Freshwater metagenomes from lakes in Japan

This study describes the microbial communities of four lakes in Japan using high throughput metagenomic sequencing with long- and short read technologies (Oxford Nanopore and Illumina). Water samples were taken from two different depths representing the epi- and hypolimnion (5 m and 50-150 m depending on the depth of the lake) at the deepest part of Lake Biwa, Lake Inawashiro, Lake Chuzenji and Lake Toya. 3-28 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.