An international research team led from Uppsala University in Sweden has identified a metabolic shift in ancient microbes that helps explain how Earth’s first complex cells arose from a merger of simpler organisms. The study, published in Nature, assembled hundreds of new genomes from Asgard archaea, the closest known relatives of all complex life, and found that their descendants adapted to use oxygen in ways that would have made the original fusion event possible. Drawing on a large international collaboration described in a recent news release, the authors argue that this shift in energy metabolism created the ecological conditions for an archaeal host cell to partner with, and eventually internalize, an oxygen‑using bacterium. The findings fill a long-standing gap in understanding how single-celled organisms gave rise to the plants, animals, and fungi that populate the planet today.
A Massive Genomic Haul From Coastal Mud
For roughly two billion years, life on Earth consisted of nothing but single cells similar to modern bacteria. Then something changed. A simple archaeal cell somehow absorbed a bacterium, and that captured microbe eventually became the mitochondrion, the energy-producing organelle inside every human, animal, and plant cell. Pinpointing how that partnership started has been one of biology’s hardest puzzles, in part because the organisms involved left no fossils. The new study attacks the problem with data: the team sifted through 15 terabytes of environmental DNA and assembled more than 13,000 microbial genomes, including hundreds of new Asgard archaea, as detailed in the primary genomic analysis of these deep-branching lineages.
Among those, the researchers report 404 new Asgardarchaeota metagenome-assembled genomes, 136 of which belong to the class Heimdallarchaeia, the group most closely related to eukaryotes. Sediment samples came from sites around the world, including variably oxygenated coastal deposits in the Bohai Sea cataloged under the PRJNA743900 project. A clear pattern emerged from the global dataset: Asgard archaea are especially abundant in coastal sediments where oxygen levels fluctuate with tides, storms, and seasons. That distribution turns out to be a critical clue, because it suggests these microbes were routinely exposed to changing redox conditions and may have evolved unusually flexible metabolisms as a result.
Oxygen as the Missing Link
Archaea are typically methane-producing microbes that thrive without oxygen, yet the new genomic reconstructions show that many Asgard lineages broke from that pattern and acquired the ability to metabolize oxygen or at least detoxify it. Enzymes involved in aerobic respiration and oxidative stress defense appear repeatedly in the reconstructed genomes, implying that the ancestors of modern Asgard archaea were already experimenting with oxygen-based energy pathways. This metabolic flexibility matters because the bacterium that became the mitochondrion was an oxygen-breathing organism. For the two cells to live together, the archaeal host needed to tolerate, and eventually benefit from, the oxygen its partner consumed, a scenario the Uppsala-led authors emphasize in their overview of the work.
Molecular clock analyses of ancient gene duplications place the arrival of the mitochondrial endosymbiont shortly after the Great Oxidation Event, the period roughly 2.4 billion years ago when photosynthetic bacteria flooded Earth’s atmosphere with oxygen for the first time. By comparing rates of sequence change across conserved genes, the team infers that the archaeal host lineage was already present in shallow marine settings when oxygen began to accumulate, and that the acquisition of bacterial partners followed not long after. That timing aligns with independent clock-based estimates of early eukaryote diversification reported in a complementary chronological study, which also suggests multiple bursts of complex-cell evolution rather than a single clean split. Together, these lines of evidence support a picture in which oxygen was not merely a background condition but an active driver of the symbiosis that produced mitochondria.
Tentacles, Cytoskeletons, and the Entangle Model
Genomic data alone cannot show how one cell physically swallowed another. But laboratory work on living Asgard archaea has started to fill in the mechanics. A landmark cultivation effort succeeded in growing a member of the Lokiarchaeota group in the lab, revealing small, slow-growing cells that extend long, branching protrusions into their surroundings. Reporting on that work, observers noted that these tentacle-like extensions, together with the cells’ close association with bacterial partners, make Asgard archaea compelling candidates for the kind of physical interactions needed to capture a symbiont, an idea highlighted in coverage of early insights into complex life. More recently, cryo-electron tomography of a cultured Asgard archaeon revealed an elaborate actin-based cytoskeleton dubbed Lokiactin, complete with extensive protrusions that could facilitate close contact with neighboring cells.
