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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.

Human activities and climate change threaten coldwater organisms in freshwater ecosystems by causing rivers and streams to warm, increasing the intensity and frequency of warm temperature events, and reducing thermal heterogeneity. Cold‐water refuges are discrete patches of relatively cool water that are used by coldwater organisms for thermal relief and short‐term survival. Globally, cohesive management approaches are needed that consider interlinked physical, biological, and social factors of cold‐water refuges. We review current understanding of cold‐water refuges, identify gaps between science and management, and evaluate policies aimed at protecting thermally sensitive species. Existing policies include designating cold‐water habitats, restricting fishing during warm periods, and implementing threshold temperature standards or guidelines. However, these policies are rare and uncoordinated across spatial scales and often do not consider input from Indigenous peoples. We propose that cold‐water refuges be managed as distinct operational landscape units, which provide a social and ecological context that is relevant at the watershed scale. These operational landscape units provide the foundation for an integrated framework that links science and management by (1) mapping and characterizing cold‐water refuges to prioritize management and conservation actions, (2) leveraging existing and new policies, (3) improving coordination across jurisdictions, and (4) implementing adaptive management practices across scales. Our findings show that while there are many opportunities for scientific advancement, the current state of the sciences is sufficient to inform policy and management. Our proposed framework provides a path forward for managing and protecting cold‐water refuges using existing and new policies to protect coldwater organisms in the face of global change.

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Since 2006, the Restigouche River watershed, eastern Canada, has been affected by nuisance growths of the mat‐forming diatom, Didymosphenia geminata. In 2010, in view of the potential impacts of this alga on the local Atlantic salmon fishery, we created a volunteer monitoring network to assess D. geminata mat severity within the watershed. Over the course of 6 monitoring summers, more than 1,200 observations of D. geminata mat severity were reported in 20 subwatersheds of the Restigouche River basin. Observations were mapped to illustrate the yearly severity of D. geminata mats throughout the watershed. Metrics were then extracted from this dataset to assess the spatial and temporal variability of mat severity. At the reach scale, D. geminata occurrence was predominantly found in riffles compared to any other river habitat type. At the watershed scale, a two‐sample Kolmogorov–Smirnov test highlighted a significant effect of maximum spring discharge on mean annual D. geminata mat severity, indicating that when maximum spring discharge is high, severity of D. geminata mats in the following months is significantly lower. Additionally, maximum spring discharge explained 71% of the variability in annual mat severity. This study contributes to the understanding of mat severity dynamics and illustrates the value of volunteer monitoring networks for studying complex ecosystem dynamics.

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