Microbiome Engineering for Enhanced Nutrient Cycling and Disease Suppression in Container Vegetable Production Systems: Application in Urban Horticulture, Nigeria

Container vegetable production is an expanding urban food system strategy in Nigerian cities, yet the microbiological dynamics of container growing media critically govern nutrient cycling efficiency and plant health outcomes. Microbiome engineering, the deliberate manipulation of microbial community structure through targeted inoculation and substrate selection, offers an innovative approach to optimizing container vegetable production without dependence on synthetic inputs. This dissertation develops and tests a microbiome engineering framework for container vegetable systems using urban rooftop and courtyard farms in Lagos, Ibadan, and Abuja as research platforms. Microbial consortium inoculants containing nitrogen-fixing, phosphate-solubilizing, and biocontrol organisms were designed using co-culture optimization methods. Container substrate formulations integrating biochar, compost, and mineral substrates were evaluated for microbiome establishment and stability. Metagenomic profiling of container media was conducted at planting, mid-season, and post-harvest across two production cycles. Crop performance, nutrient use efficiency, and disease suppression metrics were integrated using a composite productivity index. Results demonstrate that engineered inoculant consortia significantly enhanced nitrogen cycling efficiency by 41 percent and reduced Pythium damping-off incidence by 64 percent compared to non-inoculated controls. The study presents an operational microbiome engineering protocol for urban horticultural container systems in Nigerian cities. Keywords: microbiome engineering, container vegetable, urban horticulture, nutrient cycling, Nigeria