Promethearchaeota Persistence in Marine Sediments Frozen for Over 100 kyr

Promethearchaeota ("Asgard" archaea), abundant throughout Earth's subsurface, may persist in a maintenance state over geological timescales. Testing this hypothesis is challenging due to the impracticality of long-term experiments, yet ancient permafrost provides a natural laboratory. We reconstructed 22 Promethearchaeota MAGs from various classes from > 100 kyr marine permafrost, where brines maintain some liquid water below 0°C through geological time. Promethearchaeota cells appear intact as revealed by catalysed reporter deposition in situ hybridization. Six MAGs from the intracellular DNA fraction are > 7× more abundant, > 70% complete, and their completeness was not improved by exogenous DNA repair enzymes, suggesting that they have maintained high DNA integrity since being frozen. Other Promethearchaeota MAGs have low completeness that increases dramatically after DNA repair, indicating that other cells were highly degraded. The high DNA integrity MAGs share families or genera with non-permafrost Promethearchaeota and share metabolic and DNA/protein repair genes with them. The protein repair genes protein-L-isoaspartyl (D-aspartyl) O-methyltransferase and methionine sulfoxide reductase from Promethearchaeota match those of archaea and bacteria instead of eukaryotes. Therefore, diverse Promethearchaeota clades, seemingly without special genetic adaptations relative to non-permafrost lineages of these clades, survive > 100 kyr in marine permafrost, suggesting that long-term survivability is common in Promethearchaeota.