Abstract
Summary The traditional view of carbon cycling within the pelagic zone of freshwater lakes has consisted of methane production within the anoxic sediment, followed by diffusive flux and ebullition through the water column. Methanogenic archaea have been shown to be present within the water columns of freshwater lakes; however, little is known about whether these methanogenic communities are distinct from those in the sediment or how these communities change over space and time. We used the methanogen‐specific phylogenetic marker mcrA to perform a 3‐year study focusing on the community structure of methanogens within the sediment and anoxic hypolimnion water layer of five humic lakes in WI , USA . The hypolimnion and sediment communities were distinct in composition, richness and phylogenetic diversity. Hypolimnion communities displayed a temporally stable biogeographical pattern among lakes, which was driven by both lake‐specific environmental variables and barriers to dispersal. We conclude that the hypolimnion comprised communities of methanogens that are distinct from those in the sediment, differentiated among lakes, and likely have unique ecological roles and evolutionary trajectories in these anaerobic environments.