Marine recirculating aquaculture systems (marine RAS) are increasingly utilized for their high productivity and minimal environmental impact. However, effective nutrient management and biosecurity measures remain crucial for sustainable operation of marine RAS. This study successfully established a simultaneous nitrification and denitrification (SND) process using a biofloc technology (BFT)–ultrafiltration (UF) combined approach. A stable autotrophic marine nitrification system was rapidly initiated within 23 days using a ceramic ring (CR)–granular activated carbon (GAC)–UF process (CGUF), followed by the substitution of polyhydroxyalkanoates (PHA) for GAC filter to achieve rapid start-up of SND in 24 h (CG/PUF). Soluble reactive phosphate (SRP) was removed in-situ via biofloc adsorption. The co-existence of ammonia-oxidizing archaea (Candidatus_Nitrosopumilus) and denitrifying bacteria (Stenotrophomonas, Ruegeria and Ilumatobacter) synergistic promoted the SND start-up in CG/PUF process. Stenotrophomonas emerged as the keystone species which closely linked to amoA/B/C, hao and nosZ genes (p < 0.05). The CG/PUF process effectively enhanced the biosecurity of marine RAS, with 100 % elimination of potential pathogens (Vibrio and Tenacibaculum). UF membrane could maintain fluxes at 15 L∙ m−2∙ h−1 (LMH) for 180 days, with a 2-day intermittent hydraulic flushing keeping transmembrane pressure below 50 kPa. These findings provide insights for broader application of BFT–UF combined process in marine RAS.
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