Microbial footprints of tomato domestication

Although plant domestication has significantly altered crop genetics and phenotypes, its effects on the taxonomic and functional diversity of plant-associated microbiomes are not well understood. This thesis investigates how the tomato domestication has influenced the diversity, structure, and functional potential of root-associate microbiomes by integrating field studies, controlled experiments, and quantitative genetics. Field exploration of the wild tomato Solanum pimpinellifolium in its native habitat in Sourthern Ecuador revealed a deterministic rhizosphere microbiome dominated by Enterobacteriaceae, Rhizobium, Fusarium, and Aspergillus. Bacterial metagenomic evidence showed traits that support adaptation to harsh environments. Experiments comparing wild and domesticated tomatoes grown in native, agricultural, and greenhouse soils demonstrated that both plant genotype and soil environment influence rhizosphere composition with domesticated tomato displaying microbiomes aligned with managed soils. These shifts suggest that domestication has inadvertently reduced beneficial microorganisms and microbial functions related to motility, chemotaxis and stress response, which were observed in their wild counterparts. Further analyses showed that the wild tomato relies on its native soil microbiome. Specifically, Actinobacteriota such as Actinoplanes, provided protection against the endemic insect Prodiplosis longifila. These bacteria exhibited functional traits associated with secondary metabolism and nutrient transport. Finally, using a recombinant inbred line population, we identified plant genomic regions associated with the differential recruitment of key bacterial taxa, such as Cellvibrio in wild and Streptomyces in domesticated tomato. These associations revealed reciprocal links between plant and bacteria regarding plant nutrient uptake, stress tolerance, and metabolic functions. Together, these findings demonstrate that domestication has reshaped tomato–microbiome interactions by altering microbial diversity and functions that are crucial for plant stress resilience. This work highlights the importance of reintegrating beneficial native microbial partners into breeding programs to support more resilient and sustainable agricultural systems.