Crop rotation stage has a greater effect than fertilisation on soil microbiome assembly and enzymatic stoichiometry

Agronomic practises, such as fertilisation and crop rotation, affect soil microbial communities and functions. However, limited information is available regarding the relative importance of fertilisation and crop rotation stages in determining the soil microbiome and assembly processes. In addition, insights into the connections between the soil microbiome and enzymatic stoichiometry are scarce. In this study, soil samples were collected from a wheat–rice rotation system that received mineral and organic fertiliser inputs for 6 years to investigate soil microbiome assembly, and the relationship between the soil microbiome and enzymatic stoichiometry. Our results revealed that the crop rotation stage strongly affected the soil microbial community structure, assembly, and enzymatic functions compared to that of the fertilisation regime. Enzymatic stoichiometry results and vector analysis implied that mineral and organic fertilisation could alleviate the microbial N limitation. However, no-manure fertilisation led to microbial P limitation during the wheat stage. The decreases in soil pH mainly drove microbial P limitation due to the acidification induced by the mineral fertilisers. Microbial N/P limitation correlated more strongly with the bacterial assembly than with fungal assembly. Moreover, co-occurrence network analysis showed that ecological relationships between microbial taxa and enzymes were more complex during the wheat stage than that during the rice stage. Microbial nodes linked to acid phosphomonoesterase correlated significantly with the soil pH. Our study highlights the distinct responses of the soil microbiome to fertilisation in different crop-rotation stages, and provides novel insights into connections between microbial assembly and enzymatic stoichiometry.