Biofilter disinfection increases the colonization success of opportunistic bacteria in the recirculating aquaculture system (RAS)

There is concern that the biofilm in the nitrifying biofilters can act as a reservoir for pathogenic bacteria in recirculating aquaculture systems (RAS); thus, disinfection of the biofilter after each production cycle is currently considered a method to prevent disease outbreaks. Whether regularly disinfecting the biofilters is a proper bacterial management practice in the RAS is still controversial and is an ongoing debate among RAS operators, scholars, and the authority. This study investigated the effect of biofilter disinfection on the colonization success of opportunistic bacteria in RAS. We ran a fish experiment in two identical small laboratory scale RAS (mini-RAS), one running with disinfected biofilter and the other with a non-disinfected biofilter (control, i.e., a mature nitrifying biofilter). Afterwards, both systems were challenged by introducing four bacterial strains, previously isolated from salmon fry, representing the genera Proteus, Pseudomonas, Psychrobacter, and Flavobacterium. Each bacterial strain was added to both mini-RAS at a final concentration of about 1.25 × 105 cells/mL. The bacterial communities of the rearing water and biofilters’ biofilm were characterized by Illumina sequencing of 16S rDNA amplicons, and the relative abundances of the ASVs representing the four added bacterial strains were determined. Our results revealed that the relative abundance of the added bacterial strains was significantly higher in the biofilters’ biofilms and rearing water of mini-RAS with a disinfected biofilter, indicating the higher colonization success of the strains in that system. On day 8 post-challenge, in the biofilm samples of the disinfected biofilter, the average relative abundances of Flavobacterium, Pseudomonas, and Psychrobacter isolates were 4.0 ± 1.3%, 1.79 ± 0.11%, and 0.23 ± 0.05%, respectively, while the control (mature) biofilter showed relative abundances not exceeding 0.006%. The bacterial communities in the biofilm carriers and rearing water in the mini-RAS with a disinfected biofilter also exhibited lower stability over time. Furthermore, in terms of proportions, we observed a reduction of nitrifiers and an increase of Gamma-proteobacteria in the bacterial communities of the biofilm and the rearing water of mini-RAS with a disinfected biofilter. Our findings suggested that biofilters disinfection may increase the risk of opportunistic bacterial invasion in RAS. The results can contribute to formulating better biofilter management practices to optimize the bacterial communities in the RAS and ultimately promote the fish's health and welfare.