How these strange cells may explain the origin of complex life

In many submerged regions, murky mud shelters strange life-forms that seem to be the key to one of the biggest mysteries of life on Earth.

These creatures belong to a domain of life called the archaea: single-celled microorganisms that look much like bacteria under a microscope. Ten years ago, a new group called the Asgard archaea was identified in sediments from the North Atlantic Ocean. They are nothing like us: They live mostly in places with little or no oxygen, and they are almost unbelievably ancient, with a lineage tracing back perhaps 3 billion years. Yet their DNA shows that the Asgard archaea sit startlingly close to humans on the tree of life.

In 2015, game-changing research made the case that these odd microbes can explain the origin of eukaryotes, the domain of life that includes organisms made of cells containing a membrane-bound nucleus. Since then, an explosion of studies has added to evidence that the Asgard archaea are the key to the birth of all known complex life.

The rise of the eukaryotes was one of the most important events in Earth’s history. If it had not occurred, there would be no great white sharks, no towering redwood trees, no hovering hummingbirds and no people. Just slimy layers of bacteria and archaea, everywhere. And the Asgard archaea may have started it all.

“I think it’s the most exciting thing that’s happened in microbiology in a long time,” says geobiologist Daniel Mills of Heinrich Heine University of Düsseldorf in Germany.

Exactly how the Asgard archaea gave rise to eukaryotes, and why it happened when it did, is still being thrashed out by researchers. But based on the evidence so far, the Asgard archaea seem to have evolved in multiple ways that primed them to birth eukaryotes. This suggests that the origin of complex life on Earth wasn’t an incredibly lucky chance, but something that built up over evolutionary time.

That, in turn, implies complex life may evolve more easily than many biologists suspected, in which case — if there is extraterrestrial life somewhere in the cosmos — at least some of it might be complex like us.

What were the first cells?

The oldest known living things are simple, single cells. There are two major domains: bacteria, which are familiar in part because some of them cause diseases, and the less well-known archaea. Scientists didn’t recognize how distinct the two domains are until the advent of DNA analysis in the 1970s.

The third domain, eukarya, arose later in Earth’s history. Compared with the older groups, eukaryotic cells are usually much larger. They also have more internal structure. Each eukaryotic cell has a nucleus, an enclosure where the DNA is stored. Most also have many stubby structures called mitochondria, which supply them with energy. Unlike bacteria and archaea, eukaryotic cells can group together to form large multicellular organisms with distinct tissues like muscle and bone.

“If eukaryotes never originated, we wouldn’t be here,” Mills says.

How and why eukaryotes formed are profoundly difficult questions because the differences between eukaryotes and their bacterial and archaeal cousins are vast. One group of microbiologists in the 1960s called the divide “the greatest single evolutionary discontinuity to be found in the present-day world.”

For many biologists, the origin of eukaryotes also seemed extremely unlikely. All eukaryotes today are descended from the same common ancestor, and nobody has ever observed new eukaryotic cells forming, either in the wild or in the lab. This has long implied that eukaryotes formed only once, and that it was “a chance event,” Mills says.

Then came a crucial clue.

How Loki’s Castle changed the game

In July 2008, researchers discovered a series of hydrothermal vents on the Arctic Mid-Ocean Ridge, between Scandinavia and Greenland. Each vent is a chimney that pumps out black, chemical-rich water at temperatures of 310° to 320° Celsius. The team that found the vent system called it Loki’s Castle, after the Norse trickster god.

Subsequent expeditions collected sediments from the surrounding seabed, which were home to communities of archaea. Initial genetic studies suggested there was something unusual about these archaea. They “seemed to be somehow closer to eukaryotes than what we knew before,” says Anja Spang, now an evolutionary microbiologist at the Royal Netherlands Institute for Sea Research in Den Burg.

“I’ve always been fascinated by the question of how eukaryotic cells evolved,” says Spang, who at the time was doing a postdoc at Uppsala University in Sweden. The newfound microbes looked potentially relevant, so she resolved to “reconstruct the genomes of these organisms.”

