16S rRNA gene amplicon sequencing of microbial trapping devices (MTDs) in an aquifer in the Ammer floodplain near Tuebingen, Germany.

Microorganisms catalyze the turnover of reactants in the subsurface, determining the fate of major groundwater constituents and contaminants, such as nitrate. Nitrate was injected into a well into an anaerobic aquifer in the Ammer floodplain near Tuebingen, Germany. Microbial trapping devices (MTDs) were installed in a second well 1.6m away from the nitrate injection. The sediment-associated microbial community in the MTDs was monitored by 16S rRNA sequencing over time. Microbial 16S rRNA genes were amplified using primers 515F and 806R targeting the V4 region. Library preparation steps (Nextera, Illumina) and sequencing were performed using Illumina MiSeq sequencing system (Illumina, USA) at the Institute for Medical Microbiology and Hygiene (MGM) of the University of Tuebingen (Germany).