A paleolimno-metagenomic exploration of Lake Constance sediments : Ancient DNA records of environmental change

During the 20th century, many lakes of the Northern Hemisphere were affected by increasing human population and urbanisation along their shorelines and in their catchment areas, leading to, for example, eutrophication. Ecosystem monitoring commenced only after these changes became apparent, precluding any examination of timing and dynamics of the initial community change and of comparisons of the pre- and post-impact communities. With improving DNA extraction and sequencing methods, historical changes in lake communities can now be examined through DNA of organisms that have been living in the past, which is archived in lake sediments. Peri-Alpine Lake Constance (Germany), which underwent a well-documented, mid-century period of eutrophication followed by re-oligotrophication, and which is now experiencing warmer temperatures, was chosen as a model system in this study. Sediment cores with of up to 73 cm in length, reaching back to the early 18th century, were taken from different basins and sites of Lake Constance and analysed for the deposited sedimentary DNA (sedDNA). I focussed on plankton organisms, such as algae and other protists, cyanobacteria, Fungi and parasitic protists, and on aquatic plants as well as on the terrestrial vegetation along the shorelines and catchment area. This was done by PCR-amplicon sequencing using four genetic markers that reconstructed the aquatic microbial eukaryote (18S rRNA gene fragment), diatom (rbcL fragment), cyanobacteria (cyanobacteria-specific 16S rRNA gene fragment) and plant communities (trnL intron fragment) across the different sediment cores from Upper and Lower Lake Constance. For ecological inferences, the relative read abundances and overall diversity, i.e., alpha and beta diversities, were analysed for each group, and their temporal responses were examined in relation to environmental change, in particular the phosphorus loading of Lake Constance. A general trend reconstructed by the sedDNA-analyses was that a higher alpha diversity was observed in the deeper and, thus, older sediment layers, from where an overall loss of diversity was indicated towards younger sediment layers, independent of the sampling sites. All groups,with exception of diatoms showed an earlier and stronger community shift relative to the strong eutrophication phase of the 1950s: break points with loss of diversity were detected for the microbial eukaryote and cyanobacteria biomarkers as early as in the 1920s and for the terrestrial plant community as early as the 1900s. Diatoms, which are traditionally used as paleolimnologic proxies due to their microfossils, showed the latest response in the sedDNA analyses. In addition, for the 1990s, the microbial eukaryote, cyanobacteria and diatom markers each indicated another break point, towards increasing diversity, which corresponded to the increasing re-oligotrophication of Lake Constance by that time. Accordingly, a strong correlation between the community changes and the phosphorus loading of Lake Constance was indicated for these markers. The different plankton-markers showed furthermore that the overall diversity values after re-oligotrophication reverted to values similar to those of the pre-eutrophic phase, but that their present community composition is significantly different. This suggested that the ecosystem Lake Constance has not reverted back to the initial community, i.e., was not reversible, but that it is changing further. A significant correlation of climate warming with community change in the recent times could be demonstrated for the cyanobacteria and for both terrestrial and aquatic-plants. In addition, analyses show temporal congruency among specific taxonomic groups and interactions between them suggested an increased influence of biotic interactions from the 1970s onwards - independent of the physicochemical-abiotic stressor; however, this needs to be confirmed with further analyses. For the changes of the terrestrial-plant community starting at around 1900, a high correlation with human land-use change and with individual historical events was detected. These included the building of the island Reichenau dam and the subsequent planting of Populus trees, as well as meteorological events such as major flooding and extensive freezing of the lake. In addition, a shift in the plant community towards plants with economic value was detectable. The aquatic plant community for comparison showed a much lower degree of diversity change by sedDNA-analysis. In conclusion, with these studies I successfully analysed sedDNA from physiologically and phylogenetically divergent uni- and multi-cellular organisms from sediment cores taken from multiple sites across Lake Constance. I was able to reconstruct the historical perturbations of these communities on a centennial timescale and thereby their response to natural and anthropogenic changes. The inferences discussed in this thesis not only pave the way to a more comprehensive understanding of the aquatic and terrestrial community dynamics within and around a large and heterogeneous aquatic system such as Lake Constance, but also highlight the potential of using sedDNA metabarcoding for long-term environmental monitoring.publishe