Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Plant-Microbe Interfaces: Disentangling Microbial-Mediated Plant Stress Tolerance with Synthetic Communities and Automated Phenotyping


David J. Weston1* (, Jun Lee1, Sara S. Jawdy1, Leah Burdick1, Kelsey Carter2, Alyssa A. Carrell1, Dale A. Pelletier1, Christopher W. Schadt1, Larry York1, John Lagergren1, Wellington Muchero1, Kuntal De1, Melissa A. Cregger1, Dana L. Carper1, Paul E. Abraham1, Robert L. Hettich1, Mitchel J. Doktycz1


1Biosciences Division, Oak Ridge National Laboratory; 2Environmental Sciences Division, Oak Ridge National Laboratory



The overriding goal of the Oak Ridge National Laboratory Plant-Microbe Interfaces (PMI) Science Focus Area is to predictively understand the productive relationship between a plant host and its microbiome based on molecular and environmentally defined information. Populus and its associated microbial community serve as the experimental system for understanding this dynamic, complex multi-organism system. To achieve this goal, the team focuses on: (1) defining the bidirectional progression of molecular and cellular events involved in selecting and maintaining specific, mutualistic Populus-microbe interfaces; (2) defining the chemical environment and molecular signals that influence community structure and function; and (3) understanding the dynamic relationship and extrinsic stressors that shape microbiome composition and affect host performance.


Recent studies have shown that microbes from extreme environments can confer plant stress tolerance. Such studies have led to the hypothesis that microbiomes adapted to harsh environmental conditions can benefit host plants in similar environments. However, the magnitude of these benefits, underlying microbial dynamics, and driving genetic mechanisms remain unclear. The current study employs synthetic community (SynCom) approaches, paired with high-throughput phenotyping and physiological assays, to dissect the specific roles of microbial strains and communities in plant thermotolerance. To quantify microbial benefits on plant growth and physiology across temperatures, SynComs were constructed with selected bacteria and applied to axenic tissue culture Populus trichocarpa x deltoides within a calcined clay medium. Bacteria were selected and prioritized based on phylotyping data from PMI field sites. The SynCom–host systems were then exposed to a range of temperatures (9°C to 28°C). These systems were enclosed for 3 weeks to ensure community establishment, and then containers were opened for an additional 4 weeks and subjected to automated phenotyping. The addition of a single Variovorax bacterial strain significantly enhanced plant growth and photosynthetic efficiency. Further investigation using a heterologous quantitative trait loci (QTL) study identified a seven-gene interval associated with microbially conferred thermotolerance. Interestingly, genetic analysis revealed a proteosome interacting protein (PIP) essential for the plant to benefit from the Variovorax strain. Future studies are integrating this newly found microbially mediated abiotic stress response pathway with known induced system resistance (ISR) and systemic acquired resistance (SAR) pathways. This knowledge paves the way for developing climate-resilient plants by harnessing the power of beneficial microbes and genetics.

Funding Information

Oak Ridge National Laboratory is managed by UT-Battelle, LLC for DOE under contract no. DE-AC05-00OR22725. The Plant-Microbe Interfaces Science Focus Area is supported by the DOE Office of Science through the GSP, BER Program under FWP ERKP730.