Turning waste into substrates enhance rooftop tomato production through microbial mediation

Urban agriculture is emerging as a valuable strategy to mitigate the challenges posed by rapid urbanisation and global population growth. Among its forms, productive rooftops stand out as a sustainable solution, enabling food production, organic waste recycling, and the creation of green spaces by repurposing underutilized roofs. Leveraging natural resources, including plant-associated microbiomes, offers further potential to sustainably improve productivity and food quality. However, microbial communities inhabiting different organic amendments, such as compost and biochar (BC), remain poorly studied despite their relevance in shaping plant–substrate interactions. The Madreenroof project, conducted on the rooftop of the Instituto de Ciencias Agrarias (ICA-CSIC) in the city of Madrid, aimed at investigating how different organic biomasses (i.e., spent coffee grounds, coffee silverskin, and seaweeds) composted with or without BC affect substrate properties, microbial communities, and tomato productivity. A commercial peat-based substrate was used as a benchmark. Our results showed that feedstock type was the primary factor influencing substrate chemical and physical properties, and thus microbial communities. While BC addition improved compost quality, its role in shaping microbial communities was less pronounced than that of the feedstock. Alternative substrates exhibited higher phosphorus concentrations, pH, and electrical conductivity than peat. Microbial analysis revealed that bacterial diversity was higher in alternative substrates, yet their overall taxonomic structure remained relatively consistent across treatments, indicating functional redundancy. Notably, we identified distinct microbial communities associated with each feedstock. Communities enriched in the composted seaweed biomass substrate were significantly and positively correlated with increased tomato yield. These findings highlight the dual role of organic substrates in directly influencing plant growth through their physicochemical traits and indirectly through microbiome modulation. Selecting appropriate organic materials not only boosts rooftop vegetable production but also enriches urban microbial diversity in otherwise underexploited spaces.