No boundaries, no benefits: The role of root defense barriers in microbiome assembly

Agricultural production currently relies on chemical fertilizers and pesticides to safeguard plant health. An alternative is to strategically boost the relationship between plant roots and soil beneficial microbes. Plant roots have evolved defense mechanisms to deter microbial pathogens, while still allowing beneficial microbes to establish. Mechanistic understanding of how defense components enable a homeostatic relationship with the commensal and beneficial members of the soil, can enable design of crop varieties that leverage the interaction with the microbiome. In this project, we systematically characterized the role of key components of the plant immune system in the interaction with soil microbes. In Chapter 2 we screened Arabidopsis mutants with defects in chemical and structural defense barriers in the interaction with a beneficial bacterium, Pseudomonas simiae WCS41. While this bacterium promotes plant growth in the wild type, we showed that in plant mutants with defense barrier defects the beneficial effects were compromised. Our findings highlight the delicate balance underlying beneficial plant–microbe interactions, where the loss of many defense barriers can result in the loss of beneficial effects, though the mechanisms involved differ depending on the specific defense barrier affected. In order to evaluate the impact of these defense barrier defects on the interaction with complex soil communities, in Chapter 3 we developed a spatially resolved root sampling protocol, from plants grown in natural soil. Spatially resolved sampling allowed us to evaluate the impact of the defense barrier defects on the root colonization process from soil, in Chapter 4. We detected specific changes to bacterial community composition in the rhizosphere in almost all of the mutants with chemical defects. In contrast, mutants with defects in structural barriers led mainly to changes in the endosphere. These findings revealed root compartment specific mechanisms of microbiome assembly from soil. Finally, in Chapter 5 we evaluated the effect of activating key hormone defense signaling pathways in 22 plant species from the Brassicaceae family. We found that microbiome assembly is differential between the two major defense pathways: those regulated by the hormones Jasmonic acid and Salicylic acid (SA), indicating that the microbiome is an extension of the plant’s defense strategy. We found that the activation of the SA defense pathway led to phylogenetically congruent microbiomes, suggesting evolutionary conserved mechanisms of microbiome recruitment under biotic stress. These results support the idea that plant defenses not only play a role in deterring pathogenic microbes, but also are critical for a homeostatic relationship with the microbiome. We propose that breeding targets defense signaling pathways and root defense barriers in a way that supports the recruitment of beneficial microbes, alongside the targeted application of bioinoculants aligned with these engineered defenses.