Spatiotemporal Variations in Microbial Community Structure and Assembly Mechanisms Within Recirculating Aquaculture Systems for Mandarin Fish (Siniperca chuatsi)

) is a carnivorous fish species endemic to China with significant economic value. The Recirculating Aquaculture System (RAS) has exhibited promising application prospects in the culture of this species. However, the role of the succession patterns of microbial community structure in maintaining the ecological function and stability of this system remains poorly understood. Therefore, this study employed 16S rRNA high-throughput sequencing to analyze community characteristics, assembly mechanisms, co-occurrence networks, and potential functions across different functional zones and culture cycles. The results indicated that, temporally, alpha diversity decreased significantly during the T4 stage due to stress from nutrient accumulation and metabolic waste, accompanied by a distinct succession of dominant taxa. As the system entered the T5 stage, self-purification capacity improved, and microbial diversity gradually recovered. Spatially, significant differences in microbial composition were observed across environments, reflecting the strong influence of environmental specificity on community structure. Analysis of assembly mechanisms revealed that stochastic processes played a dominant role in driving the microbial community, particularly during the T3-T4 stages and within the YCS and TSC zones. Conversely, microbial dispersal was limited in the GC and LHC zones due to habitat barriers. Co-occurrence network analysis demonstrated that microbial interactions were predominantly competitive, with the network structure shifting from loose to modular over time. Spatially, differentiation arises due to varying functional requirements. Functional prediction identified chemoheterotrophy as the core metabolic function. Furthermore, the nitrogen transformation pathway shifted from predominantly denitrification to urea hydrolysis and nitrate reduction as the culture period progressed. These findings highlight the risk of nitrite and ammonia nitrogen accumulation in later stages and provide a theoretical basis for the optimization and management of RAS for Mandarin fish.