Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems

Soil microbiomes support agricultural ecosystems, but how they and their functions respond to fertilization across cropping systems is not well known. This study tested 36 years of phosphorus (P), nitrogen (N), and manure application on soil bacterial communities, functionality, and crop productivity in three highland cropping systems on China’s Loess Plateau: continuous alfalfa (AC, legume), continuous winter wheat (WC), and a grain-legume rotation (GLR: winter wheat–millet–pea–winter wheat). Long-term fertilization significantly affected soil bacterial communities with system-specific responses: fertilization increased bacterial richness and diversity in AC but decreased them in GLR; WC showed little change in alpha diversity. Manure-inclusive fertilization increased differences among systems. Bacterial communities were primarily associated with soil organic carbon (SOC) and nitrogen in WC and GLR, but with available phosphorus (OP) in AC. Crop productivity correlated with the abundance of fertilization-responsive taxa in all systems. The study emphasizes distinguishing legume and non-legume systems when assessing long-term fertilization effects on soil microbiomes.