Metagenomes reveal the effect of crop rotation systems on phosphorus cycling functional genes and soil phosphorus avail–ability

The use of different cropping systems affects soil phosphorus (P) availability. Microbes play a main role in regulating soil P cycling. Currently, there is a knowledge gap on the effects of the long-term use of different crop rotation systems on microbial functional genes involved in P cycling on soil P availability. In this study, metagenomics was used to determine microbial functional genes involved in P cycling in a 12-year experiment that included three crop rotation systems: wheat–maize rotation (WM), wheat–cotton rotation (WC), and wheat–soybean rotation (WS). WS had a significantly higher AP content than WC (37.3%) and WM (41.5%). Further analysis of the soil microbial population showed that WS mainly enriched the abundance of Proteobacteria, Actinobacteria, and Firmicutes from the phylum to genus levels. For the P-cycling genes, WS significantly increased the P-cycling gene abundance of organic P mineralization (phoD, phnA, and phnP) compared with WC and WM. WC enhanced the microbial function of the Inorganic P solubilization genes gcd and gppa. WM enhanced the function of polyphosphate degradation, and the abundance of genes spoT and ppnK was significantly increased in WM soil compared with WC and WS soil. In addition, our structural equation model and network analysis showed that the organic P mineralization gene abundance had a significant effect on the available P content; the effect coefficients were 0.73, and the organic P mineralization genes phoD, phnA, and phnP, which were enriched in WS soil, were keystone genes in the process of increasing the soil-available P. Our results highlight the relationship between P cycle functions and cropping systems, which also has implications for enhancing P availability through the use of different crop systems in agricultural production.