Differential roles of fertilization, soil compartment, and crop phenology in shaping the soil microbiome of maize

Identifying sustainable fertilization strategies is essential to maintaining crop productivity while preserving soil health and functionality. In this study, we evaluated the individual and combined effects of fertilization type (struvite, compost and sludge), soil compartment (bulk and rhizosphere), and maize phenological stage (germination and blooming) on crop yield, nutrient availability, and the soil microbiome in a Mediterranean agroecosystem. Maize yield was maintained by the partial substitution of NPK with struvite and its combinations with compost or sludge. These treatments increased Olsen P (by 30%-40%) and water-soluble N contents (by 22%) particularly at blooming and harvest. Alkaline phosphatase and urease activity, together with bacterial and fungal biomass, were enhanced under organic and organo-mineral amendments (>15%), with consistently higher values in the rhizosphere. Phenological stage and soil compartment were the main drivers of changes in microbial biomass and activity, while fertilization influenced specific microbial groups. Further, amplicon sequencing revealed that fungal communities were more responsive to fertilization than prokaryotic ones. Crop phenology exerted the strongest effect on community composition and richness, particularly for fungi. Fungal taxa such as Cladosporium and Mortierellales showed stage and treatment-specific dynamics, reflecting their potential role in nutrient mobilization. Moreover, the relative abundance of Nitrososphaera under treatments with higher water-soluble N highlighted its critical role on N cycle in this agroecosystem. Overall, our results underscore the value of combining organic amendments with mineral fertilizers to enhance nutrient use efficiency and sustain microbial-mediated soil functions. Further, this study highlights the importance of spatial (soil compartment) and temporal (phenological stage) dimensions when evaluating the effect of agricultural management practices in the soil microbiome of maize. • Substitution of NPK fertilization with organomineral fertilizers maintain crop yield. • Organomineral fertilization sustain nutrient availability during peak nutrient demand. • Struvite acts as a slow release P and N source, boosting nutrient efficiency. • Crop phenology strongly drives microbial dynamics, linking plant growth to succession.