From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)

Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This study aims to understand the effect of depth and biotic factors on these communities, to better unravel their origins and to compare their composition with the communities detected in groundwater. To do so, we collected samples from two profiles (~0–50 m) in aquifer sites in the Laurentians (Quebec, Canada), performed DNA extractions and Illumina sequencing. The results suggest that changes in geological material characteristics with depth represent a strong ecological and phylogenetical filter for most archaeal and bacterial communities. Additionally, the vertical movement of water from the surface plays a major role in shallow subsurface microbial assembly processes. Furthermore, biotic interactions between bacteria and eukaryotes were mostly positive which may indicate cooperative or mutualistic potential associations, such as cross-feeding and/or syntrophic relationships in the terrestrial subsurface. Our results also point toward the importance of sampling both the geological formation and groundwater when it comes to studying its overall microbiology.