Spatial and temporal dynamics of thaumarchaeota in deep European lakes

In past decades the focus of research on archaea has changed from studies solely in extreme environments to a variety of moderate ecosystems, mainly marine and terrestrial. The work in this thesis aims to elucidate archaeal ecology in deep freshwater lakes, thereby enhancing knowledge on the archaeal and bacterial contribution to biogeochemical cycling of nitrogen, i.e. aerobic ammonium oxidation in these lakes. A properly functioning nitrogen cycle is part of a healthy lake ecosystem, preventing eutrophication. Understanding the way in which different organisms convert nitrogen compounds helps to describe how a lake ecosystem functions. Freshwater habitats are described to play a major role in the conversion of reactive nitrogen compounds to gaseous products before they reach the ocean. However, Thaumarchaeota, which are suggested to play an important role in nitrification, are scarcely studied in lacustrine settings. We found Archaea to be present in 29 European lakes at all water depths, forming lake specific community compositions. In a vertical and seasonal study of oliogotrophic Lake Lucerne we found that Archaea are well represented (average 6 x 10 4 cells/ml) and belong to the phylum Thaumarchaeota. Bacterial nitrifiers lag behind in both the presence of amoA genes and gene transcripts, suggesting an active and influencing role of freshwater thaumarchaeota in nitrification in this environment. Different populations and smaller numbers of thaumarchaeota thrive at surface water compared to deeper waters. No correlation was found between ammonium oxidizing archaea (AOA) or bacteria (AOB) and the prevailing ammonium concentrations, which were near detection level. At the surface water, a correlation was found between AOA gene and gene transcript numbers, nitrate concentrations and numbers of mixotrophic algae. In conclusion, Archaea thrive in freshwater lakes and thaumarchaeota show a niche separation in surface and deeper waters and are likely active in nitrification, as the amoA gene transcripts are abundant and ammonium, though low in concentration, can be available locally through an intensified cycling of nitrogen