Crop rotation-driven change in physicochemical properties regulates microbial diversity, dominant components, and community complexity in paddy soils

Crop rotation is a production practice to promote a more diversified plant community in rice field, thereby enhancing agroecosystem sustainability and production efficiency under an increasing demand for food and energy. The regulation of rotations of rice with different crop on soil microbiomes and their relationships with key soil physicochemical drivers has not been understood enough. To address this, soils of 0–20 cm and 20–40 cm layers subjected to four rotation regimes (rice-rice, tobacco-rice, rice-oilseed rape, and rice-rice-oilseed rape) were collected from a long-term (>20 year) field experiment. Compared with the rice-rice, the other three rotations significantly increased surface soil porosity and the content of soil total nitrogen (N), available phosphorus (P), total potassium, and organic matter, as well as improved soil aggregate composition but decreased soil bulk density (P < 0.05). Rotation patterns and soil layers independently or interactively explained the variation in microbial diversity and community composition in soil, with a greater impact of the rotation regimes (9.3–49.7%; P < 0.05). The rotation systems of rice-oilseed rape and rice-rice-oilseed rape showed a higher soil microbial diversity and co-occurrence of the community species compared with other two systems. The components of the genus Clostridium , Pedobacter , and Gp1 were the dominant hubs (with a larger number of edges) in bacterial communities, and the members of the Mortierella , Ascomycota, and Agaricales were the hubs in fungal communities. The co-occurring networks between the members of bacterial and fungal communities in the four systems showed same keystone taxa that mainly belong to fungal genus Mortierella , Fusicolla , Paranamyces , and Pseudeurotium . The microbial diversity and community composition were positively correlated with soil NH 4 + -N-to-NO 3 - -N ratio, available P content, total N content, and soil aggregates, and meanwhile, those variables were the creadible predictors of the community changes. These findings highlighted the advantage of rice rotations with oilseed rape in improvement of soil fertility and production by mediating soil microbiome and physicochemical property relationships. • Rice-oilseed rape rotation increased soil microbial diversity and species co-occurrence. • Mortierella , Fusicolla , and Paranamyces were main hubs of microbial co-occurring network. • Microbial community trait was correlated with inorganic N, available P, and soil aggregates. • Soil NH 4 + -N: NO 3 - -N was main predictor of bacteria diversity and community composition. • Rice-oilseed rape rotation showed an advantage in enhancing soil biology fertility.