Coordination of microbe-host homeostasis by crosstalk with plant innate immunity

Nat Plants. 2021 Jun;7(6):814-825. doi: 10.1038/s41477-021-00920-2. Epub 2021 May 24.


Plants grown in natural soil are colonized by phylogenetically structured communities of microbes known as the microbiota. Individual microbes can activate microbe-associated molecular pattern (MAMP)-triggered immunity (MTI), which limits pathogen proliferation but curtails plant growth, a phenomenon known as the growth-defence trade-off. Here, we report that, in monoassociations, 41% (62 out of 151) of taxonomically diverse root bacterial commensals suppress Arabidopsis thaliana root growth inhibition (RGI) triggered by immune-stimulating MAMPs or damage-associated molecular patterns. Amplicon sequencing of bacterial 16S rRNA genes reveals that immune activation alters the profile of synthetic communities (SynComs) comprising RGI-non-suppressive strains, whereas the presence of RGI-suppressive strains attenuates this effect. Root colonization by SynComs with different complexities and RGI-suppressive activities alters the expression of 174 core host genes, with functions related to root development and nutrient transport. Furthermore, RGI-suppressive SynComs specifically downregulate a subset of immune-related genes. Precolonization of plants with RGI-suppressive SynComs, or mutation of one commensal-downregulated transcription factor, MYB15, renders the plants more susceptible to opportunistic Pseudomonas pathogens. Our results suggest that RGI-non-suppressive and RGI-suppressive root commensals modulate host susceptibility to pathogens by either eliciting or dampening MTI responses, respectively. This interplay buffers the plant immune system against pathogen perturbation and defence-associated growth inhibition, ultimately leading to commensal-host homeostasis.

MeSH terms

  • Arabidopsis / genetics
  • Arabidopsis / immunology*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / immunology
  • Gene Expression Regulation, Plant
  • Host-Pathogen Interactions / immunology
  • Host-Pathogen Interactions / physiology*
  • Microbiota*
  • Pathogen-Associated Molecular Pattern Molecules
  • Phylogeny
  • Plant Diseases / immunology
  • Plant Diseases / microbiology
  • Plant Immunity / physiology*
  • Plant Roots / genetics
  • Plant Roots / growth & development
  • Plant Roots / microbiology*
  • Plants, Genetically Modified
  • Pseudomonas / physiology


  • Arabidopsis Proteins
  • Pathogen-Associated Molecular Pattern Molecules