The samples were taken from oxygen stratified lake Alinen Mustajarvi in the beginning of September 2013. The lake was sampled at 13 depths with a 20-cm-long acrylic tube sampler (Limnos vol. 1.1 L). About 500 ml of lake water was filtered through 0.2 um polycarbonate filters, which were frozen in -78 C until further analysis. The DNA was extracted from the filters using Mobio PowerSoil DNA extraction kit (MO BIO Laboratories). Shot gun metagenomic libraries were prepared from 10 ng of genomic DNA. First, the genomic DNA was sheared using a focused-ultrasonicator (Covaris E220) and subsequently, sequencing libraries were prepared with the Thruplex FD Prep kit from Rubicon Genomics according to the manufactures protocol (R40048-08, QAM-094-002). Library size selection was made with AMPure XP beads (Beckman Coulter) in 1:1 ratio. The prepared sample libraries were quantified using KAPA Biosystem's next-generation sequencing library qPCR kit and run on a StepOnePlus (Life Technologies) real-time PCR instrument. The quantified libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform with a TruSeq paired-end cluster kit, v3, and Illumina's cBot instrument to generate a clustered flowcell for sequencing. Sequencing of the flow cell was performed on the Illumina HiSeq2500 sequencer using Illumina TruSeq SBS sequencing kits, v3, following a 2x100 indexed high-output run protocol.