Bacterial diversity in carbonate rock aquifers of the Hainich Critical Zone Exploratory

In this study we investigated the community structure of groundwater bacteria in two superimposed limestone aquifer assemblages in the Hainich Critical Zone Exploratory (Thuringia/Germany). Samples were obtained from 8 different wells along a groundwater observation transect with sampling depth ranging from 12 to 88 m depth. Community structure was assessed by amplicon sequencing using the Illumina MiSeq platform, targeting the V3-V5 region of the bacterial 16S rRNA gene. Sequence analysis was performed for three different time points (August 2014, August 2015, November 2015). In addition, we analysed the community structure of nirS-type denitrifiers in the same groundwater samples obtained in August 2014 targeting nirS genes by Illumina MiSeq.