Thiosulfate- and hydrogen-driven autotrophic denitrification by a model consortium enriched from groundwater of an oligotrophic limestone aquifer

In this study we investigated the community structure of nirS-type denitrifying bacteria in two superimposed limestone aquifer assemblages in the Hainich Critical Zone Exploratory (Thuringia/Germany). Samples were obtained from 4 different wells along a groundwater observation transect with sampling depth ranging from 12 to 88 m depth. Community structure was assessed by amplicon sequencing of nirS genes using the Illumina MiSeq platform. Sequence analysis was performed for five different time points (July 2014, January 2015, March 2015, June 2015, August 2015). In addition, we enriched chemolithoautotrophic denitrifiers from groundwater and followed changes in the structure of the enriched consortium during two microcosm experiments. Community structure was assessed by MiSeq Illumina amplicon sequencing of bacterial 16S rRNA genes targeting the V3-V5 region.