Ancient marine sediment DNA reveals diatom transition in Antarctica

Abstract

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.

Fig. 1. IODP Exp. 382 Site Map.

Coring sites at which sedaDNA sampling was performed include U1534 (Falkland Plateau), U1536 (Dove Basin) and U1538 (Pirie Basin). Map adapted from IODP and created using ref. .

Fig. 2. Relative eukaryote abundance across all samples using SSU, LSU and SSU + LSU reference databases.

Pie charts were generated based on relative abundances (phylum level) determined after running shotgun data against the SILVA 132 SSU (a), LSU (b), and combined SILVA SSU + LSU (c) databases. Taxa that contributed <1% on average across all samples are summarised as’Other (rare) Eukaryota’. Source data are provided as a Source Data file.

Fig. 3. Relative eukaryote abundance at IODP Exp. 382 Sites U1534, U1536, U1538.

Relative abundance of eukaryotes is shown at phylum-level as derived from sedaDNA at Exp. 382 Sites U1534 (Hole C) (a), U1536 (Hole B) (b) and U1538 (Holes C and D) (c) post combined SSU + LSU alignment. Taxa abundant with at least 1% on average across all samples are shown separately, less abundant taxa are grouped as ‘Eukaryota.rare’. Left axis shows the estimated age (where an age but no bar is shown, no eukaryote reads were identified in that sample). For sample details see Table 1. ML = mudline. The arrow indicates the first sample in which the transition to an increased relative diatom (Bacillariophyta - olive) abundance was detected at Site U1538. Total eukaryote read count: 71,214 reads. Source data are provided as a Source Data file.

Fig. 4. Abundance of photosynthetic organisms at IODP Exp. 382 Sites U1534, U1536, U1538.

Abundance of the psbO gene (read counts) determined at Exp. 382 Sites U1534 (Hole C) (a), U1536 (Hole B) (b) and U1538 (Holes C and D) (c). Left axis shows the age estimate (where an age but no bar is shown, no psbO reads were identified in that sample; for sample details see Table 1). ML = mudline. Figure based on normalised data (subsampled to 1.1Mio reads), total psbO read count: 42 reads. Source data are provided as a Source Data file.

Fig. 5. Relative diatom abundance at IODP Exp. 382 Sites U1534, U1536, U1538.

Relative abundance of diatoms is shown at lowest taxonomic level resolved from sedaDNA at Exp. 382 Sites U1534 (Hole C) (a), U1536 (Hole B) (b) and U1538 (Holes C and D) (c), post combined SSU + LSU alignment. Left axis shows the estimated age (where an age but no bar is shown, no diatom reads were identified in that sample). For sample details, see Table 1. ML = mudline. Arrows indicate the start of increased, consistent presence of C. affinis (14.5 ka) and H. sinensis (12.7 ka) at Site U1538. Total diatom read count: 27,707 reads. Source data are provided as a Source Data file.

Fig. 6. Depth profiles of eukaryote sedaDNA damage and geochemical parameters.

Plotted against depth (metres below seafloor, mbsf) are a the proportion of eukaryote sedaDNA damage (based on SSU + LSU alignments), and all geochemical parameters that showed positive correlations with the proportion of eukaryote sedaDNA damage, including, b ammonia, c alkalinity, d sulfate, e phosphate, f temperature and g silicon. Source data are provided as a Source Data file.