Compost chemodiversity regulates soil organic matter transformation pathways and plant biochemical quality

The valorization of agro-food waste through composting represents a key strategy to enhance soil organic matter (SOM) quality and functionality while supporting circular agriculture. Beyond organic carbon inputs, the molecular composition and chemodiversity of composts can influence SOM transformation pathways, microbial activity, and plant–soil interactions. However, the extent to which compost chemodiversity shapes soil biodiversity and associated ecosystem functions remains insufficiently understood. In this study, we evaluated the effects of three composts differing in feedstock origin on soil–plant–microbiome interactions in a carrot pot experiment. The composts included: (i) green compost from horticultural residues and coffee husks (GrC), (ii) manure-based compost from bovine manure and straw (MaC), and (iii) a 1:1 mixture of the two (MiC), compared with a mineral-fertilized control. Plants were grown for 90 days, after which soil and plant compartments were analyzed for physicochemical properties, nutrient uptake, soil microbial community structure and functional potential, and plant metabolomic profiles.Compost applications significantly enhanced plant growth and nutritional quality. MiC and MaC increased plant biomass and nutrient accumulation. Metagenomic analyses showed that compost treatments modulated soil microbial diversity and functional pathways related to organic matter decomposition, and plant growth promotion, with MiC inducing the highest bacterial richness. Untargeted LC-QTOF-MS metabolomics revealed compost-specific patterns in carrot secondary metabolites. Overall, our findings demonstrate that compost chemodiversity acts as a key driver of SOM functional dynamics, soil biodiversity, and crop biochemical quality, highlighting the potential of tailored organic amendments to enhance soil health and agroecosystem multifunctionality.