16S and 18S rRNA amplicon sequencing of coastal microbial communities across the salinity gradient of the Baltic Sea in pelagic, benthic, and biofilm environments

The data was collected within the framework of the BaltVib project to analyze the current pelagic and benthic composition of the microbiological community along the salinity gradient of shallow coastal waters in the Baltic Sea, with a specific focus on Vibrio bacteria both within and outside of eelgrass meadows (Zostera marina). Additional to samples collected for sequencing, physico-chemical environmental parameters, cell counts (flow cytometry), and gene copy numbers of target organisms were quantified. Both prokaryotes and eukaryotes were targeted in the pelagic environment using V3-V4 16S rRNA (NovaSeq and MiSeq) and V4 18S rRNA gene (MiSeq) amplicon gene sequencing, respectively. The prokaryotic communities in sediment and biofilm were sequenced with MiSeq.