Recirculating aquaculture systems (RAS) are increasingly used in salmon smolt production as they enable flexible production cycles with reduced freshwater use and time in net-pens at sea. Maintaining good water quality is essential in RAS, and the microbiota is key in this. It is important to maintain a stable community of nitrifying bacteria in the biofilter, and the water microbiota can affect fish health. Small particles typically accumulate in RAS, and this can negatively impact the microbiota by facilitating growth of heterotrophic bacteria. This can be detrimental for biofilter functioning, water quality, and fish health.
In the MikroRAS study, funded by the Norwegian Seafood Research Fund, we conducted an experimental study with six identical pilot-scale RAS stocked with Atlantic salmon. Three systems were operated at high and three at low particle loads (Figure 1). We followed the systems for four months through the freshwater and brackish phases and conducted a simulated transport followed by further sampling over three months in salt-water flow through systems (simulating open sea-cages). We have utilized amplicon and shotgun sequencing to investigate the microbiota of the RAS environment (water, biofilter) and salmon (gut, gill, and skin). We relate the microbiota data to water quality metrics and particle size distribution as well as fish health and performance.
Our results show that particle load had limited impact on biofilter functioning and water quality, although we observed trends towards more favourable conditions in the low particle load RAS. The RAS operated at a low particle load had lower levels of ammonia and nitrite, likely due to nitrifying microorganisms in the biofilter facing less competition from heterotrophic bacteria. Initially, in the freshwater phase, the RAS microbiota was surprisingly unperturbed by the difference in particle load. However, after transition to brackish water, the newly established saline-tolerant microbiotas diverged strongly between the RAS with high and low particle loads. We observed minimal mortality and the fish remained healthy throughout the study. However, the salmon in RAS with low particle load trended towards increased feed intake and growth, resulting in heavier fish with a higher condition factor at the end of the RAS phase. The study ultimately aims to help optimise operational parameters in RAS, thereby improving fish welfare, cost-effectiveness, and sustainability of salmon production in RAS.