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Infectious agents are key components of animal ecology and drivers of host population dynamics. Knowledge of their diversity and transmission in the wild is necessary for the management and conservation of host species like Atlantic salmon ( Salmo salar). Although pathogen exchange can occur throughout the salmon life cycle, evidence is lacking to support transmission during population mixing at sea or between farmed and wild salmon due to aquaculture exposure. We tested these hypotheses using a molecular approach that identified infectious agents and transmission potential among sub-adult Atlantic salmon at marine feeding areas and adults in three eastern Canadian rivers with varying aquaculture influence. We used high-throughput qPCR to quantify infection profiles and next generation sequencing to measure genomic variation among viral isolates. We identified 14 agents, including five not yet described as occurring in Eastern Canada. Phylogenetic analysis of piscine orthoreovirus showed homology between isolates from European and North American origin fish at sea, supporting the hypothesis of intercontinental transmission. We found no evidence to support aquaculture influence on wild adult infections, which varied relative to environmental conditions, life stage, and host origin. Our findings identify research opportunities regarding pathogen transmission and biological significance for wild Atlantic salmon populations.

Blooms of the river benthic diatom Didymosphenia geminata are an enigma because they occur under phosphorus-poor conditions. A recent proposal that ferric–ferrous iron redox shifts sequester the additional phosphorus needed to stimulate and sustain D. geminata blooms does not agree with published experimental data showing that blooms only occur when cells are phosphorus-limited. The “iron hypothesis” also infers that blooms would be favoured in rivers with elevated iron, and management should target iron. Surveys of rivers around the world affected by D. geminata show that blooms most often occur in iron-poor rivers. Phosphorus uptake experiments conducted under realistic environmental conditions with living D. geminata colonies showed no effect of iron enrichment on phosphorus uptake. Iron does not solve the mystery of D. geminata growth causing nuisance blooms worldwide.

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