Maintaining water quality in recirculating aquaculture systems (RAS) is critical to fish health and production efficiency. Biofilters play a central role in removing nitrogenous waste via microbial nitrification and denitrification but can also act as reservoirs for pathogens, raising concerns about pathogen carryover between production cycles. Chemical disinfectants, such as sodium hydroxide (NaOH) and peracetic acid (CH₃CO₃H), are used to mitigate these risks, though they also eliminate beneficial nitrifying bacteria. This study evaluated microbial diversity, functional capacity, and succession of biofilter communities following disinfection in a large-scale Atlantic salmon Salmo salar RAS facility.
16S rRNA gene sequencing identified taxonomic shifts during biofilter re-maturation and revealed delayed recovery of key nitrifiers, including Nitrosomonas and Nitrospira. Pathogen-associated genera, such as Flavobacterium and Aeromonas, were detected throughout the sampling period, highlighting concerns about persistence or re-introduction.
Long-read metagenomics provided a transkingdom perspective, identifying microbial taxa beyond bacterial profiles, including archaea, fungi, and other eukaryotes. Functional metabolic analyses and metagenome assembly to strengthen aquaculture-specific microbial databases. From two pooled metagenomic samples, 35 high-quality metagenome-assembled genomes (MAGs) were recovered. Shared nitrogen cycling genes, such as amoB, hao, nirK, nirS, and nosZ, were detected across MAGs and biofilter zones, though zonal differentiations in composition and function were detected as well.
This study demonstrates biofilters support diverse and resilient microbial communities but emphasizes vulnerabilities, including delayed recovery of nitrifiers and persistence of potential pathogens post-disinfection. Refining disinfection protocols and improving biofilter management strategies is essential to enhance microbial recovery and reduce pathogen risks within RAS production.