| Summary: | ENVS 4902 Environmental Science Undergraduate Honours Thesis The Committee on the Status of Endangered Wildlife in Canada considers Atlantic salmon (Salmo salar) in the outer Bay of Fundy to be endangered. Despite decreases in fishing pressure since wild Atlantic salmon were overfished in the 1960s and 1970s, Atlantic salmon abundances have continued to drop across Atlantic North America, including in the Bay of Fundy. Atlantic salmon have been important for fisheries and are important for nutrient transfer across aquatic environments. Understanding factors that perpetuate Atlantic salmon declines is crucial for wild salmon population recovery efforts and restoration of the historical and ecological roles of the species. Salmon aquaculture currently poses a threat to outer Bay of Fundy wild Atlantic salmon. Pathogen transfer from open-net aquaculture farms into the surrounding water column is a potential risk for wild salmon. However, agents of oceanic Atlantic salmon mortality, and specifically how Atlantic salmon populations are impacted by marine salmon farms, remain largely undocumented in the literature. This study aimed to address knowledge gaps surrounding the impacts of marine aquaculture on wild Atlantic salmon by answering the question: how does the richness of pathogens differ around open-net Atlantic salmon marine aquaculture farms compared to fallow farms and non-farm areas in Passamaquoddy Bay, NB? Ocean water was sampled adjacent to active and fallow open-net pen salmon aquaculture sites, as well as at non-farm sites, in Passamaquoddy Bay. Water was filtered to capture pathogen eDNA in the water column. Quantitative PCR analysis of filters showed no detection of RNA from Piscine orthoreovirus or Atlantic salmon coldwater vibriosis (Atlantic salmon pathogens) and no detection of Atlantic salmon DNA or RNA at any of the tested sites, with the exception of one active site (where a small amount of Atlantic salmon DNA was detected). These results reveal potential issues with experimental design, including possible challenges associated with sampling distances from the net pens and tidal effects, pre-filter clogging, and bleach contamination. Avenues to address these challenges have been presented and should be considered by future studie
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