Composition of bacterial and eukaryotic communities in oligotrophic groundwater of the Hainich Critical Zone Exploratory

In this study we investigated the community structure of bacteria and eukaryotes in two superimposed limestone aquifer assemblages in the Hainich region (Thuringia/Germany). Samples were obtained from 10 different wells along a groundwater observation transect with sampling depth ranging from 5 to 88 m depth. Community structure was assessed by amplicon sequencing using Illumina MiSeq, with the primer combination Bakt_0341F/Bakt_0785R for the bacterial 16S rRNA gene and EukA7F/Euk516R for eukaryotic 18S rRNA genes. Sequencing was performed on both the DNA and RNA level for selected groundwater samples and time points. In addition to SSU rRNA genes, we targeted genes encoding for RubisCO form IA (cbbL), form IC (cbbL), and form II (cbbM).