Metagenomic reconstruction of prokaryotes and eukaryotes using shotgun sequenced sedimentary ancient DNA in Upper Lake Constance

Bacteria and archaea are ubiquitous, high in biomass and extremely diverse. Although known to respond actively to environmental changes, their various habitats and assorted assemblages have resulted in the under-characterisation of prokaryotes in paleoecological studies. Here we present a detailed analysis of an ancient prokaryote metagenomic time-series from the sediment of Lake Constance spanning the last 13,500 years. Shotgun-sequenced DNA was taxonomically classified by mapping to over 6700 bacteria and 280 archaea reference species in the curated modern database GTDB. We distinguish different components of sedimentary bacterial assemblages and investigate their respective dynamics: Occurrences of short-term assemblages, which mainly consist of low-abundance taxa, are shown linked to the Pleistocene-Holocene transition, local hydrodynamics, and changes in human-driven landscape and trophic state. These assemblages display high taxonomic diversity. Certain lineages harbouring microbes possibly involved in soil function modulation, nitrogen fixation and pathogenesis, expanded during the Middle Ages known for intensified human impact. Taxa that persisted throughout the Holocene are generally aquatic and abundant in DNA sequences, but many went extinct in the 90s after the lake returned to oligotrophic state after decades of anthropogenic eutrophication. Sediment-dwelling microbes, identified through their lower degree of DNA damage, show several occasions of turnover coinciding with climate- or human-driven changes in sedimentary input. Through combining analyses based on taxonomy, bioinformatic networks and DNA damage, we point to the multiple sources and temporal development of prokaryotes in Earth's subsurface, and consequently, demonstrate their power to disentangle interwoven ecosystem history of various causes, intensity and duration. Complex interactions between humans and the environment led to incessant ecosystem changes in the Holocene. Ancient DNA-based paleoecology is powerful to recover nature's past but dynamics across taxonomic lineages are still inadequately characterised. In this study, we sampled a sediment core from Lake Constance and shotgun-sequenced 34 sedimentary DNA libraries to reconstruct the community (re)assembly processes in the last 13.5 thousand years. Through focusing on organisms showing similar patterns of impact during periods of fast change, we present transformations of communities associated with millennia-scale natural and human-driven environment changes. The Pleistocene-Holocene transition witnessed the disappearance of a diverse, largely herbaceous vegetation and the establishment of other long-persisting and abundant organisms. This process of initial establishment continued for ~3000 years, accompanied by a minor vegetation turnover in the early Holocene. The Mesolithic-to-Neolithic transition at 7500 years BP, ~500 years afterthe Holocene Thermal Maximum, is marked by a quick change in vegetation, and a trend began from the Neolithic Age where the detection of long-term taxa became variable, while new taxa, including plants, animals and pathogens related to human livelihood, were continuously introduced or re-established until the end of the Middle Ages. Overall, the sediment record of Lake Constance since the end of the Pleistocene shows constant changes and a steady increase in alpha diversity that peaked during 2000 to 500 years BP, and a sharp decrease in DNA sequence count since the Middle Ages suggests a biomass decline for both plant and non-plant organisms.