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At high latitudes, lake whitefish (Coregonus clupeaformis) and others in the closely related Coregonus species complex (CSC) including cisco (C. autumnalis and C. sardinella) can be diadromous, seasonally transitioning between freshwater lakes and the Arctic Ocean. CSC skin- and intestine microbiomes were collected, facilitated by Inuit fishers at sites on and around King William Island, Nunavut, at the northern range limits of lake whitefish. Community composition was explored using 16S rRNA gene sequencing and microbiota distinctly grouped depending on fishing site salinity. Overall, lake whitefish intestine communities were more variable than those of the two cisco with higher Shannon diversity, suggesting that lake whitefish and their microbiomes could be susceptible to environmental stress possibly leading to dysbiosis. Lake whitefish showed lower condition (K) in the ocean than in freshwater rivers, whereas cisco condition was similar among distinct seasonal habitats. Taken together, the impact of changing habitats on fish condition and microbial composition may inform approaches to CSC health in fisheries and aquaculture, in addition to being relevant for northern Indigenous peoples with subsistence and economic interests in these resources.

Concern about salt levels in freshwater habitats receiving road de-icer runoff has inspired the development of “eco-friendly” formulations that are intended to be less toxic to aquatic organisms, but few experiments have determined that these products are environmentally benign. Mesocosms containing lake water were established for 6 weeks to compare traditional road salt with two newer de-icers, one an inorganic mixture of chloride salts and the second of beet extract and brine. Amplicon sequencing and algal blocking sequences facilitated the identification of differentially impacted bacterial taxa. Ironically, although there was only a minor effect on bacterial structure at high road-salt concentrations, there was an increased relative abundance of salt-resistant genera in the mixed-salt formulation. After amendment with the beet brine de-icer, there was a turnover of taxa coincident with a 68-fold decrease in dissolved oxygen, with decreased diversity and displacement by anaerobic genera indicating a shift across a threshold to a new, apparently stable state, suggesting mesocosm recovery was unlikely. Overall, although we applaud the sentiment behind the formulation of less-damaging “eco-friendly” de-icers, they appear to have more negative environmental impacts than the traditional road salt that they were made to replace.