Enhanced sedimentary ancient DNA (sedaDNA) retrieval from Antarctic diatoms

Diatom microfossils are key environmental indicators and an important proxy in paleoenvironmental reconstructions. Sedimentary ancient DNA (sedaDNA) complements microfossil analysis by detecting poorly preserved diatoms and distinguishing morphologically similar taxa, painting a more detailed picture of the past. However, retrieving diatom sedaDNA in marine environments can be challenging due to trace amounts being preserved in the sediment record. Optimising existing protocols is thus essential to maximise diatom sedaDNA yield. This study compares six methods to determine the best approach for recovering diatom sedaDNA from Antarctic marine sediment cores. The same six samples from two sites - U1536C (West Antarctica) and KC02 (East Antarctica), were extracted. Post shotgun sequencing, the methods were evaluated based on diatom sedaDNA recovery, fragment length, and species diversity. Results showed that method performance in retrieving the highest number of Bacillariophyta (diatom) reads is primarily driven by site (R² = 0.593, p = 0.001) and sample age (R² = 0.401, p = 0.001), while the extraction method had minimal influence (R² = 0.001, p = 0.064). The SiMAG method proved highly effective in U1536C but was entirely ineffective in KC02, where the COM Short method successfully recovered diatom sedaDNA. Other methods, including COM QG, PPKIT, and PB, consistently resulted in low sedaDNA yields. Differences in the diversity and the relative abundance of taxonomic classes were also seen across methods (χ2 88.04 to 99,664.17). This study serves as a focal point for experiments aiming to maximise diatom sedaDNA recovery enabling accurate reconstructions of Antarctic marine ecosystems.