Chemical dialogues in the rhizosphere Interactions between solanaceous crops, their microbiome, and eavesdropping pathogens

Plants communicate with soil microorganisms through specialized metabolites released into the rhizosphere. These chemical interactions are especially important under nutrient-limiting conditions, where plants recruit beneficial microbes to support growth and nutrient acquisition. However, the metabolites and mechanisms involved in this process remain poorly understood. In this thesis, I investigate how root-exuded metabolites shape the tomato rhizosphere microbiome, particularly under nitrogen deficiency. Using multi-omics analyses, virus-induced gene silencing, metabolite profiling and microbial assays, I show that tomato actively modulates its rhizosphere through changes in specialized metabolism. I demonstrate that strigolactones, including solanacol, influence the recruitment of beneficial bacteria, suggesting a broader role for these molecules beyond their established function in arbuscular mycorrhizal symbiosis. I further show that manipulating cycloartenol-derived triterpenoid pathway genes alters both the tomato root metabolome and the associated microbiome, providing causal evidence that specific metabolic pathways contribute to microbiome assembly. This thesis also explores the ecological role of solanoeclepin A, a triterpenoid known as a hatching factor for potato cyst nematodes. I show that a solanoeclepin A precursor functions as a rhizosphere signaling molecule under nitrogen deficiency and is associated with the recruitment of specific growth-promoting microbial taxa. In addition, I demonstrate that soil microbes can influence solanoeclepin A production, thereby disrupting nematode hatching. Together, these findings reveal that plant and microbial metabolism are tightly interconnected in the rhizosphere and provide new insights for improving sustainable agriculture through microbiome-based strategies.