Autecology of crenarchaeotal and bacterial clades in marine sediments and microbial mats

The focus of this thesis was the autecology of the Miscellaneous Crenarchaeotal Group (MCG), a phylum-level clade of Archaea occurring mostly in marine sediments. Sequences of MCG 16S rRNA genes have been retrieved from a wide range of marine and terrestrial habitats, such as deep subsurface sediments, hydrothermal sediments, mud volcanoes, estuaries, hot springs and freshwater lake sediments. MCG members seem to have no general preferences for a particular temperature or salinity. So far, not a single member of the elusive MCG has been cultured. They show a high intragroup diversity with percent identity values of 16S rRNA as low as 77%. Since MCG sequences are frequent in sulfate-methane transition zones (SMTZ) of deep sea subsurface sediments, MCG were assumed to be the dominant archaeal population which might greatly contribute to biogeochemical cycles in the deep biosphere. However, quantitative data on the abundance and activity of MCG are still largely lacking. Therefore, in this doctoral thesis, a polyphasic approach was applied for the quantification and visualization of MCG in marine habitats using different molecular methods such as slot-blot hybridization, quantitative PCR and fluorescence in situ hybridization. MCG-specific oligonucleotide probes and primers were designed and used for the quantification. It was shown that in general the relative abundance of MCG strongly increased with depth. In methane-rich surface sediments MCG abundances were below 3% of total Archaea. In contrast, MCG constituted a major part of the archaeal community with 15-100% in subsurface SMTZ. My results provide the first quantitative data on the high abundance of MCG in deep subsurface sediments and are inline with a major role of MCG in biogeochemical cycling in these habitats. In this thesis, cells of MCG were visualized for the first time by CARD-FISH. The cell shape was coccoid and the cell diameter was 0.4-0.5 µm. Signals were weak, but still clearly detectable with CARD-FISH suggesting that MCG are not only abundant, but also active in subsurface sediments. The single cell identification protocol developed in this doctoral thesis will in the future facilitate further quantitative investigations of the autecology of MCG. Further experiments performed in the course of this doctoral thesis addressed the quantification and visualization of particular bacterial populations such as Chloroflexi and Aquificae in microbial mats and marine sediments.