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

The Gippsland Lakes is the largest estuarine system in Australia. Over the last 2 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 arrival, creating chronic salinisation in the system. However, the biological impacts of this historic shift are unclear. Here, we use shotgun metagenomics of environmental DNA from historical sediments of Lake King and Lake Victoria to detect ancient microbial DNA and track past ecological changes in prokaryotic communities. Sedimentary prokaryotic communities changed with core depth, organic matter levels and European arrival. Specifically, we observed an increase in sulfate-reducing bacteria (e.g., Desulfobacterales) and organic matter enrichment in the upper layers of the sediment cores of the Gippsland Lakes, which could reflect a period of eutrophication caused by higher rates of organic deposition and marine intrusion post-European arrival. However, while some species presented authentic ancient DNA signals, the shifts in community composition probably reflect changes in indigenous sediment-dwelling microorganisms in response to geochemical changes of the sediment. Overall, these observations suggest that historic waterway management practices may influence microbial systems today and that sedimentary microbial communities can change in response to both natural biogeochemical dynamics along the depth profile and past environmental conditions.