Prokaryotic assemblages recovered by sedimentary DNA record natural and human-driven disturbances over the past 13 500 years in a cultural landscape.

Bacteria and archaea are under-characterized in palaeoecological studies, despite their ubiquity, high diversity, and tight integration with the abiotic, biotic, and human-influenced environments. The complexity of their assemblages and difficulties in separating living- from paleo-prokaryotes render research challenging. Here we present an ancient metagenomic time-series of prokaryotes from a sediment core of Lake Constance, spanning the last 13 500 years of natural and anthropogenic impact. We mapped DNA to reference genomes and characterised the DNA damage of taxa as collectively increasing with time. By constructing co-abundance networks, we recognize major assemblage groups, containing both dead and living microbes, that show specific dynamics: Short-term and often low-abundance assemblages are linked to the Pleistocene-Holocene transition, floods, and human activities. Noticeably, certain lineages harbouring microbes common in human-impacted environments expanded during the Middle Ages and Modern time. Some abundant taxa associated with various freshwater and soil environments persisted through millennia. By extricating different sources and trajectories of change, we demonstrate the power of prokaryotic sedimentary DNA in revealing nature- and human-caused long-term eco-evolutionary consequences.