Ancient marine sediment DNA reveals diatom transition in Antarctica
Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.
Polar ecosystems are highly vulnerable to ongoing climate change, and rapidly melting ice-sheets and changes in oceanography and in marine ecosystems are expressed on all levels of the food web1,2,3. Antarctica is arguably the most susceptible polar region to climate, evidenced in the fact that West Antarctica has warmed 2.4 ± 1.2 °C between 1958 and 2010, making it one of the fastest-warming regions globally4. Understanding how Southern Ocean organisms respond to climate variability, including throughout past climate shifts, is thus of key importance to predict how the Antarctic marine ecosystem will evolve in the near future.
Sedimentary ancient DNA (sedaDNA) analysis studies ancient genetic signals preserved in sediments. Because genetic traces of all organisms, fossilising and soft-bodied, can potentially be preserved in sediment records, the analysis of sedaDNA holds enormous potential to go beyond standard environmental proxies and allow reconstruction of entire ecosystems5,6. Yet, the recovery of sedaDNA is complicated, as only trace-amounts of DNA are preserved and they are fragmented and degraded, which makes sedaDNA prone to contamination from modern environmental DNA5,7. Recent improvements in sedaDNA techniques, including in anti-contamination measures during field work, laboratory work, and the use of bioinformatic DNA damage analysis, now permit authentication of sedaDNA detected in sediment samples6,8,9,10,11.
It is yet to be determined, however, how far back in time marine organisms can be detected using sedaDNA tools. So far, the oldest authenticated sedaDNA is from ~400,000-year-old terrestrial (cave) sediments12, and ~650,000-year-old subarctic permafrost deposits13. In polar marine ecosystems, eukaryote sedaDNA has been recovered from up to ~140,000-year-old sediments in the Arctic14,15,16 and <25,000-year-old sediments in the Antarctic7. Deep polar marine environments are ideal locations for sedaDNA research because of favourable DNA preservation14,15. They feature constantly low temperatures (~0 °C) and low oxygen (~5 mL L−1), and UV radiation is absent17,18,19.
In 2019, IODP Expedition 382 ‘Iceberg Alley and Sub-Antarctic Ice and Ocean Dynamics’ set out to investigate the long-term climate and oceanographic history of the Antarctic Ice Sheet (AIS). Five sites (U1534–U1538) were drilled east of the Drake Passage, two shelf sites at 53.2°S, the northern edge of the Scotia Sea (U1534, U1535), and three abyssal/deep sites at 57.4°–59.4°S in the Scotia Sea (U1536, U1537, U1538) (Fig. 1). Continuously deposited late Neogene sediments were recovered, which form the basis for ongoing investigations into reconstructing AIS mass loss and associated changes in oceanic and atmospheric circulation20,21,22,23.