| Summary: | The objectives of this thesis were the establishment of molecular approaches in the diversity investigation of eukaryotic protists in the Southern Ocean and the delivery of a comprehensive and taxon detailed overview of protist assemblages in the Pacific sector of the Southern Ocean, especially in the Amundsen Sea. The molecular approaches used to achieve these goals were automated ribosomal intergenic spacer analysis (ARISA) and 454-pyrosequencing. First, the hypothesis that distinct protist community assemblages characterize large-scale water masses was tested. The composition and biogeography of late summer eukaryotic protist assemblages along a transect from the coast of New Zealand to the eastern Ross Sea was determined. Distinct biogeographic patterns defined by the different oceanic regions were revealed. Different water masses harboured different microbial communities, and environmental gradients limited their dispersal. Picoeukaryotes were of minor importance throughout the investigated transect and were nearly absent south of the Polar Front. Dinoflagellates, Syndiniales, and small stramenopiles dominated the Subantarctic Zone, whereas the importance of diatoms increased southwards, in the Polar Frontal Zone, the Antarctic Zone and the Subpolar Region. South of the Polar Front, haptophytes were the dominating group. Second, the investigation focused on the Amundsen Sea to see if the protist community assemblages vary in different areas of a single large-scale water mass. The composition and structure of late summer eukaryotic protist assemblages along a west-east transect in the Amundsen Sea were analysed. Characteristic communities offshore and inshore were revealed. In general, total chlorophyll a and microeukaryotic contribution were higher in inshore samples. Diatoms were the dominating group across the entire area, at which Eucampia sp. and Pseudo-nitzschia sp. were dominating inshore and Chaetoceros sp. was dominating offshore. At the eastern most station, the assemblage was dominated by ...
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