Our Closest Microbial Relatives, Grown in the Laboratory at Last
Every animal, plant and fungus — including every reader of this article — is made of eukaryotic cells: cells with a nucleus and other membrane-bound compartments inside, and, in most cases, mitochondria that were once free-living bacteria. How such complex cells first emerged remains one of the biggest mysteries in biology.
A leading hypothesis is that a complex cell began when an archaeal cell formed a close partnership with a bacterium that eventually became the mitochondrion. The archaea thought to be closest to that ancestor are called Heimdallarchaeia, part of a group called Promethearchaeota. Until now, however, they had never been grown in the laboratory, so ideas about their internal structure and way of life rested on DNA found in the environment, not on direct observation.
That has changed. A collaborative team led by Hiroyuki Imachi and Masaru K. Nobu of the Japan Agency for Marine-Earth Science and Technology (JAMSTEC), including Satoshi Nakagawa of Kyoto University, has for the first time isolated and cultivated two strains of Heimdallarchaeia. Their findings were published in the journal Nature, and reported by Kyoto University on 29 October 2026.
Simple inside, busy on the surface
In 2020, the same JAMSTEC team first cultivated a related organism, strain MK-D1, from deep-sea sediment, and proposed a model, called the E3 model, for the origin of eukaryotes. Later studies of environmental DNA suggested Heimdallarchaeia might already have complex internal structures, or the ability to use oxygen, like eukaryotes. Because they had never been grown in the laboratory, those suggestions remained unverified.
Direct examination gave a different picture. The internal structure of both new strains was simple, lacking membrane-bound organelles such as a nucleus. Instead, the cell surface was complex, extending multiple long, branching membrane protrusions. Those protrusions helped the cells attach to other microorganisms and form symbiotic partnerships.
Both strains were oxygen-independent, meaning they live without oxygen. One had several systems to protect itself from oxygen and could grow even when small amounts of oxygen were initially present, as long as oxygen-utilising bacteria were also present in the culture.
Partnership first, complexity later
The researchers draw three conclusions. First, the archaeal ancestor of eukaryotes may have remained simple on the inside. Second, surface structure-mediated symbiosis is the first biological connection found in archaea between structural complexity and symbiosis. Third, the early partnership may have begun in an environment with low levels of oxygen, with the bacterial partner helping the anaerobic archaea cope with oxygen — until one archaeon eventually took the bacterial ancestor of mitochondria inside its cell, leading to major changes in structure and metabolism and, ultimately, to the ancient eukaryote.
In other words, complexity may not have started with elaborate internal machinery. It may have started at the surface, with reaching out, holding on, and living together. The newly cultivated strains now provide experimental models for testing that idea directly, by studying their cell structures and interactions with microbial partners.
For students, this is a reminder that classification is not just naming things. Archaea, bacteria and eukaryotes are the three great branches of life, and the boundary between the simple and the complex turns out to be a story of partnership — one that scientists could only confirm by growing the organisms and watching them live. Book your first lesson and compare verified biology tutors for help with cells, evolution and GCSE or A-level biology, online, in person or in a group class.
Sources:
- Kyoto University, “Capturing our closest archaeal relatives offers clues to the origin of eukaryotes”, 29 October 2026, reporting Imachi et al., “Eukaryotes’ closest relatives are internally simple syntrophic peptidotrophic archaea”, Nature (2026), DOI: 10.1038/s41586-026-11170-7: https://www.kyoto-u.ac.jp/en/research-news/2026-10-29-2