16S rRNA and ITS amplicon sequencing of four different field sites in the Ammer catchment area near Tuebingen, Germany

Microcosm experiments to determine the impact of glyphosate application on the microbial community structure and abundance of four different agricultural soils from the Ammer valley, Germany with a history of glyphosate application. The aim of the study was to evaluate if glyphosate application caused any changes on the microbial community structure and in case these changes were found, to provide clues on potential glyphosate degraders or glyphosate-susceptible taxa in the soil environment. Pristine or contaminated soil was incubated for 60 days and samples were taken in the beginning (0 days), after 28 days and at the end of the study (60 days). Microbial 16S rRNA genes were amplified using primers 515F and 806R targeting the V4 region, and subsequently library preparation with Nextera 2nd step PCR and sequencing on Illumina MiSeq, v2, 2x250 bp were performed. Fungal ITS regions were amplified using primers ITS1-F and ITS2, and subsequently library preparation with Nextera 2nd step PCR and sequencing on Illumina MiSeq, v3, 2x300 bp were performed.