Although rice cultivation holds potential for restoring unproductive saline-alkali soils and increasing food production, the mechanisms underlying the relationship between microbial functions and soil element turnover remain unclear. To clarify this relationship, this study investigated the soil physicochemical properties and microbial functions during remediation in saline-alkali soil by rice cultivation over 2, 4, 6, 8, 11, 12, 20, and 23 years. The results indicated rice cultivation markedly improved soil nutrients, soil nutrient stoichiometry, and soil aggregate stability. Additionally, rice cultivation significantly increased the microbial functions involved in nutrient cycling, such as nitrogen fixation, carbon fixation, methanogenesis, dissimilatory sulfate reduction, and thiosulfate oxidation. However, these nitrogen (N), carbon (C), and sulfur (S) cycle-related functions exhibited a similar “increase-peak-decrease” successional pattern with the years of remediation, reaching optimal levels when rice was continuously grown for 11–16 years. Furthermore, correlation analysis demonstrated that the succession of soil microbial N, C, and S functions during saline-alkali soil restoration closely related to changes in soil properties, particularly the availability of phosphorus (P). Therefore, we propose to prioritize the management of P during saline-alkali soil remediation. In conclusion, this study provides a comprehensive understanding of the microbial N, C, and S functions and soil P in the remediation of saline-alkali soils mediated by rice crop.
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