Permafrost microbial communities follow shifts in vegetation, soils, and megafauna extinctions in Late Pleistocene NW North America

Abstract We analyzed the microbial constituent of sedimentary ancient DNA sequence data recovered from subarctic loessal permafrost sediments dating between 30,000 and 4000 years ago. These data were originally studied for paleo‐ecological shifts in plants and animals associated with the Pleistocene–Holocene transition. Here, we explore whether there were changes in microbial communities paralleling the transition from distinctive cold‐adapted Ice Age megafauna and vegetation communities—the mammoth steppe ecosystem—toward the expansion of woody shrubs, extirpation of grazing megaherbivores, and development of the boreal forest. We observe a clear shift in the relative proportions of prokaryotic taxa after ca. 13,300 years ago associated with the collapse of the mammoth steppe. These data are consistent among study sites and between replicates processed with different methodologies (shotgun sequencing and targeted capture), which highlights that the “off‐target” fraction of metagenomic data used to study macro‐ecosystems can also be used to investigate synchronous changes in microbial communities. Functional analyses were performed with SEED and KEGG databases where we observed a shift in methane metabolism pathways after ~13,100 years ago, which suggests that there was a shift in methanogenesis away from animal gut microflora at the end of the Pleistocene. There does not appear to be a significant shift in the overall diversity of microbial communities despite the observed taxonomic and functional changes.