Northern lakes disproportionately influence the global carbon cycle and may do so more in the future depending on how their microbial communities respond to climate warming.  Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada.  We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost thaw and subsequent changes in groundwater connectivity, interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects.  Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity.  Finally, we found an increase in sugar utilisation genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.

This table contains seasonal and daily field and laboratory data for samples collected from 19 lakes in Alberta and the Northwest Territories between 2018 and 2019. General information includes lake name, permafrost region, location coordinates, size and depth. Meteorological information includes mean annual precipitation, mean annual air temperature, precipitation and pressure. Chemical measurements are the average of measurements taken over the entire 2018–19 sampling period. Daily measurements for specific conductivity (COND) are also reported. Chemical parameters measured were: water temperature, dissolved oxygen, specific conductivity, pH, dissolved organic carbon, total nitrogen, ions (Na, Mg, K, Ca, Mn, Fe, Cu, Zn, P, S, NH₄, NO₃ Cl, PO₄, SO₄), chlorophyll A. Further information regarding units and descriptions of each parameter can be found under the “Sample Information” tab in the spreadsheet.