Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms

Abstract

The spread of infection from reservoir host populations is a key mechanism for disease emergence and extinction risk and is a management concern for salmon aquaculture and fisheries. Using a quantitative environmental DNA methodology, we assessed pathogen environmental DNA in relation to salmon farms in coastal British Columbia, Canada, by testing for 39 species of salmon pathogens (viral, bacterial, and eukaryotic) in 134 marine environmental samples at 58 salmon farm sites (both active and inactive) over 3 years. Environmental DNA from 22 pathogen species was detected 496 times and species varied in their occurrence among years and sites, likely reflecting variation in environmental factors, other native host species, and strength of association with domesticated Atlantic salmon. Overall, we found that the probability of detecting pathogen environmental DNA (eDNA) was 2.72 (95% CI: 1.48, 5.02) times higher at active versus inactive salmon farm sites and 1.76 (95% CI: 1.28, 2.42) times higher per standard deviation increase in domesticated Atlantic salmon eDNA concentration at a site. If the distribution of pathogen eDNA accurately reflects the distribution of viable pathogens, our findings suggest that salmon farms serve as a potential reservoir for a number of infectious agents; thereby elevating the risk of exposure for wild salmon and other fish species that share the marine environment.

Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong

“…Another important aspect of adopting environmental DNA-based monitoring in fish farms is its non-destructive sampling approach [28,50,51]. Traditionally parasites burden is monitored in fish farms by handling animals, use of anesthetics, and preventive bath treatment, which are stressful for fish and can predispose animals getting sick after any of these procedures [52].…”

Atlantic salmon farms are a likely source of Tenacibaculum maritimum infection in migratory Fraser River sockeye salmon

“…While time spent in the vicinity of individual farms is low (Rechisky et al 2021), approximately 30 active farms, each farm holding 500 000 to 1 000 000 fish, lie along the main sockeye migration route between the Fraser River and the Alaska border in any given year (DFO, Figure 1). These farms can elevate the concentration of infectious agents faced by migrating juvenile sockeye (Shea et al 2020), and depending on agent, elevated infectivity can extend for tens of kilometres beyond the confines of a farm (Krkošek et al 2005;Foreman et al 2015).…”

“…A cosmopolitan marine bacterium that infects fish, T. maritimum infection does not invariably cause disease but is responsible for tenacibaculosis globally and causes "mouth rot" in Atlantic salmon (S. salar) on farms in BC (Frisch et al 2018b). In a recent environmental-DNA (eDNA) study, out of 39 salmon pathogens for which presence was assessed in coastal marine waters, T. maritimum was one of the agents most strongly associated with active salmon farms (Shea et al 2020). Here, we analyse new data from migrating sockeye salmon that were not included in DFO's risk assessment (DFO 2020).…”

Sea lice(Lepeophtherius salmonis)detection and quantification around aquaculture installations using environmental DNA

“…However, several recent studies have suggested that the eDNA concentration can reflect the local biomass of fishes in marine environments (32,33). Further, it was recently shown that it is possible to identify eDNA from various aquaculture pathogens (34)(35)(36), including L. salmonis, using eDNA metabarcoding (multi-species approach) of the 18S rRNA region in a mesocosm setting. The cost of eDNA metabarcoding and the complexity of the analysis might limit the use of the eDNA metabarcoding approach in a regulatory monitoring program.…”