Salish Sea Marine Survival Project

20 5. Powerful Genetic Technologies — Genomics During SSMSP, new genetic tools were developed to assess if a fish is developing an active disease, allowing for detection before clinical signs of the disease are evident. The Strategic Salmon Health Initiative (SSHI) is a collabo- ration between Genome BC, the Department of Fisheries and Oceans led by Dr. Kristi Miller-Saunders, and the Pacific Salmon Foundation. This study has successfully demon- strated the application of a new technology from Dr. Miller's lab. During the past few years, over 28,000 samples of wild Pacific Salmon, hatchery-reared Pacific Salmon and aquaculture-reared Atlantic Salmon have been collected and analyzed using state of the art genomics methods to examine microbes (Figure 9). This study is the largest such survey ever conducted on Pacific Salmon. The data analyses have focussed on 1) developing models to relate infectious profiles with ocean survival and productivity in Chinook, Sockeye and Coho Salmon; 2) assessing the variation in infectious profiles in aquacul- ture fish from four farms; 3) producing models to assess potential for farm-wild exchange of infective agents across all salmon species surveyed, assessing pathogenic potential of top agents of interest through linkage with physiological changes at the molecular and cellular levels; and 4) looking at hatchery-wild interactions for Coho and Chinook. 6. Use of Acoustic Telemetry Acoustic tags transmit unique signals that are received and recorded by receivers suspended in the sea. If a fish tagged with an acoustic tag passes a receiver within approximately 300 metres, the receiver records that event. By strategically placing lines of receivers across the seafloor, researchers can trace the migration path of individually tagged fish (Figure 10). As part of the SSMSP, PSF has enhanced the use of acoustic tags and receivers within the Strait of Georgia. Until 2015 the existing acoustic receiver arrays allowed for fish detections in the lower Fraser River, in Juan de Fuca Strait, in north-central Strait of Georgia, and in northern Queen Charlotte Strait (yellow lines on Figure 10). While these arrays have been very useful, they could not provide sufficient resolution to assess the residence time; migration patterns, rate and timing; and survival of juvenile Pacific Salmon within the Strait of Georgia. To address these issues, PSF deployed 43 new receivers in the Discovery Islands (northern end of the Strait of Georgia/Salish Sea) and Johnstone Strait near Sayward, BC in 2015. Of these, 41 were loaned from OTN and the other two were loaned from Kintama Research. Figure 11 shows the yellow flotation collars used to protect the receivers. New technology — the Fluidigm BioMarkTM HD System can analyze samples on a scale never before conducted on fish. Up to 90 individual fish and 47 microbes (duplicated) can be examined simultaneously! This break-through allows for statistically reliable sampling for pathogens in fish for the first time. Figure 9. The SSHI achieved a milestone in 2015 when the BioMark was approved for use in Phase 2b of the project.

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