In summer 2012 the Arctic sea-ice extent declined to a record minimum. The observed rapid sea-ice melt resulted in the sinking and widespread deposition of fresh ice algal aggregates of the centric diatom Melosira arctica to the deep-sea floor (Boetius et al. 2013, Science 339: 1430). Elevated rates of oxygen consumption were measured in sediments with algal deposits to depths of 4400m, indicating remineralization by bacteria, and evidencing a response of the entire ecosystem down to the deep sea to elevated carbon flux rates. Microbial communities play an essential role in carbon and nutrient cycling not only at the seafloor but also in the sea ice and in the water column, contributing significantly to Arctic ecosystem functioning. Although warming and its associated physical changes in the Arctic will also affect bacterial communities, we still lack baseline information regarding their community composition in different Arctic environments. In this study, we sampled a wide range of Arctic environments from the surface to the deep sea during RV Polarstern expedition ARK XXVII-3 to the Central Arctic in summer 2012, in order to compare bacterial communities from sea ice, melt ponds, surface seawater, deep-sea sediment with and without algal aggregates. Analyses included molecular fingerprinting and next generation sequencing to test for differences in bacterial community structures and to identify the most abundant bacterial groups in each environment. Although certain bacterial classes (Flavobacteria, Gammaproteobacteria, Verrucomicrobia) were identified as pre-dominant community members across different environments, the structure and composition of bacterial communities showed strong environmental specificity, with distinct differences between surface and deep-sea environments. Furthermore, differences were detected between multi-year ice and first-year ice, with specific bacterial taxa only being present in multi-year ice, e.g. Verrucomicrobia, possibly entailing implications for the ongoing decline of multi-year ice in the Arctic. The detection and relatively high contribution of ice-associated genera in algal aggregates found both in melt ponds and at the seafloor, indicated a transport of surface-derived bacterial cells to the deep sea with the rapidly deposited aggregates. With the continuing thinning and retreat of Arctic sea ice during summers, export events as observed in 2012 may repeat and cause shifts in bacterial community diversity and functioning in the future.