Eco-AlpsWater project: 16S rRNA sequences determined in samples collected in 59 Alpine lakes and rivers

This dataset includes 16S rRNA (V3-V4 region) sequences obtained from HTS analyses of samples collected in 37 lakes and 22 rivers as part of the Interreg Alpine Space Eco-AlpsWater (ASP569) project. Data were collected in 2019 in the pelagic zone (planktic samples, PL) and along the shores (biofilm samples, BFM). 16S rRNA data were analysed with a specific focus on the taxonomic identification of cyanobacteria. In parallel, 18S rRNA gene sequencing was performed on the same set of samples (PRJEB49184).