The recipe for suppressiveness: modulating compost feedstock configuration shapes microbial signatures linked to tomato Fusarium wilt biocontrol

The prebiotic properties of compost promote the development of beneficial microbial communities that actively contribute to the suppression of soil-borne diseases. Metagenomics enables the identification of key taxa and the analysis of population dynamics within plant–microbiota–compost interactions. This study investigated the composition and structure of microbiomes in five composts derived from different combinations of plant- and animal-based matrices, and their role in suppressing tomato tracheofusariosis. Bacterial and fungal communities in composts and in the rhizosphere of artificially infected tomato plants grown under suppressive conditions were characterized through bioinformatic analysis of 16S rRNA (V3–V4 regions) and ITS (ITS1–5.8S–ITS2 regions) sequences, respectively. Amplicon sequencing analyses assessed taxonomic profiling, and differential abundance across ecological niches, matrix types, and levels of suppressiveness. Microbial communities showed clear clustering according to compost matrices, with significant effects on suppressive capacity. Composts derived from polyphytic residues with a high proportion of livestock matrices exhibited complex communities, where multiple bacterial and fungal taxa collectively contributed to disease suppression. In contrast, composts based exclusively on oligophytic substrates displayed a more specific suppressive pattern, involving fewer taxa influenced by lignocellulosic and aromatic compounds from tomato residues and olive oil by-products. Rhizosphere analysis of plants grown in suppressive composts revealed reduced α-diversity and increased Bray-Curtis dissimilarity to bulk samples, suggesting plant-mediated selective recruitment of beneficial microbiota. These findings highlight the combined role of compost composition and plant-driven selection in shaping microbial communities associated with disease suppression.