Traits enabling persistence of living Promethearchaeota in marine sediments frozen for over 100 kyr

Abstract

The phylum Promethearchaeota (formerly "Asgard" archaea), the microbial progenitors of all Eukaryotes, are abundant throughout Earths subsurface, who have been hypothesized to persist over geological timescales in stable environments with little cell division. We therefore examined the genetic adaptations of Promethearchaeota after being frozen for >100 kyr by comparing metagenome-assembled genomes (MAGs) from the Kolyma Lowland, Siberia, to MAGs from other marine and terrestrial sediments worldwide. We reconstructed 22 Promethearchaeota MAGs from 5 classes (Heimdallarchaeia, Gerdarchaeia, Lokiarchaeia, Helarachaeia and Thorarchaeia). Six MAGs from the intracellular DNA fraction were > 70% complete before and after DNA repair, and therefore likely represent living Promethearchaeota that have maintained high DNA integrity under cryogenic conditions through geological time. These 6 MAGs were also over 7 times more abundant than all other Promethearchaeota MAGs based on read recruitment. These permafrost Promethearchaeota MAGs are closely related to other non-permafrost Promethearchaeota lineages at the family or genus level and share metabolic potential and genes for DNA and protein repair with them. This suggests that the ability to survive for >100 kyr in permafrost is a trait that is widespread within the Promethearchaeota. No genes were more prevalent in our permafrost MAGs compared to Promethearchaeota MAGs from other environments. The lack of detectable genetic change since these groups were frozen is consistent with the predicted state of inactivity. Furthermore, although DNA repair mechanisms were present in the Promethearchaeota/Eukaryote lineage before the eukaryotic split, Promethearchaeota protein repair mechanisms emerged after the split, suggesting that adaptations to long term dormancy, or aeonophily, may set modern Promethearchaeota apart from eukaryotes. Collectively, our study expands the known habitat range of many subgroups of Promethearchaeota to ancient marine permafrost and suggests they may have extraordinary long-term survivability under cryogenic conditions through geological time.