Microbiological monitoring of an Atlantic salmon recirculating aquaculture system (RAS) – Health and quality assessment

Aquaculture is an important industry in Norway, particularly the production of Atlantic salmon (Salmo salar L.). Health problems and environmental impacts during the seawater stage are limiting factors for the industry. To combat these issues, closed and land-based aquaculture facilities for post-smolt production have become more popular. Although, vaccinations control several infectious diseases in Norwegian aquaculture, bacterial and viral infections and salmon lice cause losses in aquaculture and pose a threat to fish health and welfare. Also, off-flavor compounds, such as geosmin, have the potential to be important quality-limiting factors in the production of Atlantic. The change to land-based production increases the risk of accumulation of pathogenic and geosmin-producing bacteria, and little is known how such a production method affects the overall health and skin microbiota of fish. In the present study, microbiological and molecular methods were used to monitor fish health and product quality in connection to off-flavor in a land-based saltwater RAS facility. Brevundimonas vesicularis was amongst the most dominating bacteria in all samplings, whilst bacteria such as Chryseobacterium indologenes were only present in freshwater fish mucus samples. Overall, less bacterial diversity was observed in the second saltwater RAS sampling. Geosmin-producing bacteria were identified in most of the samples, with an increase of target DNA in the saltwater RAS samplings, particularly in RAS biofilm. The results presented in this study indicate that monitoring of bacterial microbiota of fish skin, RAS biofilm, and biofilters by traditional bacteriology methods could be used to reveal wound problems in an aquaculture facility. Aliivibrio wodanis was isolated from fish and environment during a period with ulcer problems in the RAS facility and could thus potentially be used as a biomarker for wound development. Quantitative PCR was established and used as a method for early detection of pathogens important in Norwegian aquaculture and geosmin-producing bacteria. This approach can be used to implement changes in production quickly if pathogens or geosmin-producing bacteria are detected.