Mature nitrifying biofilters counteract invasion by rapid-growing heterotrophic bacteria in recirculating aquaculture systems (RAS)

Nitrifying biofilters are essential components of recirculating aquaculture systems (RAS) for nitrification. Beyond this primary function, their role in shaping the microbial environment for fish remains underappreciated. We previously hypothesized that mature biofilters would resist bacterial invasions and suppress the proliferation of rapid-growing heterotrophic bacteria. We performed two experiments to test this hypothesis: first, in small-scale RAS with Atlantic salmon ( Salmo salar ) fry, and second, in laboratory-scale moving-bed bioreactors (MBBRs). Two treatment groups were compared: systems with a mature biofilter (control) or with a perturbed biofilter induced by hydrogen peroxide disinfection. The systems were then challenged by introducing four strains representing rapid-growing heterotrophic bacteria genera: Flavobacterium , Proteus , Pseudomonas , and Psychrobacter . Microbial communities of biomedia-biofilm and water were analyzed using 16S rRNA gene amplicon sequencing (Illumina). In both experiments, microbial communities in the biofilm and water of perturbed systems had substantially higher relative abundances of these strains eight days post-addition, indicating significantly greater invasion success ( p < 0.01). Furthermore, the perturbed systems showed significantly higher relative abundances of Gammaproteobacteria and Flavobacteriia ( p < 0.01), classes of which encompass many genera associated with opportunistic bacteria and fish pathogens. Our findings emphasize that the biofilter is crucial for optimizing the microbial environment in RAS by counteracting invasion and suppressing unfavorable bacterial growth. Understanding the negative consequences of biofilter perturbation, for example, by disinfection, on the microbial environment in the system, beyond impaired nitrification, is crucial for developing effective management strategies in RAS. • Mature biofilters reduced invasion success of rapid-growing bacteria in RAS. • Perturbed biofilter increased invasion success and promoted rapid-growing bacteria. • Biofilter perturbation may compromise microbial environments in RAS. • Beside nitrification, biofilters contribute to stable microbial conditions in RAS.