From small RNA to metabolites – how eucalypts meet up with ectomycorrhizal fungi

Wong JWH1, Lutz A2, Natera S2, Wang M3, Ng V3, Grigoriev I3, Martin F4, Roessner U2, Anderson I1 and Plett J1

  1. Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia.
  2. School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia.
  3. U.S. Department of Energy Joint Genome Institute, Walnut Creek, USA.
  4. INRA, UMR 1136, INRA-Nancy Universite, Interactions Arbres/Microorganismes, 54280 Champenoux, France.

Ectomycorrhizal (ECM) fungi are often associated with roots of forest trees, bringing benefits to their hosts including enhanced nutrient uptake and increased stress tolerance. How trees communicate with ECM fungi prior to physical interaction, and how this pre-symbiotic exchange of signals differs from plant-pathogen interactions, is largely unexplored. With a focus on this pre-symbiosis stage, we aim to decipher the communication routes between the model tree Eucalyptus grandis and one of its associated ECM fungal species: Pisolithus microcarpus. Considering the roles of metabolites and RNAs in plant-microbial signalling as determined by previous studies, we examined ECM fungi-eucalypt molecular interaction with a combined use of RNA-seq, small RNA-seq and untargeted metabolite profiling.We identified significant changes in both the metabolome and transcriptome (including both small RNAs and RNAs) of eucalypt roots during this pre-symbiotic period with P. microcarpus. These results suggest that eucalypts are able to respond to the presence of ECM fungi prior to physical contact. We then further investigated whether these changes were activated by internal gene regulation of eucalypt roots, or by the trafficking of fungal signals. With our small RNA-seq data, we observed a significant portion of small RNA reads detected in eucalypt roots are originated from P. microcarpus rather than E. grandis. Amongst these fungal reads, we identified one species of fungal small RNAs that putatively targets defense-related R genes of the plant host during pre-symbiosis. Additionally, with the use of isotopic labeling in conjunction to untargeted metabolite profiling, we also identified some ECM fungi-derived metabolite signals in eucalypt roots. Therefore, by dissecting the molecular signals in eucalypt roots using a multi-omics platform, our research suggests that both small RNAs and metabolites are signals used by ECM fungi to prime their host plant during this pre-symbiotic stage of interaction.