Researchers have successfully cultivated two strains of Heimdallarchaeia from gas field biofilm samples, revealing simple internal cellular structures alongside complex surface membrane protrusions. This achievement offers physical specimens to test long-held theories regarding how complex eukaryotic cells originated from ancient microbial partnerships.
Sampling Microorganisms From the Southern Kanto Gas Field
Deep beneath the surface in Chiba Prefecture, Japan, the Southern Kanto gas field holds subsurface gas reservoirs within turbidite sandstones. In an old marine forearc basin, brine erupts from production wells. From a gas production well designated as KTG3, a collaborative research team collected biofilm samples from the wall of a separator discharge outlet positioned twenty to forty centimeters below the water surface. These materials were gathered following brine eruptions on 29 August 2019, 16 July 2020, and 11 May 2023.
Cultivating Heimdallarchaeia Strains in the Laboratory
A collaborative team led by Hiroyuki Imachi and Masaru K. Nobu of the Japan Agency for Marine-Earth Science and Technology, alongside Satoshi Nakagawa of Kyoto University, isolated and cultivated two strains belonging to Heimdallarchaeia. Environmental DNA studies previously indicated that this group sits among the closest known archaeal relatives of eukaryotes, the domain that encompasses plants, fungi, animals, and humans. Although researchers long suspected that these microorganisms might possess complex internal structures or the capacity to process oxygen like modern eukaryotes, because they had never been grown in the laboratory, their cell organization and physiology remained unverified.
This successful isolation follows earlier work from 2020, when the research team cultivated strain MK-D1 from deep-sea sediment, which led them to propose the E3 model for eukaryote origins. Direct examination of the newly grown Heimdallarchaeia strains revealed that their internal organization remains surprisingly basic. The cells lack a nucleus and other membrane-bound organelles, showing that the archaeal ancestor of eukaryotes stayed internally simple.
For scanning electron microscopy analysis, archaeal cells were preserved using 2.5% weight-per-volume glutaraldehyde, incubating under anoxic conditions for two hours at their optimum growth temperatures before spending the night at four degrees Celsius. To acquire wide-area perspectives, researchers stitched one hundred individual frames into a ten-by-ten grid, operating with an acceleration voltage of one kilovolt and a beam current of thirteen picoamperes.
Surface Protrusions and Symbiotic Partnerships Under Oxygen Limits
While the inside of each cultivated cell is uncomplicated, the exterior tells a different story. High-resolution imaging using transmission electron microscopy and quick-freeze deep-etch electron microscopy uncovered complex cell surfaces featuring multiple long, branching membrane protrusions. These structural extensions enable the archaea to attach to neighboring microorganisms, forming direct physical connections that facilitate symbiotic relationships.
Physiological tests showed that both strains are fundamentally oxygen-independent anaerobes.
Implications for the Ancestry of Eukaryotic Cells
The findings support the hypothesis that early partnerships began in low-oxygen environments where an aerobic partner helped an anaerobic archaeon handle oxygen exposure. Over evolutionary time, one such archaeon likely engulfed a bacterium that eventually transformed into the mitochondrion, restructuring cellular metabolism and launching the lineage that became eukaryotic life.