Dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea

Here we report a comprehensive dataset covering spatiotemporal variations in prokaryotic and eukaryotic microbial communities and physicochemical parameters in the Baltic Sea. Within 13-months (Jan 2019-Feb 2020), we took 346 water samples during monthly cruises at 19 stations along the salinity gradient. We performed 16S and 18S DNA metabarcoding and microscopy based counting, and saw that both salinity and season are strongly reflected in the dataset. It provides unique opportunities for both technical and ecological analyses, and is valuable for both environmental monitoring and as a biodiversity reference for future studies, in the context of eutrophication and the prospect of climate change.