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

Fruits are primarily linked to seed dispersal. However, they might also play a key role in the assembly of the plant microbiome and microbial inheritance. We propose that fruit decomposition directly influences the plant microbiome and plant fitness. Additionally, we hypothesized that fruit decomposition alters the microbiomes of soil and seedlings. We used amplicon sequencing to analyse microbial communities associated with the soil, rhizosphere, and phyllosphere of tomato and chili plants grown with and without their fruit. We demonstrated that fruit decomposition decreased the germination rate and phyllosphere microbial diversity, and influenced the phyllosphere and rhizosphere community composition. Moreover, fruit decomposition increased soil microbial diversity and drastically altered microbial community composition as well as predicted microbial functions. Soil physiochemical properties were influenced by fruit decomposition, resulting in high organic carbon accumulation and distinct availability of crucial elements such as sulfur, magnesium, and potassium. The phyllosphere and rhizosphere microbiomes showed differences, with fruit and seed treatments driving unique microbial enrichments in each compartment, which subsequently resulted in distinct predicted functions. This study provides evidence that fruits may have an alternative function beyond seed dispersal in plant microbial assembly and microbial inheritance, potentially shaping the development and success of plant offspring.