Sample collection was carried out as part of the ‘multi omic’ approach of the MIMAS (Microbial Interaction in MArine Systems) project (www.mimas-project.de). Surface water was collected on 11 February 2009 and weekly from 31 March 2009 until October 2009. Water samples (total volume 360 l) from the Kabeltonne site at Helgoland Roads in the North Sea (54°11.18′N, 7°54.00′E) were collected at a depth of 0.5 m and processed immediately at the Biological Station Helgoland. The water was pre-filtered through a 10 μm and a 3 µm pore-size filter. For harvesting a 0.2 -μm-pore-size filter was used. At each time point 10 l and 15 l of seawater were filtered onto 8 filters for genomic DNA extraction. All filters were stored at −80°C until future usage. Details can be found in Teeling et al. (22 (link)). In this study, 16S rDNA pyrotag analysis with Roche’s 454 FLX Titanium technology was performed using samples from: 11 February 2009, 7 April 2009 and 14 April 2009. Results from 16S rDNA diversity analysis gained from metagenome studies of the same sampling dates (22 (link)) were used for comparison.