Shotgun metagenomic sequencing of Lake Slone sediment.

Lake sediments not only store the long-term ecological information, but are also a source of sedimentary ancient DNA (sedaDNA). Here, by combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedaDNA we were able to paint a comprehensive picture of the fluctuations in trophy and microbial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of Roman and Early Medieval periods, and correlated these to increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply – hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest employment of the fibre count analysis as an additional and independent proxy.