The terrestrial subsurface harbors unique microbial communities that play important biogeochemical roles and allows studying a yet unknown fraction of the Earth’s biodiversity. The Saint-Leonard cave in Montreal city (Canada) is of glaciotectonic origin. Its speleogenesis traces back to the withdrawal of the Laurentide Ice Sheet, 13 000 years ago, during which the moving glacier dislocated the sedimentary rock layers. Our study is the first to investigate the microbial communities of the cave. By using amplicon sequencing, we analyzed the taxonomic diversity and composition of bacterial, archaeal and eukaryotes communities living in the groundwater (0.1µm- and 0.2µm-filtered water), in the sediments and in surface soils. We identified a microbial biodiversity typical of cave ecosystems. Communities were mainly shaped by habitat type and harbored taxa associated with a wide variety of lifestyles and of metabolic capacities. Although we found evidence of a geochemical connection between the above soils and the cave’s galleries, our results suggest that the community assembly dynamics are driven by habitat selection rather than dispersal. Furthermore, we found that the cave’s groundwater, in addition to being generally richer in microbial taxa than sediments, contained a considerable diversity of ultra-small bacteria and archaea.

Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiome in two distinct aquifers located in the region of Vaudreuil-Soulange (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested low contribution of surface environments to groundwater microbiome except for months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.