Eukaryotes’ closest relatives are internally simple syntrophic peptidotrophic archaea

Abstract Eukaryotes are theorized to have an origin associated with the archaeal phylum Promethearchaeota (formerly Asgard archaea) 1–3 . The first cultured representatives revealed valuable insights 4,5 but are still distantly related to eukaryotes, leaving many unknowns regarding eukaryogenesis. Here we report the isolation of two strains, HC1 and SC1, that belong to the archaeal lineage that branches closest to eukaryotes (Heimdallarchaeia); 6–8 these isolates are members of a pure co-culture and a tri-culture with methanogenic partners. Both are obligately anaerobic, syntrophic, peptide-degrading and mesophilic archaea that produce protrusions and vesicles but lack persistent internal membrane structures, like Promethearchaeales 4,5 . All Promethearchaeota isolates demonstrate behaviour focused on cell construction and membrane structures rather than division, in contrast to typical prokaryotes 9 . Strain HC1 possesses genes associated with aerobic lifestyles (such as cytochrome c oxidase (Cox)) but co-cultures cannot grow under (micro)oxic conditions. Meanwhile, the strain demonstrates growth under microoxic conditions when in the presence of aerobes, suggesting that Cox supports oxygen detoxification rather than respiration. Comparative genomics provides evidence that, like HC1, Cox-possessing Heimdallarchaeia studied to date probably do not respire oxygen. The wide conservation of anaerobiosis, cell structure without persistent intracellular membranes and membrane protrusions across Promethearchaeota suggest that the archaeal ancestor of eukaryotes may have had such physiological features. In this cultivation-informed scenario for eukaryogenesis, the archaea–eukaryote transition would involve a steep transition in cell structure and physiological shift from anaerobiosis to (facultative) aerobiosis 10 , with early interactions between the archaeal host and mitochondrial ancestor probably occurring under low-oxygen conditions and at least partially mediated by oxygen detoxification.