Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

Sedimentary ancient DNA (sedaDNA) offers a novel approach to investigating past marine ecosystems-from the smallest bacteria to phytoplankton and their predatorsover geological timescales. Knowledge about such paleo-food webs can provide broad-scale biological context to paleoceanographic and environmental reconstructions. However, the field of marine sedaDNA research is still in its infancy; community reconstructions are complicated by the minuscule amounts of ancient DNA preserved in the sediments. Consequently, the identification of most prokaryotes and eukaryotes in sedaDNA is difficult, and sedaDNA sampling, extraction, and analysis require optimized procedures and rigorous contamination control to ensure that the sedaDNA signal is authentic and not overridden by modern environmental DNA. This article describes some of the latest developments in marine sedaDNA research, including the use of metagenomics to study past marine food webs, and new experimental and computational techniques to maximize taxonomic resolution, particularly that of eukaryotes. An example of bioinformatic techniques designed to increase taxonomic insight is presented, demonstrating the breadth of paleogenetic signals that could be extracted from marine sediments. With ongoing improvements in genetic reference databases, sedaDNA extraction techniques, species-specific enrichment approaches, and computational tools, marine sedaDNA will continue to improve our understanding of how marine ecosystems evolved in concert with changing environmental conditions.