Glimpse of past dynamics: A new set of phytoplankton primers for sedaDNA

Sedimentary ancient DNA (sedaDNA) offers an important opportunity for investigating long-term community dynamics. Nevertheless, sedaDNA is challenging since DNA is degraded and fragmented over time. Of particular interest for such sedaDNA studies are phytoplankton communities, which are sensitive environmental indicators and important producers in aquatic systems. So far, only a few suitable metabarcoding primers for sedaDNA targeting phytoplankton exist. In this study, we introduce new metabarcoding primers targeting cyanobacteria and dinoflagellates. They amplify short, ~200-bp ribosomal 16S and 18S DNA fragments. We compared these primers against published ones, uncovering distinct communities captured by different primer sets. The newly designed dinoflagellate and cyanobacterial primers revealed unique sets of amplicon sequence variants (ASVs) compared to published primers, highlighting the impact of primer choice on describing community composition. We also explored the effect of amplicon length on metabarcoding success over a sample age. Observed trends suggest that amplification success decreases with longer amplicons, probably as a result of DNA degradation in older sediment samples. Lastly, strong DNA preservation challenges emerged in sediment samples older than 7000 BP, corresponding with oxic phases of the Baltic Sea bottom water. This emphasizes the importance of age, sediment type, and preservation conditions when interpreting sedaDNA results. Despite limitations in temporal resolution, the study shows that sedaDNA-based fluctuations in the phytoplankton community are consistent with well-known environmental stages. More research is necessary to understand (1) DNA preservation and its impact on reconstructed communities and (2) impact of abiotic conditions on phytoplankton communities.