Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS

Recycling aquaculture system (RAS) requires well-functioning microbial communities to support fish welfare and to minimize the risk of spreading diseases. In this study of a marine post-smolt RAS we searched for groups of bacteria containing known salmon pathogens in a 16S RAS library that covered samples from four different sites over a year. In the first of the four production cycles included, there was a severe outbreak of fish skin ulcers associated with over 50 % loss of the fish population. To study the presence of potentially pathogenic bacteria from various habitats in the RAS, we used a refined 16 S rRNA gene library approach. The short library sequences of 250 bp were aligned towards 16 S sequences of recognized fish pathogenic bacteria 750-1500 bp long. The latter sequences were widely defined and gathered from GenBank into a fish pathogens database (FPD) prior to the alignment. Pathogen-relatives detected were Moritella viscosa, Psychrobacter immobilis and Aeromonas salmonicida, all with 100 % similarity; Tenacibaculum dicentrarchi, Pseudoalteromonas piscicida, Mycobacterium simiae, Aliivibrio wodanis and Fransicella philomiragia that had 97-99 % similarity and Shewanell puterfaciens, Flavobacterium johnsoniae, Piscirickettsia salmonis, and Bacillus mycoides that had 90-95 % sequences similarity. The pathogen-relatives habituated differently in the RAS as their relative abundances changed between the sites and over time in response to changing operational conditions. The biofilter biofilm was a unique site due to its remarkable low abundance of the pathogen-relatives, whereas three pathogen-relatives with high similarity to classical salmon winter ulcers strains were highly present in the fish skin ulcers. All pathogen-relatives identified were also detected in the production water, three of them at high relative abundance. Thus, we recommend the fish skin and the production water as the best sampling sites for pathogens early warning and specific screening approaches. •A 16S gene fish pathogen database (FDP) was generated and aligned to a 16S gene library from a marine post-smolt RAS.•The alignment of databases identified 12 pathogen-relatives in the RAS, to whom the distribution was further investigated.•The production water and fish skin were recommended as the best sampling sites for pathogens early warning approaches in the RAS.