Microbial diversity in European alpine permafrost and active layers

TLDR

Permafrost is a largely understudied genetic resource, and its thawing under global warming is expected to accelerate microbial carbon turnover and reveal unknown microbial diversity, yet temperate mountain permafrost remains poorly explored compared to polar regions. We used a unique experimental design with high‑throughput ribosomal marker sequencing to characterize the microbiota at the long‑term alpine permafrost site Muot‑da‑Barba‑Peider in eastern Switzerland, approximately 12,000 years old. The permafrost microbiota was more diverse than that of active layers, enriched in Patescibacteria, yeasts, and lichenized fungi with streamlined genomes and anaerobic fermentative traits, offering an unprecedented view of temperate mountain permafrost microbial life and informing future ecological trajectories under warming.

Abstract

Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world.