The candidate phyla radiation (CPR) is a diverse group of uncultured bacterial lineages with poorly understood metabolic functions. CPR bacteria can represent a large proportion of the total planktonic microbial community in subarctic thermokarst lakes, but their functional roles remain unexplored. We applied sequential water filtration and metagenomic shotgun sequencing to a peatland permafrost thaw lake, and found high proportions of CPR bacteria in both summer and winter (> 40% of 16S rRNA reads in the 0.02–0.22 μm pore‐size fraction). The metagenome‐assembled genomes of CPR bacteria representatives showed capacities to degrade and ferment permafrost‐ and peatland‐derived organic matter. Potential products of their metabolic activities included acetate, CO2, and hydrogen, implying a syntrophic relationship with other community members, including methanogens and methanotrophs. The results indicate biogeochemical interdependencies in organic matter utilization within thermokarst microbial communities, with CPR members playing a key intermediate role in carbon and methane cycling.

Permafrost thaw lakes including thermokarst lakes and ponds are ubiquitous features of Subarctic and Arctic landscapes and are hotspots of microbial activity. Input of terrestrial organic matter into the planktonic microbial loop of these lakes may greatly amplify global greenhouse gas emissions. This microbial loop, dominated in the summer by aerobic microorganisms including phototrophs, is radically different in the winter, when metabolic processes shift to the anaerobic degradation of organic matter. Little is known about the viruses that infect these microbes, despite evidence that viruses can control microbial populations and influence biogeochemical cycling in other systems. Here, we present the results of a metagenomics-based study of viruses in the larger than 0.22 µm fraction across two seasons (summer and winter) in a permafrost thaw lake in Subarctic Canada. We uncovered 351 viral populations (vOTUs) in the surface waters of this lake, with diversity significantly greater during the summer. We also identified and characterized several phage genomes and prophages, which were mostly present in the summer. Finally, we compared the viral community of this waterbody to other habitats and found unexpected similarities with distant bog lakes in North America.

Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the “top down” forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.

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