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Climate warming is proceeding rapidly in the polar regions, posing a threat to ice-dependent ecosystems. Among the most vulnerable are microbial-dominated epishelf lakes, in which surface ice-damming of an embayment causes a freshwater layer to overlie the sea, creating an interface between distinct habitats. We characterized the physicochemical and biotic environment of Milne Fiord epishelf lake (82° N, Canada) in three successive summers (2010–2012), and on one date of profiling (5 July 2011) we collected samples for high through-put amplicon sequencing of variable regions of small subunit rRNA to characterize the microbial community (Eukarya, Bacteria and Archaea). Potentially active water column communities were investigated using reverse-transcribed rRNA, and phytoplankton were further characterized by accessory pigment analysis. Cluster analysis of pigment data showed a demarcation between freshwater and marine communities, which was also evident in the sequence data. The halocline community of Eukarya was more similar to the deeper marine sample than to the freshwater surface community, while the Archaea and Bacteria communities at this interface clustered more with surface communities. In 2012, conductivity-depth profiles indicated shallowing of the freshwater layer and mixing across the halocline, accompanied by lower picocyanobacteria and higher picoeukaryote concentrations. Picocyanobacteria cells were more evenly distributed throughout the water column in 2012, implying partial deep mixing. Several mixotrophic taxa of Eukarya were more abundant in the freshwater layer, where low nutrient concentrations may favor this lifestyle. Unusual features of Milne Fiord microbial communities included benthic taxa not previously reported in marine water columns (notably, the archaeon Halobacteriales), and dominance by taxa that are typically present in sparse concentrations elsewhere; for example, the Chlorophyte group Radicarteria and the betaproteobacterium Rhodoferax. Milne Fiord epishelf lake is the last known lake of this kind remaining in the Arctic, and the fate of this distinct microbial ecosystem may ultimately depend on the stability of the Milne Fiord ice shelf, which has experienced a negative mass balance over the past half century.

Microbial Community Structure and Interannual Change in the Last Epishelf Lake Ecosystem in the North Polar Region