Final Activity Report Summary - PAPHOS (Prokaryotic activity and phylogeny of oceanic systems) Prokaryotic plankton is the major drivers of biogeochemical cycles in the ocean. While the abundance and diversity of prokaryotic communities is well-known in surface waters, our knowledge about the bacteria and archaeal communities in the mesopelagic (200-1000 m depth) and bathypelagic (1000 - 5000 m depth) realms of the ocean, comprising about 70% of the ocean's volume, is rather rudimentary. Using fluorescence in situ hybridisation, it has been shown recently that planktonic Archaea, consisting of two major groups, the Crenarcheaota and Euryarchaeota, might account for about one-third of all prokaryotic cells in the global ocean. However, we still do not know the diversity and the functional importance of this archaeal community in deep waters and whether marine Archaea are important players in the biogeochemical cycles of the open ocean system. This project was mainly focused on the characterisation of the functional role and the diversity of microbial communities in meso- and bathypelagic waters of the North Atlantic. The first aim of this study was to examine the variability of bacterial and archaeal assemblages in different water masses of the eastern North Atlantic and to assess the prokaryotic diversity in its meso- and bathypelagic waters.T-RFLP (terminal restriction fragment length polymorphism) and cloning techniques, applied to the 16S rRNA gene, were used to decipher the community composition of bacterial and archaeal assemblages. Within distinct water masses, the composition of bacterial and archaeal communities was largely maintained even over large distances while vertical differences were pronounced. Based on our analyses, we conclude that for deep-water prokaryotic biogeography, the water masses exert more influence on the prokaryotic community composition than simply depth and that there is a pronounced stratification of the prokaryotic communities with distinct subsurface, meso- and bathypelagic clusters over large distances.The second aim of this study was to investigate the ecological significance of the crenarchaeotal nitrification in meso- and bathypelagic waters of the North Atlantic.Quantitative analyses of both archaeal and bacterial amoA genes (gene encoding for the ammonia monoxygenase alpha subunit) were performed to determine the ammonia oxidising bacterial and archaeal diversity in the deep waters of the North Atlantic. The archaeal amoA abundance was about one order of magnitude higher than that of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. The analyses revealed that throughout the North Atlantic, the abundance of archaeal amoA genes decreases drastically from subsurface waters to 4000 m depth and from the subpolar to the equatorial deep waters leading to pronounced vertical and latitudinal gradients in the ratio of archaeal amoA to crenarchaeal 16S rRNA genes. This coincides with an increasing age of these waters masses and concomitantly, a decrease in the ammonia concentrations. Thus, only a minor fraction of the bathypelagic Crenarchaeota is putatively oxidising ammonia as energy source in the temperate and subtropical North Atlantic. This study suggests that, in the North Atlantic, bathypelagic Crenarchaeota are not autotrophic ammonia oxidisers but most likely utilise organic matter, hence live heterotrophically.