Global long-term agricultural experiments reveal consequences of mineral fertilization for soil microbiomes

Mineral fertilizers have sustained food security for decades, yet the long-term impacts on soil microbial communities underpinning soil health remain virtually unknown. We combine standardized field surveys with a meta-analysis to assemble a global dataset of 501 long-term agricultural experiments (≥5 years, median duration 25 years) to evaluate the impacts of sustained mineral fertilization on soil properties and microbial communities. Long-term mineral fertilization increases soil organic carbon by 14% and decreases soil pH by 0.31 units on average relative to unfertilized controls. Soil organic carbon accumulation largely explains increased microbial biomass carbon and living bacterial biomass. Mineral fertilizer-induced acidification primarily reshapes dominant bacterial taxa, with the relative abundance of Proteobacteria increasing and Firmicutes declining, whereas fungal community composition remains stable. Virulent bacteriophages increase in association with shifts in bacterial hosts. Microbial activities reveal a decoupling of more nitrogen- and phosphorus-acquisition enzymes from the unchanged production of carbon-mineralization enzymes. Microbial communities are taxonomically reorganized without reducing richness or promoting fungal pathogens. These responses are evaluated in the context of agroecosystem type, fertilization regime, and cropping regime. Our findings provide global-scale evidence for the consequences of long-term mineral fertilization on soil health, which is integral to guiding fertilizer management for sustainable agriculture.