16S amplicon sequencing of lake water: Lake Chuzenji epilimnion
To analyze the community structure of planktonic bacteria, 16S rRNA gene amplicon sequencing was performed for the filter samples collected at the epilimnion, metalimnion and hypolimnion of each lake. From the Sterivex filter samples, DNA was extracted us the PowerWater Sterivex DNA Isolation Kit (Qiagen, Hilden, Germany). From the DNA samples, sequencing libraries were prepared according to the Illumina 16S Metagenomic Sequencing Library Preparation protocol and then subjected to Illumina MiSeq sequencing. The resulting reads were processed with QIIME, an open-source bioinformatics platform for microbial community analysis.