Plant mechanisms involved in recruitment of disease-suppressive microbiota

Plants are not solitary organisms but coexist with microorganisms in their environment, including both pathogenic and beneficial species. These interactions are important for plant health, stress resilience, and agricultural productivity. Rather than being passive hosts, plants actively shape their associated microbiota through immune signaling and metabolic regulation in response to environmental signals. Together, plants and microbes form feedback processes that influence plant performance in both natural and agricultural ecosystems. This thesis focuses on the concept of the soil-borne legacy (SBL), a phenomenon whereby pathogen attack leads to the establishment of a disease-suppressive soil microbiome and enhanced disease resistance in plants grown subsequently in the same soil. In Arabidopsis, foliar infection by Hpa conditions the soil such that plants grown later in that soil show increased resistance to Hpa, providing a concrete example of SBL formation. Using the Arabidopsis-Hpa interaction as a model, this thesis investigates how foliar Hpa infection induces plant systemic responses that reprogram root gene expression and reshape the rhizosphere microbiome, thereby elucidating the mechanisms underlying SBL formation. By integrating time-resolved transcriptomics, gene regulatory network analysis, and functional genetics, this work examines the host regulatory pathways underlying SBL formation. Leaf infection rapidly reprograms root gene expression, characterized by changes in salicylic acid and jasmonic acid defense pathways and coordinated changes in secondary metabolism, which are required for the recruitment of disease-suppressive microbiota. Further investigation revealed that SBL formation depends on the integration of immune and environmental signals, highlighting a key role for light signaling. Functionally, SBL confers broad-spectrum disease resistance, involving systemic immune priming and microbiome transmission between the rhizosphere and phyllosphere. Collectively, this thesis demonstrates the plant regulatory mechanisms underlying the establishment and function of the SBL, showing how plant-mediated immune signaling and environmental sensing are integrated to shape disease-suppressive microbiota. By linking plant regulatory networks to microbiome assembly and downstream immune outcomes, it provides mechanistic insight into plant-centered control of microbe-mediated protection.