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The ‘microbial village that helped raise a eukaryote’

Though they were first on Earth billions of years ago, stromatolites and mats continue to form in Shark Bay, a World Heritage-listed site in Western Australia.

It was here that A/Prof. Burns and colleagues collected samples and eventually isolated a member of the Asgard archaea – a group of unique microbes thought to be closely related to the ancestors of eukaryotes, which are the cells that make up all plants and animals, including humans.

A long-standing theory in biology suggests the first eukaryote arose when an ancient archaeon and a bacterium formed a close partnership, with one eventually engulfing the other. This union gave rise to mitochondria – the powerhouse of cells.

But what scientists have been missing is direct evidence of how such relationships might have looked in practice. This study provides the first visual evidence of an Asgard archaeon physically interacting with a bacterium through fine, tube-like structures known as 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

While genetic sequencing revealed the organisms’ DNA lurking within the samples, cultivating the microbes to observe them in action was difficult.

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

Asgard archaea are notoriously difficult to cultivate outside their natural environment, so the team was unable to grow them in isolation. A/Prof. Burns says this is a finding that could also be significant.

“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.

The breakthrough came with electron cryotomography, a high-resolution 3D imaging technique that allowed researchers to see structures at the scale of a millionth of a millimetre.

The images revealed the two organisms physically linked by bacterial nanotubes. The archaeon also appeared to sprout chains of budded vesicles and elaborate tube-like structures. Each microbe made compounds that the other could use, including vitamins, nutrients and hydrogen.

Coauthor Associate Professor Debnath Ghosal from The University of Melbourne says capturing the first direct physical interaction between an Asgard archaeon and a bacterium is especially exciting.

“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 Michie from 91ɫ��Ƭ says the research included an element of deep learning – a type of machine learning.

“We used this to predict the structures of proteins in these microbes,” A/Prof. Michie 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 likens archaea to ‘companions’. Under the harsh conditions that batter microbial mats, this kind of cooperation, even at the microscale, could be vital for survival.

An ancient but living story

Coauthor Associate Professor Iain Duggin from the University of Technology Sydney says it’s amazing to imagine that these microbes could have been in partnership in these environments for millions of years, giving rise to complex life – including humans.

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

The newly identified 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 ties to Country are recognised by native title. Malgana elders, rangers and community actively work in Shark Bay caring for Country, protecting wildlife and restoring the land.

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

The naming process involved consultation with Kymberly Oakley, the world’s foremost Malgana language expert. Malgana elders were also consulted for appropriate words that could be respectfully used in the naming of the new microbe. The elders granted permission to incorporate language that allowed the Malgana culture to be recognised and celebrated.

For scientists, these microbial communities offer a rare window into early Earth. For Traditional Owners, they are part of a cultural heritage that continues to be cared for and protected.

A/Prof. Burns hopes to uncover more microbial partnerships, expanding what he calls a “little primordial Asgard soup”, to help scientists piece together the earliest chapters 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.”

The microbes show how life depended on cooperation to survive – which A/Prof. Burns says is just as essential today.

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