First cultures show the closest known archaeal relatives of complex cells are simple inside

Researchers led by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) have isolated and grown two strains of Heimdallarchaeia for the first time. They are considered the closest known archaeal relatives of eukaryotes, the branch of life that includes animals, plants and fungi, and studies of environmental DNA suggest that eukaryotes arose from within the group. A 2023 genome analysis in Nature, for example, placed eukaryotes as a sister lineage to Hodarchaeales, an order inside Heimdallarchaeia. That placement is still debated: a 2025 study in Nature, based on 223 newly assembled Asgard genomes, concluded that eukaryotes branched off before the sampled Heimdallarchaeia lineages diversified, not from within Hodarchaeales. The new study, led by Hiroyuki Imachi and Masaru K. Nobu, was published in Nature on October 28, 2026.

The cells turned out to be simple inside. Neither strain has a nucleus or any other membrane-bound organelle, the internal structures that set eukaryotic cells apart. Their surfaces are complex instead: both build long, branching membrane protrusions and release vesicles, and the protrusions attach them to the methane-producing microbes they need in order to grow.

Three years from a gas well

The source was a biofilm on the wall of KTG3, a gas production well in the Minami-Kanto gas field on the Boso Peninsula in Chiba Prefecture, according to JAMSTEC's Japanese-language release. The well intermittently spouts oxygen-free ancient seawater containing methane, so the biofilm is exposed to air from time to time. After about three months in filtered well water with added methane, archaea of the wider group made up about 0.3% of the culture. Leaving traces of oxygen in the medium raised the share of Heimdallarchaeia to 1.8%.

About three years after the first sampling, the team had a pure co-culture of one strain and a single partner, a methane-producing archaeon of the genus Methanocalculus. They named the strain Margulisarchaeum peptidiphilum HC1, after Lynn Margulis, who proposed the endosymbiotic theory, and for its preference for proteins. A second species, strain SC1, was isolated the same way, with methane-producing partners. The cells are spheres, about 1.3 micrometers across for HC1 and 0.9 for SC1.

Oxygen as a hazard, not a fuel

Some researchers had proposed that Heimdallarchaeia might already have complex internal structures or the ability to breathe oxygen, as most eukaryotes do. Both strains proved to be anaerobes that live on proteins and pass the hydrogen or formate they produce to their methane-making partners. HC1 carries genes for cytochrome oxidases, enzymes known from oxygen respiration, but not a complete electron transport chain. It could not grow when traces of oxygen were left in its medium unless oxygen-consuming bacteria were also present, which suggests the enzymes protect it from oxygen rather than let it use oxygen for energy.

Genome comparisons point the same way. Heimdallarchaeia with such genes studied so far probably do not respire oxygen, the authors write, and JAMSTEC says a new genome-based test indicates that members of the wider phylum, Promethearchaeota (formerly called Asgard archaea), all rely on anaerobic metabolism. The analysis also indicates that these archaea cannot make about half of the amino acids they need, a pattern JAMSTEC compares to the essential amino acids that humans and many other eukaryotes must get from food.

A simple ancestor, then a merger

In a leading hypothesis, the first eukaryote formed when an archaeon from this phylum teamed up with a bacterium, which over time turned into the mitochondrion. The new cultures point to an archaeal partner that was still simple inside, with its internal complexity arising only after the merger, a scenario JAMSTEC says its results strongly support. The oxygen findings suggest the partnership may have started in low-oxygen surroundings, where oxygen-consuming partners may have protected the oxygen-sensitive archaeon.

The same researchers needed 12 years to grow MK-D1, the first cultured member of the phylum, which they reported in 2020. JAMSTEC says the new strains are easier to handle than earlier cultures such as MK-D1. Next, the team plans to study how the protrusions and vesicles form and what they do, and how the partnerships with other microbes are established and maintained.