Fixed-bed baffled reactors packed with carbon fiber (CFBR), polyurethane, or non-woven fabrics were developed to support microbial nitrification–denitrification reactions for nitrogen removal from synthetic aquaculture wastewater. The CFBR showed the best performance, with a short hydraulic retention time and low C/N ratio. Microbial communities in the reactor’s biofilms and deposited sludge were analyzed using high-throughput sequencing and quantitative polymerase chain reactions. The biofilms efficiently enriched the nitrifying and denitrifying bacteria in the CFBR. Moreover, bacteria capable of denitrification under aerobic conditions were detected in the aerobic chamber biofilm, showing positive correlations with the main nitrifiers and denitrifiers, which provides potential synergistic interactions for simultaneous nitrification–denitrification in the aerobic chamber. A network analysis revealed that the CFBR had more complex cooperative interactions than others. This study provides insights into the influence of different carrier materials on biofilm formation, proving that the CFBR has potential applications in aquaculture wastewater treatment.
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