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Genomic Science Program

Systems Biology for Energy and the Environment

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Genomic Science Program

Science Focus Area: Oak Ridge National Laboratory

Plant-Microbe Interfaces

Populus-microbiome interface diagram
The Populus-microbiome interface encompasses diverse biological components and physical and temporal scales that result in dynamic functional processes. Events at the molecular and cellular levels lead to specific, mutualistic host-microbe selection and underpin host performance and community formation. Furthermore, the structure of the microbial community depends on specific and nonspecific relationships that vary based on the physical location and dynamic chemical environment defined by the host. These molecular- and cellular-level events can vary over the lifetime of the tree and respond to changes in seasons. Understanding the connections between molecular-level processes, biological organization, and host function is a long-term goal of the Plant-Microbe Interfaces SFA at Oak Ridge National Laboratory (ORNL). [Courtesy ORNL]

  • Principal Investigator and Laboratory Research Manager: Mitchel J. Doktycz1
  • Technical Co-Managers: Dale A. Pelletier1 and Timothy J. Tschaplinski1
  • Co-Investigators: Jin-Gui Chen1, Melissa A. Cregger1, Omar N. Demerdash1, Joseph C. Ellis1, E. Peter Greenberg2, Caroline S. Harwood2, Robert L. Hettich1, Daniel A. Jacobson1, Udaya C. Kalluri1, Jessy L. Labbé1, Francis M. Martin3, Joshua K. Michener1, Jennifer L. Morrell-Falvey1, Wellington Muchero1, Mircea Podar1, Scott T. Retterer1, Christopher W. Schadt1, Amy L. Schaefer2, Claire Veneault-Fourrey3, Rytas Vilgalys4, David J. Weston1, Xiaohan Yang1
  • Participating Institutions: 1Oak Ridge National Laboratory; 2University of Washington, 3INRAE (National Research Institute for Agriculture, Food, and Environment), 4Duke University
  • Project Website:

The Plant-Microbe Interfaces (PMI) Science Focus Area (SFA) led by Oak Ridge National Laboratory is directed toward understanding the dynamic interface that exists between plants, microbes, and their environment. This interface is the boundary across which a plant detects, interacts with, and may alter its associated biotic environment to maintain or improve its performance. Project efforts focus on revealing the mechanistic bases underpinning the selection of symbiotic plant-microbe partnerships, determining the chemical environment that structures the host plant’s microbiome, and evaluating how the host plant and its microbiome respond to environmental challenges. For example, various tree species of the genus Populus, commonly known as eastern cottonwood, black cottonwood, or aspen, serve as hosts to diverse microbial associates and make for an ideal experimental platform. This genus of fast-growing tree species is a leading candidate for bioenergy production and a dominant perennial component of many North American temperate forests. PMI research seeks to define the relationships among Populus spp. and their microbiomes in natural settings, dissect the molecular signals and gene-level responses of the organisms to changing conditions, and rebuild the complexity of these systems using sequence-characterized plants and microbes. Extensive, project-derived collections of diverse, genome-defined hosts and microbial species are leveraged for relating functional events to genomic information. Measurement and interpretation of these complex systems are facilitated using advanced analytical tools and computational approaches. Ultimately, an improved fundamental understanding of plant-microbe interfaces and the genomic underpinnings of information, energy, and material exchange among and between interacting organisms are long-term goals of this research. These efforts will lead to a better understanding of symbiotic relationships and of natural routes to influencing ecosystem responses to global climate change, cycling and sequestration of chemical elements in terrestrial environments, and development and management of renewable energy sources.

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