Objectives  By analyzing the effects on soil fertilization and phoD gene community structure and diversity under different crop rotation systems in Panxi plateau, this paper is aimed to further understand the soil phosphorus (P) circulation mechanism in plateau habitat and to establish a reasonable crop rotation system.

  Methods  In this study, the fallow non-rhizosphere soils under five different crop rotation systems in Panxi plateau were selected as the research objects. Using chemical analysis and high-throughput sequencing technology, the physical-chemical properties, the phoD community structure and gene diversity of soil were investigated.

  Results  Under different crop rotation systems, soil available P content increased significantly compared with barely roots. However, total nitrogen (TN), alkali-hydrolyzed nitrogen (AN) and soil organic carbon (SOC) contents decreased obviously(P < 0.05). Acid phosphatase activity (ACP) was higher than alkaline phosphatase (ALP) and neutral phosphatase(NP) in soil, which was the highest under Maize-flue-cured tobacco crop rotation system (13358 U g⁻¹). Shannon diversity index of phoD gene was the highest under Maize-flue-cured tobacco crop rotation system and lowest under buckwheat (Fagopyrum tataricum)-flue-cured tobacco crop rotation system. phoD gene community structure had obvious differences under different crop rotation systems. Proteobacteria and Actinobacteria were the main phylums under different crop rotation systems, and Bradyrhizobium was the mutual advantage species in all patterns. RDA analysis showed that SOC and pH were the main factors stimulating the development of phoD gene community structure.

  Conclusions  Compared with barely roots, crop rotation systems changed soil fertilization and phosphatase activity obviously and developed different phoD gene community structure of soil. In five crop rotation systems, Buckwheat (Fagopyrum tataricum)-flue-cured tobacco crop rotation system had the most significant effect on phoD gene diversity index and Maize-flue-cured tobacco crop rotation system had the most significant effect on soil fertilization contents and ALP activity.