Phosphorus (P) fertilization affects plant diversity and ecosystem function by changing the abundance and composition of functional soil microorganisms and genes. Understanding the mechanisms regulating the soil carbon (C), nitrogen (N), sulfur (S), and P cycle across different P fertilizer inputs is crucial to the management of P in sustainable agroecosystems.

We investigated whether soil functional microorganisms affected the coupling of the abundance of soil C, N, P, and S genes under long-term (up to 14 years) P fertilizer input (0, 21.8, 43.6, and 87.2 kg P ha⁻¹ yr⁻¹) on the Loess Plateau of China.

Long-term P fertilizer input resulted in the increased abundance of soil functional microorganisms and the expression of soil C cycle genes but decreased soil P cycle genes. The relative abundance of ecological clusters (including bacteria, fungi, and archaea) was significantly correlated with functional genes related to the C, N, P, and S cycles. Soil Actinobacteria, Proteobacteria, Cyanobacteria, Bacteroidetes, and Chloroflexi were the keystone taxa mediating soil nutrient cycling in wheat fields. Both Mantel’s test and structural equation modeling indicated that the shifts in soil available C and P were the major factors driving the coupling of soil functional microorganisms and genes.

The changes in soil microorganisms and genes can drive soil nutrient cycling and promote crop growth, suggesting that their relationship can provide new insight for understanding the microbial mechanisms of soil P turnover in sustainable agroecosystems.