Environmental selection shapes the formation of groundwater microbiomes

Here we took advantage of the Hainich Critical Zone Exploratory (Germany) which allows disentangling spatial patterns to identify drivers of groundwater microbiome formation and differentiation in oligotrophic carbonate-rock aquifers along a 5.4 km transect. Groundwater samples were collected from groundwater of different depths across two aquifer assemblages on a three-month basis for three years. Based on 16S rRNA gene amplicon sequencing, we show that environment selection drives the spatial assembly of groundwater microbiomes, with dissolved oxygen, ammonia and nitrate as the major determinants.