design: RNA was extracted from 2 g sediment of each sample using Qiagens RNeasy PowerSoil Total RNA kit following the manufacturers guidelines. RNA concentrations were measured using a Nanodrop2000 (Thermo Fisher Scientific, Germany) and RNA integrity was assessed on an Agilent Bioanalyzer 2100 system. Around 2 g of total RNA of each sample were used as starting material for the gene expression profiling. To enrich messenger RNA in prokaryotic samples, an rRNA depletion was performed using the NEBNext rRNA Depletion Kit for Bacteria following the manufacturers instructions. Afterwards, the NEBNext Ultra II Directional RNA library Kit was used for sequencing library preparation. Quality checked libraries were then sequenced on an Illumina NextSeq 2000 machine, generating 2x150 nt reads.