Natural systems, from simple microbes to complex, highly diverse ecosystems, hold secrets of life that fascinate curious minds, drive scientific inquiry, and offer biological solutions to many energy and environmental challenges facing us today. Even the simplest of these systems, the single microbe, is so complex that we do not yet possess a full understanding of how a living system works, how life processes are regulated at the molecular level, and how organisms interact with and modify their environments.
The Department of Energy (DOE) Genomic Science program (formerly called Genomics:GTL) is driven by a grand challenge in biology: understanding biological systems so well that we can develop predictive, computational models of these systems (see figure above, Genomic Science Program Goal and Objectives). By revealing the genetic blueprint and fundamental principles that control plant and microbial systems relevant to DOE missions, the Genomic Science program is providing the foundational knowledge underlying biological approaches to producing biofuels, sequestering carbon in terrestrial ecosystems, and cleaning up contaminated environments. The fundamental scientific advances emanating from this program are transferable to a broad range of application areas and lay a foundation for new generations of industrial biotechnologies.
Addressing extremely complex science questions that span all scales of biology, research supported by DOE’s Genomic Science program requires the collective expertise of scientists from many disciplines and the coordinated application of a wide range of technologies and experimental approaches—genome sequencing, gene expression profiling, proteomics, metabolomics, imaging, research technology development, and computational biology. Research is conducted at national laboratories, national user facilities, and universities and includes single-investigator projects, multi-institutional collaborations, and fundamental research centers. The Genomic Science program is run by the Office of Biological and Environmental Research (BER) within DOE’s Office of Science.
In addition to supporting the Genomic Science program, BER is collaborating with other governmental agencies to advance genomics. A research program jointly sponsored by BER and the U.S. Department of Agriculture (USDA) Cooperative State Research, Education, and Extension Service supports genome-based approaches to accelerate plant breeding programs and improve potential bioenergy crops.
The DNA code—the genome—is the starting point to understanding any biological system. The genomes of individual organisms and systems of organisms (e.g., plants, microbes, and their communities and ecosystems) contain the information and operating capabilities that determine structure and function across multiple scales of biological organization. Exploring biological systems across all scales in a comprehensive and integrated way is essential to understanding how these systems operate in nature or in more applied contexts related to new technology endpoints for DOE missions (see figure below, DOE Genomic Science Program, A Mission-Inspired Fundamental Research Approach). The biological systems investigated by researchers in the Genomic Science program include protein and molecular interactions, pathways, and vast interconnected networks within whole cells, communities, and ecosystems.
Systems biology is the holistic, multidisciplinary study of complex interactions that specify the function of an entire biological system—whether single cells or multicellular organisms—rather than the reductionist study of individual components in isolation. As a leader in systems biology research, the Genomic Science program builds on a foundation of sequenced genomes to identify the common fundamental principles that drive living systems. These principles guide the translation of genomic code into functional molecules underlying biological system behavior. For example, understanding these principles could determine the biological mechanisms controlling changes in the production of cellulose-degrading enzymes in an industrial bioreactor or the amount of carbon stored in a plant’s roots under different environmental conditions. Knowledge of these common principles revealed by studying organisms for one DOE mission inevitably will lead to breakthroughs in basic biology important to other DOE and national needs.
In addition to funding a broad portfolio of single-investigator and team projects that target microbial and plant systems relevant to DOE missions, the Genomic Science program supports three fundamental research centers focused on bioenergy production. The genome sequences of organisms studied in these projects are provided largely by the DOE Joint Genome Institute, an important user facility and a world leader in generating sequences of microbes, microbial communities, plants, and other organisms.
By leveraging the increasing availability of sequences from whole organism genomes and environmental samples (metagenomes), Genomic Science researchers are using and developing advanced methods to facilitate the translation of genome sequence into predictive understanding of function. These methods cut across DOE missions in energy production, carbon cycle science, climate change, and environmental remediation. For example, technologies used to image and characterize microbes interacting with contaminants in subsurface environments could also provide insights into plant-microbe interactions that increase carbon fixation and biomass yield in plants or carbon accumulation in soils.
For more information about specific research projects, see our Research page.
Achieving a predictive understanding of biological systems is a daunting challenge and will require the integration of immense amounts of diverse information—functional descriptions assigned to DNA sequence, molecular interactions, images of molecules or physical structures within an organism, and details about the environment in which an organism lives. These types of information typically have not been integrated and compared, and the heterogeneous mix of data emanating from the Genomic Science program will span diverse environmental conditions, spatial scales (nanometers to kilometers), and temporal scales (nanoseconds to decades). To address this grand challenge, DOE will develop a Systems Biology Knowledgebase to facilitate a new level of scientific inquiry. The Genomic Science program defines the Knowledgebase as an integrated experimental framework for accessing, analyzing, modeling, and testing diverse data on complex biological systems. In addition to empowering scientists with free and broad access to diverse data types, the Systems Biology Knowledgebase will also provide sophisticated tools for data analysis, visualization, and integration. The Knowledgebase will enable a more comprehensive understanding of how biological systems work and more accurate predictions of system behaviors— knowledge needed to develop biologically inspired solutions to some of the most pressing energy and environmental challenges.
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