Global consequences of long-term mineral fertilization on soil microbiomes

Mineral fertilization has sustained food security for decades, yet its long-term impacts on soil microbial communities underpinning soil health remain virtually unknown. We combined standardized field surveys and literature synthesis to assemble a global dataset of 501 long-term agricultural experiments (median 25 years) to evaluate the impacts of sustained mineral fertilization on soil properties, microbes and functions. A biogeochemical trade-off between organic carbon accumulation and acidification was observed under long-term mineral fertilization. Microbial biomass increased with soil organic carbon accumulation, and we found major shifts in dominant soil taxa with the relative abundance of Proteobacteria increasing and that of Firmicutes declining with acidification. Virulent bacteriophages increased, with host associations consistent with these bacterial shifts. Microbial activities revealed a decoupling of increased nitrogen- and phosphorus-acquisition enzymes without effects on carbon-mineralization enzymes. Microbial communities were taxonomically reorganized without reducing richness or promoting fungal pathogens. Our findings provide global-scale evidence on the consequences of long-term mineral fertilization for soil health, which is integral to guiding fertilizer management for sustainable agriculture.