Roots of healthy plants are colonized by complex bacterial and fungal communities. We reported that root-colonizing fungi, reproducibly detected in natural Arabidopsis populations, are often detrimental when mono-inoculated on germ-free Arabidopsis under laboratory conditions. We discovered that these fungi are very efficient at colonizing roots and causing disease due to their ability to aggressively degrade plant cell wall constituents such as pectin, one of the most abundant carbohydrates in the primary cell wall of Arabidopsis. However, the detrimental activity of these fungi is often kept in check in natural populations, illustrating the existence of mechanisms that prevent fungal dysbiosis in nature. We reported that the protective activity of the bacterial community is as important as the host's innate immune branch, involving tryptophan-derived specialized metabolites for controlling fungi in plant roots. Our results indicate that the plant innate immune system is insufficient to fully protect plants from fungal infections, and that bacterial partners residing in roots provide an additional layer of protection, which is needed for plant survival in nature. During this presentation, I will talk about which fungal genetic determinants drive root infection, how we can harness the diversity of bacterial exometabolites to protect roots against fungal infections, and also how we uncovered metabolic decoys as a new source of molecules preventing fungal diseases.
