Validation and application of fossil DNA as a recorder of past marine ecosystems and environmental conditions

The majority of planktonic species, including those that are informative in the reconstructions of past marine environmental conditions, do not produce diagnostic features (e.g., cysts, spores, or lipid biomarkers) and would therefore escape identification from the fossil record using traditional paleoecological tools (microscopy or lipid biomarker geochemistry). However, several studies have recently demonstrated that fossil DNA of planktonic species can be preserved for thousands of years and can be used for species-specific characterization using molecular biological techniques. The objectives of this thesis were to investigate the potential fate of fossil DNA and to what extent it can be used as a qualitative and quantitative biomarker for paleoecological and paleoenvironmental reconstructions. For this goal, fossil DNA of several groups of planktonic protists was analyzed in various marine settings, and validated by comparing the results to microscopical identification and lipid biomarker analyses. A Holocene sediment core from Ellis Fjord, Antarctica, spanning 2700 years of deposition was used to study taxon-specific variation in the level of preservation of fossil DNA. The results showed that post-depositional fragmentation of DNA was highest for dinoflagellates, followed by diatoms and lowest for phototrophic green sulfur bacteria (GSB) stemming from the ancient sulfidic chemocline. Dinoflagellate cysts were rare in the sediment record and despite an exponential decline in fossil dinoflagellate DNA, paleogenetics was the only approach that revealed an important shift in dinoflagellate communities around 1850 years ago, indicative of colder climate and an increased ice cover. In similar aged anoxic sediments from the much deeper (2000 m) permanently stratified Black Sea, a significant fraction (~30%) of fossil DNA of the calcifying haptophyte Emiliania huxleyi, an important species involved in global oceanic C and N cycling and a source of alkenones as a proxy for past oceanic sea surface temperatures (SST), appeared to escape fragmentation and was relatively well preserved for up to 3600 years. Fossil DNA revealed an absence of additional haptophyte species as sources of fossil alkenones indicating that no species-specific calibration of alkenone-SST is required for at least the last 3600 years. Finally, fossil DNA was studied in up to 124,000-year old eastern Mediterranean sediments to reveal the extent of DNA preservation beyond the Holocene era in organic carbon-rich sapropel layers as compared to the organic carbon-poor oxidized sediments. Despite the observation that a significant amount of plankton DNA could only be recovered from the youngest Holocene sapropel S1 (~5 to 9 kyr BP), the paleogenetics approach recorded a simultaneous community shift of non-fossilized haptophytes and dinoflagellates reflecting the changing hydrological conditions during sapropel formation. In summary, the studies reported in this thesis show that the use of fossil DNA is a promising tool for reconstructing Holocene paleoenvironmental conditions in settings where poor bottom water ventilation resulted in the deposition of organic-rich sediments