This study investigated the impact of 36 years of phosphorus, nitrogen, and manure fertilization on soil bacterial communities, functionality, and crop productivity across three highland cropping systems in China: continuous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation (GLR). Fertilization significantly altered soil bacterial communities, with system-specific responses. AC showed increased richness and diversity with fertilization, while GLR showed decreases. Manure application amplified differences among systems. Soil bacterial communities were linked to soil organic carbon and nitrogen (WC, GLR) or available phosphorus (AC). Crop productivity correlated with fertilization-responsive taxa.
