Hidden within ancient microbial structures, scientists have uncovered a partnership that may mirror one of life’s most transformative moments, the emergence of complex cells.

Stromatolites may look like unremarkable, dark rock formations, but they are anything but lifeless. These structures, along with similar microbial mats, are built by layers of microorganisms that have been shaping Earth’s surface for billions of years.

Long before forests, animals, or even simple multicellular organisms appeared, these microbial communities were already transforming the planet. By producing oxygen through photosynthesis, stromatolites helped turn Earth’s atmosphere into one capable of supporting complex life. Now, new research suggests they may also preserve clues about how that complexity first arose.

Associate Professor Brendan Burns, an evolutionary microbiologist at UNSW Sydney, is part of a research team that discovered a previously unknown microbe living in close association with another organism inside these so-called “living fossils.”

The study, conducted with scientists from the University of Technology Sydney and The University of Melbourne, could shed light on one of biology’s biggest questions: how simple cells joined together to form more complex life.

“Stromatolites could be more than ‘just’ a cradle of life where early microbial life flourished,” says A/Prof. Burns. “They could also tell us how complex life first emerged.”

The ‘microbial village that helped raise a eukaryote’

Although stromatolites first appeared billions of years ago, they are still forming today in Shark Bay, a World Heritage-listed site in Western Australia.

At this location, A/Prof. Burns and his team collected samples and eventually isolated a member of the Asgard archaea, a group of unusual microbes believed to be closely related to the ancestors of eukaryotes. Eukaryotes are the cells that make up all plants, animals, and humans.

One long-standing theory suggests that the first eukaryotic cell formed when an ancient archaeon and a bacterium entered into a close partnership, with one eventually engulfing the other. This process led to the development of mitochondria, the structures that generate energy inside cells.

Until now, scientists have lacked direct evidence showing how such partnerships might have functioned. This study provides the first visual confirmation of an Asgard archaeon physically interacting with a bacterium through tiny tube-like connections called nanotubes.

“This could be a little model for how these kinds of partnerships started and ultimately formed eukaryotes,” says A/Prof. Burns.

The long road of discovery

Genetic sequencing revealed the presence of these organisms in the samples, but growing them in the lab proved challenging.

“It took four or five years in the lab,” A/Prof. Burns says. “A lot of time, optimizing and chasing different shadows.”

Asgard archaea are extremely difficult to grow outside their natural environment, and the team could not culture them on their own. According to A/Prof. Burns, this may be an important clue.

“The fact that we could never get these organisms into pure culture is probably because they always depend on other organisms to survive,” he says.

A key breakthrough came with electron cryotomography, an advanced 3D imaging method that can reveal structures at the scale of a millionth of a millimeter (about 0.00004 inches).

The images showed the two microbes physically connected by nanotubes. The archaeon also produced chains of small vesicles and complex tube-like extensions. Each organism created compounds that the other could use, including vitamins, nutrients, and hydrogen.

Coauthor Associate Professor Debnath Ghosal from The University of Melbourne says capturing this direct interaction is a major step forward. “This discovery brings us a few steps closer towards understanding how complex cells evolved from relatively simpler microbial life forms,” A/Prof Ghosal says.

Coauthor Associate Professor Kate Mitchie from UNSW explains that the study also used deep learning, a type of machine learning.

“We used this to predict the structures of proteins in these microbes,” A/Prof. Mitchie says. “And that’s exciting because we can start to see ancient versions of the cellular machinery that later became central to complex life.”

A/Prof. Burns compares archaea to “companions.” In the harsh conditions found in microbial mats, even microscopic cooperation can be essential for survival.

An ancient but living story

Coauthor Associate Professor Iain Duggin from the University of Technology Sydney says it is remarkable to consider that these microbes may have formed partnerships in such environments for millions of years, eventually contributing to the emergence of complex life, including humans.

“It’s if we have slowly arisen from the bottom of the sea,” A/Prof. Duggin says.

The newly discovered archaeon was named Nerearchaeum marumarumayae, after the ancient Greek sea god Nereus and the Malgana word marumarumayae, meaning “ancient home.”

Malgana is one of the traditional languages of the people of central Shark Bay, whose connection to the land is recognized by Native Title. Malgana elders, rangers, and community members actively care for the region, protecting wildlife and restoring the environment.

Shark Bay also has a deep Indigenous history, with people first inhabiting the area around 30,000 years ago.

The naming process involved consultation with Kymberly Oakley, a leading expert in the Malgana language. Elders were also consulted to ensure respectful and appropriate use of language. They granted permission to include terms that recognize and celebrate Malgana culture.

For researchers, these microbial systems provide a rare glimpse into early Earth. For Traditional Owners, they remain an important part of a living cultural heritage that continues to be protected.

A/Prof. Burns hopes to identify more microbial partnerships, expanding what he calls a “little primordial Asgard soup,” to help reconstruct the earliest stages of complex life.

“But it’s not just about the organisms,” he says. “It’s about people as well. A huge collaborative effort across disciplines with many graduate students being instrumental in building this story. Part of what makes this exciting is that it’s not just discovery, but connection. Not just across many years, but at a time when these fragile ecosystems face mounting threats from climate change and human activity.”

These microbes highlight how cooperation has been essential for survival throughout Earth’s history, a principle that A/Prof. Burns says remains just as important today.

“These microbes remind us that even the smallest partners can leave the deepest mark on our history.”