Physical characteristics and chemical measurements of northern lakes in western Canada

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.