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

Plant-Microbe Interfaces: Specialized Fungal Metabolites Regulate Synthetic Fungal Communities and Their Interactions with Populus


Tomás A. Rush1* (, John Lagergren1, Christian G. Salvador2, Raphael Ployet1, Sara S. Jawdy1, Dana L. Carper1, Sameer Mudbhari1, Annegret Kohler3, Claire Veneault-Fourrey3, Rytas Vilgalys4, Dave J. Weston1, Larry York1, Paul E. Abraham1, Mitchel J. Doktycz1


1Biosciences Division, Oak Ridge National Laboratory; 2Environmental Sciences Division, Oak Ridge National Laboratory; 3Interactions Arbres-Microorganismes, INRAE, Université de Lorraine; 4Duke University



The overriding goal of the Oak Ridge National Laboratory (ORNL) 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, researchers focus 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.


Ectomycorrhizal fungi (EMF) are beneficial fungi that colonize the root tissues of multiple host plants. The interaction between EMF and their host is likely governed by metabolites, which act as direct lines of communication between organisms in the rhizosphere. However, the metabolites or signals that are produced when a fungus is alone or with a host or with other microbes are understudied. This team’s goal is to identify and characterize the repertoire of metabolites produced when EMFs are in co-culture with each other or when colonizing different Populus genotypes in tissue culture assays. Firstly, to develop a functioning EMF synthetic community, the group conducted co-culture assays between five EMFs isolated from Populus roots or within a Populus plantation. The aim was to find a combination of EMF that produce a repertoire of metabolites that promote growth of other fungal members. Since it is known that nutrient availability influences metabolite production (Rush et al. 2022; Meena et al. 2023), researchers utilized four different substrate media, two nutrient-rich and two nutrient-deprived. The group’s preliminary results determined that Hebeloma brunneifolium promoted the growth of nearly all the co-occurring fungi in a nutrient-poor environment; however, this was not reciprocal, with no growth benefit of H. brunneifolium. Laccaria bicolor and Cenococcum geophilum, regardless of the media, had the most beneficial interactions with co-occurring fungi. Based on the above results, the team determined that C. geophilum, H. brunneifolium, and L. bicolor would benefit each other for fungal growth.

Next, researchers examined how these EMFs individually impact Populus root and leaf development over time. Researchers used tissue cultures of Populus tremula x alba genotype 717-1B4 and Populus trichocarpa x Populus deltoides hybrid 52-225. Group members measured plant physiological traits (root growth and leaf development) as well as omic data (volatile organic compounds (VOCs), metabolomics, and proteomics) to determine the effect of each EMF on Populus. After 5 weeks of colonization, the team’s preliminary results determined that C. geophilum effectively colonized the root, as shown by the development of a Hartig Net, and increased root length and branching. H. brunneifolium interestingly did not colonize the host plant but still had a positive growth effect on root and shoot tissue, possibly attributed to VOCs or specialized metabolites. Lastly, L. bicolor effectively colonizes Populus tissue culture plants but showed no beneficial tradeoff with its host. Altogether, this project’s results show that researchers can construct a synthetic EMF community that will be symbiotic with each other and likely have a positive phenotypic effect on the host plant.


Meena, M. G., et al. 2023. “A Glimpse into the Fungal Metabolomic Abyss: Novel Network Analysis Reveals Relationship Between Exogenous Compounds and Their Outputs,” PNAS Nexus 2(10). DOI:10.1093/pnasnexus/pgad322.

Rush, T. A., et al. 2022. “Lipo-Chitooligosaccharides Induce Specialized Fungal Metabolite Profiles that Modulate Bacterial Growth,” mSystems 7(6). DOI:10.1128/msystems.01052-22.

Funding Information

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