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.

不同耕作制度的使用会影响土壤磷 (P) 的有效性。微生物在调节土壤磷循环中发挥着主要作用。目前，关于长期使用不同轮作制度对参与磷循环的微生物功能基因对土壤磷有效性的影响还存在知识空白。在这项研究中，利用宏基因组学确定了一项为期 12 年的实验中参与磷循环的微生物功能基因，该实验包括三种作物轮作系统：小麦-玉米轮作 (WM)、小麦-棉花轮作 (WC) 和小麦-大豆轮作（WS）。WS 的 AP 含量显着高于 WC (37.3%) 和 WM (41.5%)。对土壤微生物种群的进一步分析表明，WS主要从门到属水平富集了变形菌门、放线菌门和厚壁菌门的丰度。对于磷循环基因，与WC和WM相比，WS显着增加了有机磷矿化的磷循环基因丰度（ phoD、 phnA和phnP ）。WC增强了微生物增溶无机磷基因gcd和gppa的功能。WM增强了多磷酸盐降解功能，与WC和WS土壤相比，WM土壤中spoT和ppnK基因丰度显着增加。此外，我们的结构方程模型和网络分析表明，有机磷矿化基因丰度对有效磷含量有显着影响；效应系数为0.73，WS土壤中富集的有机磷矿化基因phoD、 phnA和phnP是增加土壤有效磷过程中的关键基因。我们的结果强调了磷循环功能与土壤有效磷之间的关系。种植系统，这对于通过在农业生产中使用不同的作物系统来提高磷的利用率也具有影响。