Freshwater and brackish metagenomes from the Baltic Sea, the Vistula River and Vistula Lagoon in Poland

This study describes the microbial communities of four freshwater or brackish sites at the Baltic coast of Poland using high throughput metagenomic sequencing with long- and short read technologies (Oxford Nanopore and Illumina). Water samples were taken from the surface (0.5-1.5 m depth) of the coastal Baltic Sea in Sopot, Vistula River and two sites at Vistula Lagoon representing freshwater and brackish conditions. 0.4-7 L of water were prefiltered through a plankton net (20 µm) and a 5-µm filter and then filtered onto polysulfone filters with a pore size of 0.22 µm until filters were clogged. DNA was extracted from the 0.22 µm filter (small, planktonic fraction) to obtain genomic DNA of the microbial community.