| Summary: | The microbial communities in recirculating aquaculture systems (RAS) are essential for optimal physicochemical water quality and fish health. Despite progress, there is still limited knowledge on microbial community dynamics in RAS and especially in commercial systems. In this thesis the temporal dynamics of the microbial community composition in RAS has been examined through studies of two commercial freshwater RAS producing Atlantic salmon fry and parr and an experiment with lumpfish juveniles reared in a seawater RAS with different water treatments. Microbiota was characterized by using 16S rRNA gene amplicon sequencing, flow-cytometry, and culture-based methods. The microbiota in rearing water and biofilter biofilm in one of the commercial RAS for salmon were variable over the 15 months period monitored. The organic matter load on the system significantly influenced the microbial communities of the system. In the second commercial RAS for salmon, fully maturated biofilters provided a more stable water microbiota with higher alpha diversities than the more immature and recently disinfected biofilter, indicating beneficial fish-microbe interactions and a more resilient system. In the experiment with lumpfish, where the hydraulic retention time (HRT) in fish tanks was long, the in-line disinfection upstream of rearing tanks had negative effects on the microbial water quality and the fish health. In comparison, for both commercial RAS for salmon where the HRT was short, we found that the in-line UV treatment led to considerably lower regrowth of bacteria in the fish tanks. In conclusion, well maturated biofilters and controlled and balanced organic loading might be characterizing a good microbial quality. In-line disinfection upstream of the rearing tanks in RAS with long HRT should be avoided, due to negative effects on microbial water quality and fish health. In RAS for salmon fry and parr production, the negative effects of the UV treatment appeared to be reduced.
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