Fruit function beyond dispersal: effect of fruit decomposition on the plant microbiome assembly

The evolutionary role of fruits has primarily been linked to seed dispersal. However, their influence on the soil and plant microbiomes subsequent to their decomposition has received no attention. We hypothesized that fruit decomposition alters the soil microbiome, and consequently the plant microbiome and performance. We used amplicon sequencing to analyze the bacterial communities in the soil, rhizosphere, and phyllosphere of tomato and chili plants grown with and without their fruit. Fruit decomposition affected soil chemistry, increased bacterial diversity and influenced bacterial community composition. Blrii41 and Sandaracinaceae and functions related to methanol oxidation and nitrification, mammalian and human gut metabolism were enriched. It also decreased germination rates and affected shoot but not root length. Fruit decomposition decreased phyllosphere microbial diversity and strongly shifted the rhizosphere and phyllosphere community composition. The plant microbiome showed increased functions related to ligninolysis, methanol oxidation, methylotrophy, and xylanolysis, among others. These results provide evidence that fruits exert a postdispersal influence on the seedling environment and the early plant microbiome assembly. This study expands the classical ecological view of fruit function and opens new directions for understanding microbial inheritance and leveraging fruit-derived microbiomes.