Using sedimentary ancient DNA to assess the historical changes of prokaryotic communities in the Gippsland Lakes

The Gippsland Lakes is the largest estuarine system in Australia. Over the last two centuries, this unique aquatic ecosystem has suffered substantial modifications mostly associated with anthropogenic impacts, including the creation in 1889 of an artificial channel to the ocean after European settlement, creating chronic salinization in the system. However, the biological impacts of this historic shift are unclear. Here, we examined sedimentary ancient DNA (sedaDNA) in historical sediments of Lake King and Lake Victoria to track past ecological changes of prokaryotic microbial communities. Sedimentary prokaryotic communities vertically changed with core depth, nutrient levels, and European settlement, suggesting that some ecological shifts over time were most likely associated with anthropogenic impact. Specifically, we observed an increase of Proteobacteria (e.g., Desulfobacterales), Bathyarchaeota, Thorarchaeota in the sediment cores of the Gippsland Lakes, which could reflect a period of eutrophication caused by higher rates of organic deposition post-European settlement. While these species presented authentic ancient DNA signals, the shifts in the community composition indicated changes in the past community structure related to the drastic changes in lake conditions associated with a reworking of physicochemical conditions at certain depths. Overall, these observations suggest that historic management practices of waterways may influence microbial systems today and that sedimentary microbial communities can change in response to both past environmental conditions and geochemical changes of the sediment during burial.