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

Plant-Microbe Interfaces: Capturing and Interpreting the Role of Populus’ Microbiome


Dale A. Pelletier* (, Paul E. Abraham, Manasa R. Appidi, Leah H. Burdick, Dana L. Carper, Alyssa A. Carrell, Robert L. Hettich, Sara S. Jawdy, Dawn M. Klingeman, Jennifer L. Morrell-Falvey, Bryan T. Piatkowski, David J. Weston, Jia Wang, and Mitchel J. Doktycz


Oak Ridge National Laboratory



The goal of the Plant-Microbe Interfaces (PMI) Science Focus Area (SFA) is to characterize and interpret the physical, molecular, and chemical interfaces between plants and microbes and determine their functional roles in biological and environmental systems. Populus and its associated microbial community serve as the experimental system for understanding the dynamic exchange of energy, information, and materials across this interface and its expression as functional properties at diverse spatial and temporal scales. To achieve this goal, the project 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.


Microbial communities play an integral role in the health and survival of their plant hosts. In ongoing efforts in the PMI SFA, researchers are capturing members of Populus’ microbiome to understand basic concepts of plant and environmental selection. Representative bacterial strains from environmental samples of Populus roots have been isolated using a direct plating approach and compared to amplicon-based sequencing analysis of root samples (Carper et al. 2021). The resulting culture collection contains 3,211 unique isolates representing 10 classes, 18 orders, 45 families, and 120 genera from six phyla, based on 16S rRNA gene sequence analysis. The collection represents a significant fraction of the natural community of plant-associated bacteria as determined by phylogenetic analysis. Additionally, a representative set of 553 strains have had their genomes sequenced to facilitate functional analyses. This culture collection allows for the exploration of microbial community function and an understanding of basic concepts of plant and environmental dependent selection.

The team is employing this collection to understand the mechanisms of microbial adaptation to Populus’ root endosphere and rhizosphere. Microbial diversity of the endosphere is low compared to rhizosphere, indicating high selectivity of this compartment for specific taxa and microbial adaptation of functions needed to compete in this unique environment. Using Populus-bacterial model systems with communities of specific Variovorax strains, researchers successfully demonstrated that they could identify bacterial strains, genes, and associated functions potentially required for fitness in Populus’ root rhizosphere or endosphere niches. L-fucose metabolism, glycoside hydrolases, pili/fimbriae production, and exopolysaccharide production were identified as important bacterial traits associated with efficient endosphere colonization. The team found the enrichment of genes in the L-fucose metabolic pathway intriguing, as metabolism of cell surface fucose residues has been implicated in enrichment of beneficial mammalian gut bacteria and suppression of pathogens. Additionally, L-fucose biosynthesis and fucosylation of cell surface macromolecules have been demonstrated to play a role in plant immune response. Researchers constructed gene deletion mutants of L-fuconolactonase in the L-fucose metabolic pathway via homologous recombination in Variovorax and confirmed this strain is defective in L-fucose growth and in Populus root colonization, relative to the wild-type strain.

In other applications of the microbial collection, the team has constructed microbial communities to elucidate organizational principles of community formation. Using genome-defined strains, systematic experiments, and computational modeling, researchers are identifying potential metabolic exchanges among species and gaining mechanistic insights into community structure. Co-culture and serial transfer experiments performed in defined media identified emergent, stable microbial communities (Wang et al. 2021; Shrestha et al. 2021). Using a complex medium environment, the effects of different initial inoculum ratios, up to three orders of magnitude, on community structure were investigated. The final compositions of the mixed communities with various starting compositions indicate that community structure is not dependent on the initial inoculum ratio. Modeling and omics analysis provide mechanistic insights into the emergence of community structure and indicate competitive relationships among the persistent organisms. These findings enlighten understanding of bacterial community formation and may guide efforts to manage rhizosphere bacterial communities. Collectively, these diverse applications of cultured representatives of Populus’ microbial community are facilitating understanding of how Populus selects microbial partners and how its microbiome is structured.


Carper, D. L., et al. 2021. “Cultivating the Bacterial Microbiota of Populus Roots,” mSystems 6(3), e01306-20. DOI:10.1128/mSystems.01306-20.

Shrestha, H. K., et al. 2021. “Metaproteomics Reveals Insights into Microbial Structure, Interactions, and Dynamic Regulation in Defined Communities as They Respond to Environmental Disturbance,” BMC Microbiology 21, 308. DOI:10.1186/s12866-021-02370-4.

Wang, J., et al. 2021. “Formation, Characterization and Modeling of Emergent Synthetic Microbial Communities,” Computational and Structural Biotechnology Journal 19, 1917–27. DOI:10.1016/j.csbj.2021.03.034.

Funding Information

Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the U.S. Department of Energy under contract no. DE-AC05-00OR22725. The Plant-Microbe Interfaces SFA is supported by the U.S. Department of Energy, Office of Science, through the Genomic Science program, Biological and Environmental Research (BER) Program under FWP ERKP730.