Water samples were collected in Fram Strait during the Polarstern cruise PS99.2 (June 24th – July 16th 2016) from Greenland shelf to west coast of Spitsbergen. For assessing bacterial and archaeal community composition 4-8 L of water were filtered with peristaltic pump through successive membrane filters of 5 µm and 0.22 µm. The extracted genomic DNA was isolated and the hypervariable V4-V5 (515F - 926R) region of the 16S rRNA was amplified and sequenced using Illumina MiSeq platform in a 2 × 300 bp paired-end run.