Sources and transport pathways of plant DNA in lake sediments: Lessons from an annually resolved record

The analysis of environmental DNA (eDNA) from sediments has become an important method to study past ecosystem dynamics, offering new perspectives for paleoecological research. Yet, the temporal and spatial variability in DNA sources and transport pathways to the sediment remain underexplored. We studied how the plant DNA signal varies between annual lamina (or varves) in the sediment from Nylandssjön, a small boreal lake in northern Sweden, between 1991 and 2020. During this time period the vegetation community composition in the catchment was stable without any known drastic changes between years. Hence, observed differences in the eDNA signal between varves (years) will be related to differences in DNA transport and preservation.

We find that the overall vegetation community structure is similar between varves (years), emphasizing the robustness of eDNA for whole-ecosystem analyses. However, both the number of taxa and genera varies considerably between varves, suggesting that there is significant between-year difference in the source area, transport, and/or preservation of DNA in the sediment. This implies that records of individual taxa – particularly more rare taxa – need to be interpreted with caution. Interestingly, some individual taxa have strong between-varve (year) fluctuations in absolute reads, suggesting differences in the transport and deposition of plant fragments could play an important role in forming the DNA signal. Our results highlight that we need a better understanding of the variability in transport pathways and deposition of DNA from the lake catchment to the sediments in order to reliably interpret eDNA signals in sediment records.