Pleistocene glacial and interglacial ecosystems inferred from ancient DNA analyses of permafrost sediments from Batagay megaslump, East Siberia

Pronounced glacial and interglacial climate cycles characterised northern ecosystems during the Pleistocene. Our understanding of the resultant community transformations and past ecological interactions strongly depends on the taxa found in fossil assemblages. Here, we present a shotgun metagenomic analysis of ancient sedimentary DNA (sedaDNA) to characterize past ecosystem-wide biotic composition (from viruses to megaherbivores) from the Middle and Late Pleistocene at the Batagay megaslump, east Siberia. The DNA records of past vegetation composition largely agree with pollen data and plant metabarcoding applied to the same samples. Interglacial ecosystems at Batagay attributed to Marine Isotope Stage (MIS) 17 and MIS 7 were characterized by forested vegetation (Pinus, Betula, Alnus) and open grassland. The microbial and fungal communities indicate strong activity related to soil decomposition, especially during the former interval. The local landscape likely featured more open, herb-dominated areas, and the mosaic vegetation supported birds and small omnivorous mammals. Parts of the area were intermittently/partially flooded as suggested by the presence of fish DNA. During MIS 3, the local ecosystems comprised cold-temperate periodically flooded grassland. A diverse megafauna (Mammuthus, Equus, Panthera) coexisted with small mammals(rodents). The MIS 2 ecosystems existed under harsher conditions, as suggested by the presence of cold-adapted herbaceous taxa. Typical Pleistocene megafauna still inhabited the area. The new approach, in which shotgun sequencing is supported by metabarcoding and pollen data, enables to investigate community composition changes and infer trophic interactions and aspects of soil microbial ecology.