When researchers first cultured an Asgard archaeon in co-culture with bacterial partners, they proposed a three-step model for how the merger could have worked: entangle, engulf, endogenize. In this scenario, the archaeal cell would initially wrap its protrusions around a bacterium, creating a stable physical association without full engulfment. Over evolutionary time, membrane remodeling and cytoskeletal innovations would allow the host to draw the bacterium inward, eventually enclosing it completely. The final step, endogenization, would involve transferring genes between the partners and integrating the bacterium’s metabolism into the host’s energy network, turning a once-independent microbe into a true organelle. The new oxygen-metabolism data strengthen this “entangle” model by showing that Asgard archaea living in fluctuating oxygen zones were already biochemically compatible with aerobic bacteria, making a long-term, intimate partnership far more plausible than if the host had been strictly anaerobic.
Where Eukaryotes Sit on the Tree of Life
The question of exactly where complex cells branch off from Asgard archaea remains actively contested. One phylogenomic analysis placed eukaryotes as a nested group within Asgard archaea, specifically as a sister to a newly proposed order called Hodarchaeales within Heimdallarchaeia, based on shared sets of informational genes and conserved protein families. That study also reconstructed the common ancestor as a heat-loving organism that gradually shifted toward cooler, moderate environments as it diversified, consistent with the idea that early complex-cell evolution played out in dynamic, shallow marine habitats rather than in the deep sea. A competing analysis, drawing on 223 nearly complete Asgard genomes and using alternative models of sequence evolution, argues instead that eukaryotes split off before the sampled Heimdallarchaeia diversified, placing the branch point deeper in the Asgard tree and implying a more ancient divergence between the host lineage and its closest archaeal cousins.
Part of the disagreement traces to chimeric genome assemblies and the difficulty of reconstructing clean evolutionary signals from environmental DNA, where fragments from different organisms can be inadvertently combined. The Uppsala-led team sought to minimize such problems by applying stringent quality filters, manually curating key genomes, and cross-checking their trees against independent gene sets. Even so, they acknowledge that the precise position of the eukaryotic root within Asgard remains provisional, and that future single-cell genomes or new cultured representatives could shift the picture again. What most researchers now accept, however, is that eukaryotes emerged from within a broader archaeal radiation rather than as a separate “third domain,” and that metabolic innovations around oxygen use were central to that transition.
A Long Prehistory of Microbial Innovation
The new work also fits into a longer narrative about how early life coped with changing planetary conditions. Geological evidence from ancient rock formations suggests that microbial ecosystems were thriving on Earth at least 3.2 billion years ago, long before oxygen became abundant. Analyses of these rocks indicate that early life could have colonized both marine and terrestrial settings under low-oxygen atmospheres, hinting at a diverse biosphere that predated the rise of complex cells by more than a billion years, as emphasized in studies of ancient microbial habitats. Against that backdrop, the Asgard archaea represent not the origin of life itself but a late, pivotal experiment in cellular complexity that capitalized on the new energy opportunities created by oxygenic photosynthesis.
By tying together environmental genomics, molecular clocks, and cell-biological observations, the Uppsala-led study offers a more coherent story of how that experiment unfolded. Asgard archaea living in patchy, oxygenated coastal sediments evolved flexible metabolisms and unusual cell shapes, setting the stage for an intimate partnership with aerobic bacteria. Over time, that partnership deepened into the endosymbiosis that produced mitochondria and, ultimately, the eukaryotic cell. While many details remain under debate, from the exact branching order of Asgard lineages to the mechanics of engulfment—the emerging picture is that complex life did not arise from a single leap but from a series of incremental innovations in some of the planet’s most unassuming microbes.
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*This article was researched with the help of AI, with human editors creating the final content.
