamental biological interest or relevance to such national priorities as productivity and sustainability of agricultural and natural resources and food-supply safety and quality.
• Nanoscale Science and Engineering. This program brings together engineering and various scientific disciplines to advance the emerging field of nanotechnology. Research areas include nanoscale investigations of biosystems; environmental processes; nanostructures and devices; multiscale multiphenomena theory, modeling, and simulation; and manufacturing processes; as well as research on societal and educational implications of nanoscale research and technology development.
• National Science and Technology Council Interagency Working Group on Microbial Genomics. This working group consists of representatives from all federal agencies that support or conduct microbial research.