The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function

Abstract Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0–45.0 mg/g; total organic carbon: 15.0–35.0 mg/g) and sustained redox homeostasis (consistently low oxidation–reduction potential: − 150 to − 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%–50% in CRCE vs. 10%–20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers ( Geobacter ), sulfur oxidizers ( Sulfuricurvum ), and nitrifiers ( Nitrospira ), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.