Plant phenotypic differentiation outweighs genetic variation in shaping the lettuce leaf microbiota

Lettuce, a widely consumed raw vegetable, harbors leaf-associated microbial communities whose understanding and prediction are crucial for plant and human health. While environmental factors are known to strongly influence plant leaf microbiomes, the role of plant-specific determinants in shaping microbial diversity remains unclear. In this study, we investigated how three key plant factors -genetic distance, plant variety and leaf micro- and macronutrient content- influence the composition and diversity of lettuce leaf bacterial communities, by analyzing 131 fully-sequenced Lactuca sativa genotypes via 16S rRNA amplicon sequencing. Our findings revealed that variety, as defined by breeders, exerts a greater influence on bacterial community diversity than genetic distance or variations in leaf nutrient levels. Together with available and detailed shoot traits they explained 13.4% of the observed bacterial diversity. Inspection of 9 specific leaf morphological traits, with further validation by MAGs analysis, showed that heart formation, head height, and venation types significantly shaped bacterial richness and evenness, mainly acting on non-hub members. These results highlight the strong relationship between leaf morphology and bacterial community structure, suggesting that phenotypic traits play an outsized but understudied role in shaping the leaf microbiota, a crucial aspect of the edible microbiome.