Clean Energy


Genomic Sciences

An ORNL researcher prepares a reaction allowing a unique DNA sequence to be inserted into a larger strand.Source: ORNL Flickr siteThe genomes of individual organisms and systems of organisms (e.g., plants, microbes, and their communities) provide the genetic blueprints that determine structure and function across multiple scales of biological organization. ORNL researchers are using genomic-based approaches to predictively understand the fundamental principles that control complex biological systems important to clean energy and environmental applications. Multidisciplinary genomic science research and communication resources at ORNL include the following:

  • Plant Systems Biology
  • Systems Genetics
  • Metabolomics
  • Plant-Microbe Interfaces
  • Biological and Environmental Research Information System

Plant Systems Biology

Plant systems biology research at ORNL seeks to explore and understand the networks of genes, proteins, metabolites, and environmental signals that lead to complex phenotypes in plant species relevant to U.S. Department of Energy (DOE) missions in energy, climate, and environment. The main goal of this research is to link genes to phenotypes using a holistic approach involving gene identification, gene expression, and phenotypic characterization. Making these connections will help identify the emerging principles related to plant functions important in biofuels development and carbon cycling and sequestration. The approaches used in this research encompass quantitative, statistical, and molecular genetics; molecular biology; model system interrogations; computational studies (in conjunction with the DOE Systems Biology Knowledgebase); synthetic biology and novel biosystems design; and fundamental studies of plant development and physiology.

As experts in these areas, ORNL researchers apply transcriptomics, proteomics, metabolomics, imaging, and bioinformatics approaches to study plant models ranging from perennial dicots and monocots (Populus, Panicum, Kalanchoe, Agave, and Clusia) to annuals (Arabidopsis) to mosses (Sphagnum). These researchers collaborate with several DOE-funded institutions (e.g., the Joint Genome Institute, Pacific Northwest National Laboratory, Lawrence Berkeley National Laboratory, Brookhaven National Laboratory, and National Renewable Energy Laboratory) and many national and international academic institutions.

Current projects center on bioenergy research; carbon sequestration, allocation, and cycling; plant responses to climate change; and plant-microbe interactions. Three specific goals include:

  • Understanding the genetic basis of plant cell wall formation to derive plant biomass with reduced recalcitrance.
  • Addressing key biological questions concerning the determinants, symbiotic associations, and mechanisms of host colonization, inter- and intraorganism signaling, and gene regulation.
  • Deconstructing the molecular basis of Crassulacean acid metabolism (CAM) photosynthesis to create synthetic CAM machinery in C3 plants for biomass production on marginal land.

Systems Genetics

The boundaries between experimental and computational research, between traditional biochemistry, microbiology, ecology, and evolutionary biology are being dissolved by interdisciplinary research enabled by genomic approaches to study biological systems.

Systems genetics research at ORNL spans multiple biological disciplines and is primarily supported by projects within DOE’s Office of Biological and Environmental Research, such as the BioEnergy Science Center and the Plant-Microbe Interfaces scientific focus area. This research also involves individual investigator–driven projects from DOE and other sponsors. Subject areas include (1) biofuels and microbial engineering, (2) the roles of individual microbial species and microbial communities in plant development and large-scale processes, (3) toxic metals cycling and bioremediation, and (4) microbial roles in carbon and nitrogen cycles under climate change scenarios.

As part of these research areas, ORNL scientists are studying organisms (e.g., archaea, bacteria, and fungi) from diverse environments, such as terrestrial geothermal and marine hydrothermal systems, soils and plant rhizospheres, subsurface aquifers, forests, and bogs. A wide range of approaches is used, including:

  • Traditional cultivation and physiology studies
  • Characterization of community diversity
  • Metagenomics
  • Single-cell genomics
  • Integrated “omics” (e.g., transcriptomics, proteomics, and metabolomics)
  • Advanced cellular isolation and imaging

Mouse genetics research involves collaboration with the University of Tennessee (UT) and is aimed at examining body responses to low doses of ionizing radiation. Research funded by other federal agencies includes studies conducted under the National Institutes of Health Human Microbiome Project.

Systems genetics scientists are integrated with UT’s research and educational system, and several are joint faculty appointees. This research area also includes postdoctoral scientists and graduate students.


Metabolomics is the analysis of the complete set of an organism’s metabolites (small molecule products of cellular processes), referred to as the metabolome. Metabolomic characterization helps determine which enzyme-mediated reactions and biochemical pathways are active and thus provides a metabolic snapshot of an organism, and can be used to determine the function of unknown genes.

ORNL metabolomics research leverages a powerful set of tools, such as metabolite separation and mass spectrometry, for phenotypic characterization of model and bioenergy-related organisms, including plants like Populus, Arabidopsis, Eucalyptus and Castanea, and microbes, such as Zymomonas mobilis, Thermoanaerobacter saccharolyticum, Caldicellulosiruptor bescii, and Clostridium thermocellum. This research is helping to answer important questions in bioenergy crop production, biomass deconstruction, biofuel production, environmental stress physiology, plant-microbe interactions (e.g., establishment of symbiosis, defense signaling, and pathogenic responses), and genomics. Goals of this research include the functional characterization of genes to accelerate the domestication of Populus for increased biomass production and drought tolerance for cultivation on marginal lands, ease of microbial deconstruction, and manipulating metabolite production for improved carbon sequestration and bioproduct formation. Work within this research area also involves developing new technologies and analytical protocols for plant physiology studies.

Plant-Microbe Interfaces

The goal of the Plant-Microbe Interfaces (PMI) scientific focus area (SFA) is to gain a deeper understanding of the diversity and functioning of mutually beneficial interactions between plants and microbes in the rhizosphere. The plant-microbe interface is the boundary across which a plant senses, interacts with, and may alter its associated biotic and abiotic environments. Understanding the exchange of energy, information, and materials across this interface at diverse spatial and temporal scales is the ultimate objective of the PMI project. Ongoing efforts focus on characterizing and interpreting such interfaces using systems comprising plants and microbes, particularly the poplar tree (Populus) and its microbial community. Understanding the inherent chemical and physical processes involved will facilitate natural routes to carbon cycling and sequestration in terrestrial environments, ecosystem response to climate change, and the development and management of renewable energy sources.

The PMI SFA integrates expertise in the areas of plant genomics, fungal and bacterial research, fungal ecology, analytical tool development, and computational biology and is based at ORNL, with collaborators at the University of Washington, Duke University, and INRA–Nancy in France. Read more at

Biological and Environmental Research Information System

Concerted communication is key to progress in cutting-edge science and public accountability. With support from DOE’s Office of Science, the Biological and Environmental Research Information System (BERIS) has for more than 20 years been the primary communication resource supporting the genome programs of DOE’s Biological and Environmental Research (BER) program. In 2009, BERIS’ focus shifted to encompass communicating all of BER’s science.

Integrating all facets of biological and environmental research is critical for spurring innovation at the most rapid pace and at the lowest cost. Moreover, scientific research involves a wide array of technologies, many just emerging, with new types of datasets that must be available to a larger, interdisciplinary research community. As such, BERIS seeks to facilitate and accelerate this integration and access through technical communication that spans diverse research areas. Key BERIS websites include


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