A strange partnership between two ancient microbes could explain one of evolution’s biggest mysteries — how simple cells first joined forces to create complex life

For billions of years, life on Earth was dominated by microscopic organisms. Long before plants, animals or humans appeared, microbial communities were already changing the planet and developing intricate ways to survive.

Now, scientists have captured something that may provide a rare glimpse into that ancient world.

Researchers studying microbial communities in Shark Bay, Western Australia, have discovered an unusual Asgard archaeon living in close association with a bacterium. High-resolution imaging revealed the two organisms physically connected by tiny tube-like structures, suggesting they may exchange materials and resources.


The finding could help scientists investigate one of biology's biggest unanswered questions: how simple microbial cells eventually came together to produce the complex cells that make up plants, animals and humans.

A microscopic relationship with enormous implications

The newly identified archaeon has been named Nerearchaeum marumarumayae. It belongs to the Asgard archaea, a group of microorganisms considered particularly important in research into the origins of eukaryotic cells.

Eukaryotes are cells with complex internal structures and include every animal, plant, fungus and human.

One leading idea about their origin proposes that an ancient archaeon formed a close relationship with a bacterium. Over time, that relationship may have become permanent, eventually giving rise to the complex cellular architecture seen in modern life.

Scientists have developed several versions of this theory, but directly observing an Asgard archaeon interacting with a bacterium has been difficult.

The new study provides an unusually detailed look at such an interaction.

Scientists found the microbes physically connected

The breakthrough came from cultures derived from microbial mats in Shark Bay.

Using electron cryotomography, a technique capable of producing detailed three-dimensional views of cells at extremely small scales, researchers observed N. marumarumayae alongside a sulfate-reducing bacterium called Stromatodesulfovibrio nilemahensis.

The images showed thin tubular structures extending from the bacterium toward the archaeon and connecting the two cells.

The tubes were only about 8 nanometres wide, far too small to see with conventional microscopy.

Researchers believe the structures may allow the organisms to interact directly, although their precise function has not yet been established. The evidence is consistent with a form of cooperation known as syntrophy, in which different organisms exchange products in a way that benefits both.

What could the microbes be exchanging?

Genetic analysis offers some clues.

The archaeon appears capable of producing compounds including hydrogen, acetate and formate. The accompanying bacterium, meanwhile, can produce amino acids and vitamins.

That creates the possibility of a biological trade: one organism supplies substances that the other can use, while receiving useful compounds in return.

The researchers caution that these metabolic relationships still need to be experimentally confirmed. But the combination of genomic evidence and direct physical contact makes the partnership particularly interesting.

If similar relationships existed in ancient microbial communities, they could have provided a pathway toward increasingly intimate cooperation between different types of cells.

The cells also revealed surprising structures

The Asgard archaeon itself proved unusual.

Researchers observed chains of small membrane-bound vesicles extending from its cell body, along with larger tube-like structures inside the cell.

Protein analysis also identified machinery related to structures found in complex eukaryotic cells, including proteins associated with membrane trafficking.

These findings are important because Asgard archaea contain many genes known as eukaryotic signature proteins. Such proteins have helped scientists investigate how the sophisticated cellular machinery found in eukaryotes might have evolved from simpler ancestors.

The study's researchers also used deep-learning methods to predict the structures of proteins produced by the microbe, offering another way to compare its cellular machinery with that of more complex organisms.

Why stromatolites matter

The discovery was made possible by an environment that resembles some conditions scientists believe existed on early Earth.

Stromatolites and microbial mats have existed for billions of years and are built through the activity of communities of microorganisms. Modern examples survive in places such as Shark Bay, where researchers can study them as living analogues of ancient microbial ecosystems.

That does not mean today's organisms are unchanged survivors from billions of years ago.

Instead, these environments provide scientists with an opportunity to examine microbial communities living under conditions that may share some characteristics with those experienced by early life.

The new findings suggest such communities may have been more than places where primitive organisms simply lived alongside one another. They may also have been environments where increasingly sophisticated biological partnerships developed.

A difficult microbe to study

Getting Nerearchaeum marumarumayae into the laboratory was itself a major challenge.

The researchers spent approximately four to five years working with the cultures. The archaeon proved difficult to grow independently, and the team was unable to establish it as a pure culture.

That difficulty may itself be significant.

If the organism relies heavily on neighbouring microbes, its dependence could reflect the importance of microbial partnerships to its survival. Researchers were ultimately able to obtain a culture highly enriched in the archaeon, reaching about 89 per cent in one culture, allowing them to examine its biology in much greater detail.

Could this be a snapshot of the road to complex life?

The researchers are not claiming to have discovered the exact organisms that became the first eukaryotic cells.

Instead, the microbes may offer something more subtle but potentially valuable: a living example of the kind of cooperation that could have helped drive eukaryotic evolution.

In one proposed scenario, an archaeon capable of producing hydrogen became increasingly dependent on a bacterium that could consume it. The two organisms would have benefited from remaining close together.

Over evolutionary time, such dependence could have encouraged progressively closer physical relationships, eventually contributing to the emergence of the complex cellular organization characteristic of eukaryotes.

The newly observed interaction does not prove that this was precisely how complex life began. But it gives scientists an actual biological system in which to investigate the idea rather than relying entirely on genetic reconstructions and theoretical models.

A new name with a connection to Shark Bay

The archaeon's name also reflects the place where the research was carried out.

Nerearchaeum marumarumayae combines a reference to Nereus, the ancient Greek sea god, with marumarumayae, a Malgana word meaning “ancient home.”

Researchers consulted Malgana language expert Kymberly Oakley as well as Malgana elders during the naming process. The inclusion of Malgana language was approved as a way of recognising the cultural heritage connected to Shark Bay.

For scientists, the region offers an extraordinary window into microbial evolution. For its Traditional Owners, it is also a living cultural landscape that has been cared for across generations.

The biggest clue may be the partnership itself

The discovery adds another piece to a puzzle that began long before humans existed.

Scientists still do not know exactly how the first complex cell emerged, or why certain microbial partnerships eventually led to the extraordinary diversity of eukaryotic life.

But seeing an Asgard archaeon and a bacterium physically connected gives researchers something they have rarely had before: a direct view of two very different microbes cooperating at the cellular level.

The next step will be to determine exactly what passes between them, how the nanotube-like connections function and whether similar partnerships exist elsewhere.

If more examples are found, these tiny organisms could provide an important window into one of the most consequential events in Earth's history — the moment when simple microbial life began taking the evolutionary steps toward becoming complex.