At first glance, stromatolites and their close relatives, microbial mats, can look like little more than dark, ancient rocks. In reality, they are densely packed, layered communities built by microbes.
Billions of years ago, before animals and plants existed, stromatolites helped release some of the earliest oxygen into Earth’s atmosphere. Now, a study published in Current Biology suggests these unusual formations may also preserve clues to another major event in Earth’s history: the emergence of complex life.
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 “living fossils.” The project, co-led with researchers from the University of Technology Sydney and The University of Melbourne, could help scientists better understand a fundamental evolutionary mystery: how relatively simple cells began cooperating and eventually gave rise to much more complex forms of 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.”
A Microbial Partnership With Ancient Roots
Stromatolites and microbial mats first appeared billions of years ago, but they have not disappeared. They still form today in Shark Bay, a World Heritage-listed site in Western Australia.
Samples collected there eventually led A/Prof. Burns and his colleagues to isolate a member of the Asgard archaea, an unusual group of microbes believed to be closely related to the ancestors of eukaryotes, which are the cells that make up all plants and animals, including humans.
One long-standing idea in biology proposes that the first eukaryotic cell developed through an intimate partnership between an ancient archaeon and a bacterium. According to this theory, one organism eventually engulfed the other, and that relationship ultimately produced mitochondria, the energy-producing structures found inside complex cells.
Scientists, however, have lacked direct evidence showing what such an early partnership might actually have looked like. The new research provides the first visual evidence of an Asgard archaeon physically interacting with a bacterium through extremely thin, 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.
Years Spent Trying to Grow an Elusive Microbe
Genetic sequencing showed that the organisms’ DNA was present in the samples, but getting the microbes to grow in the laboratory so researchers could study them directly proved far more difficult.
“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 notoriously challenging to cultivate away from their natural habitats. The researchers could not grow the organisms on their own, and A/Prof. Burns says that difficulty may itself reveal something important about their biology.
“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 researchers eventually made progress using electron cryotomography, a high-resolution 3D imaging method capable of revealing structures at the scale of a millionth of a millimeter.
The images showed the archaeon and bacterium physically connected by bacterial nanotubes. Researchers also observed the archaeon producing chains of budded vesicles along with elaborate tube-like structures. The two microbes appeared to complement one another chemically, with each producing compounds the other could use, including vitamins, nutrients and hydrogen.
Coauthor Associate Professor Debnath Ghosal from The University of Melbourne says directly capturing an interaction between an Asgard archaeon and a bacterium is particularly significant.
“This discovery brings us a few steps closer towards understanding how complex cells evolved from relatively simpler microbial life forms,” A/Prof Ghosal says.
Ancient Cellular Machinery Comes Into View
The team also incorporated deep learning, a type of machine learning, into its analysis, according to coauthor Associate Professor Kate Mitchie from UNSW.
“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 describes archaea as ‘companions’. Life inside microbial mats can be harsh, and close cooperation between organisms may provide a crucial survival advantage even at microscopic scales.
A Living Window Into Early Earth
Coauthor Associate Professor Iain Duggin from the University of Technology Sydney says it is remarkable to consider that microbes may have maintained partnerships like these 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 identified archaeon has been named Nerearchaeum marumarumayae. Its name combines a reference to Nereus, the ancient Greek sea god, with the Malgana word marumarumayae, meaning ‘ancient home’.
Malgana is one of the traditional languages spoken by the people of central Shark Bay, whose ties to country are recognized by Native Title. Malgana elders, rangers and community members continue to care for country in Shark Bay by protecting wildlife and restoring the land.
Shark Bay also has a long Indigenous history. Indigenous people first inhabited the region around 30,000 years ago.
Honoring Shark Bay’s Malgana Heritage
The process of naming the microbe included consultation with Kymberly Oakley, the world’s foremost Malgana language expert. Researchers also worked with Malgana elders to identify language that could be used respectfully in the organism’s scientific name. The elders granted permission for the Malgana language to be included so that the culture could be recognized and celebrated.
For researchers, the microbial communities of Shark Bay provide an unusual opportunity to study conditions that may resemble parts of early Earth. For Traditional Owners, the same environments form part of a living cultural heritage that continues to be protected and cared for.
A/Prof. Burns now hopes to identify additional microbial partnerships and expand what he calls a “little primordial Asgard soup,” giving scientists more pieces of the puzzle surrounding the earliest stages in the evolution 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 findings also highlight how deeply survival can depend on cooperation between organisms, something A/Prof. Burns says remains just as relevant today.
“These microbes remind us that even the smallest partners can leave the deepest mark on our history.”
