The global climate change has an unprecedented impact on the Arctic Ocean, resulting in warming of the Arctic surface air at much faster rates than the global average. The warming temperatures lead to constantly declining Arctic sea ice cover, which reached in September 2018 the sixth lowest summertime minimum extent in the satellite record (since the late 1970s). Shrinking sea ice has a strong impact on the entire Arctic marine ecosystem, through alterations of the primary production, grazers communities, and subsequently the biological carbon pump. Current predictions of entirely sea-ice free summers in the Arctic Ocean already in the second half of this century urges the need to understand the ongoing oceanographic and biological processes in order to predict how the Arctic ecosystem will respond to further environmental changes. The differentiation between natural temporal ecosystem variability and anthropogenically-induced impact of the climate change requires long-term observations. The Ocean Observing System FRAM (FRontiers in Arctic marine Monitoring), which was established in 2014, is an Arctic long-term observatory for investigating the impact of changing ocean properties and sea ice conditions of the Arctic Ocean on its marine ecosystem. The starting point for the FRAM project was the already existing long-term observatory HAUSGARTEN, situated in the main gateway between the Arctic and the Atlantic Oceans - the Fram Strait. To date, despite their importance for the biogeochemical cycling, very little is known regarding the diversity and function of microbial communities in the Arctic Ocean in general, and specifically in the Fram Strait. In the framework of FRAM, a Molecular Observatory was established, for conducting standardized molecular-based high-resolution observations of the Arctic microbial communities. This thesis was conducted as part of the FRAM Molecular Observatory, and as part of the establishment process of the observatory it contributes to the methodological and procedural standardization required for long-term microbial observations. This thesis provides a first comprehensive overview of currently existing long-term microbial observatories around the world, it provides guidelines for initial steps towards establishing a community network between them, and stresses the urgent need in community efforts towards methods standardization. Furthermore, as part of the methods standardization for long-term microbial observations, this thesis includes a performance comparison between two, broadly used in microbial oceanography, 16S rRNA gene primer sets. The main focus of the thesis is on the ecology of pelagic bacterial and archaeal communities in the Fram Strait. Its overall objective was to investigate the distribution of these communities in the Fram Strait, and to identify environmental drivers of their diversity. The observations of this thesis reveal that sea ice has a strong impact on the development of the seasonal phytoplankton bloom during the summer. As a result, sea ice conditions are affecting the bacterial diversity in surface water, and are leading to a distinct community in sea-ice free and sea-ice covered regions of the Fram Strait. However, the impact of the sea ice is not limited to the surface ocean, as it also heavily affects the vertical export of aggregated organic matter to the deep ocean. The results of this thesis also show that aggregates formed under the sea ice sink faster, and by that provide a stronger vector for transport of bacterial and archaeal taxa to the deep ocean, compared to ice-free waters. Altogether, this thesis contributes to the baseline knowledge needed for further long-term observations of pelagic microbial communities in the Arctic marine ecosystem. Furthermore, it provides an important insight into the strong impact of the sea ice on bacterial and archaeal communities throughout the entire water column, underlining the potential impact of further environmental changes on the Arctic Ocean in the light of prevalent global warming and climate change.