Long-Term Low- and Normal-Temperature Operation of Commercial Recirculating Aquaculture System Biofilters: Contrasting Microbial Communities and Predicted Nitrogen-Cycling Profiles

Microorganisms in biofilters are essential to recirculating aquaculture systems (RASs). Low temperature is an important environmental stress influencing the performance of the biofilter in RASs. However, how the microorganisms in the biofilters respond to low temperature remains unclear. In this study, we compared the microbial communities of two commercial RAS biofilters operating under low- and normal-temperature regimes across four seasons. Both biofilters generally kept low ammonia and nitrite concentrations, although the low-temperature biofilter exhibited higher nitrite levels overall with a more pronounced seasonal increase. The low-temperature biofilter also exhibited lower bacterial diversity, fewer detected taxa, and substantial shifts in community composition. The microbial communities were strongly associated with TOC, alkalinity, and inorganic nitrogen. Its co-occurrence network was smaller and more centralized, with greater clustering and shorter average path lengths, indicating highly concentrated microbial associations. Predicted nitrogen-cycle profiles also differed between the two biofilters. The predicted nitrification profile did not differ significantly, whereas the predicted denitrification profile was lower in the low-temperature biofilter. These findings indicate that the two commercial systems harbored distinctly different microbial communities, reflecting differences in specific processes. Collectively, mature RAS biofilters sustained ammonia and nitrite removal despite substantial community simplification, whereas individual predicted nitrogen-cycling processes exhibited distinct predicted patterns under the two operating regimes.