The Tomato’s Tale: Exploring Taxonomy, Biogeography, Domestication, and Microbiome for Enhanced Resilience

Plant domestication and breeding not only resulted in multiple phenotypic changes but also impacted the agricultural ecosystems in which our current crops are cultivated. Most crops to date rely on the extensive use of fertilizers and pesticides to support crop growth and health. To minimize the environmental impact of these management practices, the plant microbiome has gained renewed attention as a large yet untapped resource of microorganisms with beneficial effects on plant growth and health. In the past decade, it has become evident that the microbiome of plants plays a key role in nutrient acquisition, plant development, and tolerance to diverse abiotic and biotic stresses. Here, we review past and present knowledge of the microbiome of tomato as a model for unraveling the functional potential of plant microbiomes, the impact of domestication, and the underlying genetics of microbiome assembly and activity. We also provide perspectives on how this knowledge can be adopted to enhance crop productivity and strengthen the sustainability of agricultural management practices.