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An Evaluation of Postdepositional Controls on the Preservation of DNA in Marine Sediments

Timothy Eglinton (Marine Chemistry and geochemistry, WHOI)

Recent studies have demonstrated that preserved DNA suitable for molecular biological analysis can be recovered from anoxic lacustrine and marine sediments. This is an extremely exciting finding because it opens up the possibility for the reconstruction of past water column microbial community structure at the species and even strain level, offering an unprecedented window into past changes in the ocean primary productivity and it link to other factors, notably climate. It also provides an important means to validate and aid in the interpretation the more traditional lipid biomarker-based proxies. However, the extent to which DNA is preserved under different marine settings, the factors that influence the survival of DNA, the fidelity of the resulting sedimentary records, and relationships to lipid-based molecular stratigraphic records, remain largely unknown. These issues must be resolved before paleo-DNA records can be broadly applied in paleoecological and paleoenvironmental studies. In this project, recently funded by NSF-chemical oceanography, we will therefore: (i) analyze the early post-depositional fate of DNA from important phytoplankton members together with their corresponding lipids within laminated sediment from various anoxic marine settings which are of great interest for paleoclimatological studies. (ii) Determine the main sedimentary conditions that are conducive to the long-term preservation of the phytoplankton DNA in these anoxic marine sediments.In order to meet both goals we will undertake the following activities: (a) Perform a quantitative down-core intercomparison between lipids and DNA derived from the same precursor organisms as a measure for the level of preservation between both taxonomic markers during natural depositional conditions. (b) Perform laboratory experiments to study the fate of intracellular DNA (including cysts vs. vegetative cells), DNA associated with cell fragments, and extracellular DNA from different phytoplankton members as well as the fate of their lipid biomarkers under sulfate-reducing, and methanogenic conditions and at different incubation temperatures. (c) Determine adsorption kinetics of DNA on the marine sediment matrices and compare the preservation potential of adsorbed DNA of different phytoplankton classes.

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