Characterizing Microbial Dynamics in Pacific Salmonids Throughout Their Spawning Migration

Mucus serves as a critical first line of defense against invading pathogens as well as other environmental stressors. In anadromous and semelparous species like Pacific salmon, the environmental and physiological changes that accompany a spawning migration likely create unique challenges to a healthy microbiome. We investigated changes in the mucus microbiome throughout the long Columbia River migration in semelparous adult sockeye (Oncorhynchus nerka) salmon, as well as in iteroparous adult steelhead (Oncorhynchus mykiss) trout populations. Additionally, we characterized the microbiome of adult coho (Oncorhynchus kisutch) salmon during both their freshwater and saltwater life stages.  The mucus microbiome remained stable throughout the freshwater migration in Sockeye salmon prior to spawning, while the long duration of freshwater residency of migrating steelhead, resulted in distinct changes in the mucus microbiome but no difference in overall microbiome species diversity. The mucus microbiome of spawning coho salmon was found to be population-specific, and its composition shifted during the migration from the saltwater to the spawning grounds. There was evidence that Psychrobacter species, a marine-derived bacteria, were harbored in the mucus of spawning salmon, suggesting that salmon are transferring these microbes inland during their freshwater migration. This study combines data from three different salmonid species and provides insights into the role the microbiome plays in the health of migrating anadromous Pacific salmon, as well as the potential role salmon play in harboring and transporting marine-derived microbes to inland freshwater ecosystems.