The group’s initial attempts to isolate the archaea failed inexplicably, so Spang and her colleagues turned to a technique called meta-genomics. They collected as much DNA as they could from the sediments and used computer programs to reconstruct the genetic instruction book, or genomes, of the mystery archaea. They could then compare these mystery genomes with those of other microbes and figure out their closest relatives.

When Spang and colleagues finally generated a reliable family tree, the new group of microbes, which they dubbed the Lokiarchaeota, proved to be the closest known living relatives of eukaryotes. Their results, published in Nature in May 2015, caused a scientific sensation.

“It was a game changer,” says microbial ecologist Burak Avcı of Aarhus University in Denmark. Three things stood out. The simple fact that the Lokiarchaeota were so closely related to eukaryotes immediately raised the possibility that a member of the same group gave rise to the first eukaryotes billions of years ago. Furthermore, their genomes contained many genes that are hallmarks of eukaryotes. These genomes partially crossed the divide between complex life and simple bacteria and archaea. And crucially, some of the eukaryotic genes the team found seemed to point to an explanation for how the first eukaryotic cells formed.

How could simple cells become complex?

The basic idea for how eukaryotes may have formed goes back over a century. In 1910, Russian biologist Konstantin Sergejewitch Mereschkowsky suggested that some of the complex structures in what we now call eukaryotic cells were once free-living cells. The first eukaryote formed when one cell took up residence inside another. The intruder eventually fused with its host to such an extent that the two became inseparable.

This partnership came to be called endosymbiosis. The idea languished in obscurity for half a century until it was revived in 1967 by microbiologist Lynn Margulis. Writing as Lynn Sagan (she had been married to astronomer and author Carl Sagan), Margulis argued that the energy-giving mitochondria and two other eukaryotic structures had been formed from separate cells.

Margulis’ proposal was “groundbreaking, revolutionary work” at the time, Mills says, and today, the basic idea of endosymbiosis is textbook orthodoxy. Still, the theory of endosymbiosis raises a plethora of intractable questions, beginning with an obvious one: Which types of microbes were involved? Was the host cell an archaean or a bacterium? What about the cell that was absorbed and became the first mitochondrion?

“We did not have the host. We did not have the partner,” says microbiologist Christa Schleper of the University of Vienna in Austria.

Based on careful analyses of the genomes and biochemistry of eukaryotic cells, researchers gradually concluded that an archaeal host absorbed a bacterium. But nobody knew what kind of archaean, or how it could have achieved this. That’s where Lokiarchaeota comes in. These microbes seemed to be ideally placed to be the host cells that assimilated the bacterial ancestors of mitochondria.

Some of the eukaryote-like genes in Lokiarchaeota code for proteins that, in eukaryotes, are involved in changing the shapes of cell membranes. Using these proteins, eukaryotes can deform their cell membranes, twisting and thrusting them into new shapes.

Crucially, many eukaryotic cells can perform phagocytosis — they can engulf a large particle or another cell, trapping it inside a special compartment. In the human body, some of our white blood cells engulf harmful bacteria in this way and then digest them. If Lokiarchaeota could perform phagocytosis, then maybe a similar archaean billions of years ago used it to engulf a bacterium.

“That’s how you get a bacterium within an archaean,” Mills says.

It was a beautiful idea. But was it true? Spang and her colleagues still didn’t have any living Lokiarchaeota cells in their lab, just a reconstructed genome in their computers.

To flesh out their picture of these archaea, they looked for more. They took samples from seven watery sediments, including Loki’s Castle, Yellowstone National Park in Wyoming and the Radiata Pool in New Zealand. The DNA revealed a host of Lokiarchaeota-like microbes, such as Thorarchaeota (named by another group after the god of thunder) and Heimdallarchaeota (named after the sentinel of the Norse gods). Even more eukaryote-like genes turned up in these newfound microbes. The team decided to call the entire group the Asgard archaea, after the home of the gods in Norse mythology.

Other researchers were also identifying new Asgard archaea using similar methods. But still nobody had grown one in the lab or seen one under a microscope. Or so everyone thought.

Discovering a cell with tentacles

On May 6, 2006, microbiologist Hiroyuki Imachi and two colleagues were on the bottom of the ocean in the submersible Shinkai 6500, 2,533 meters below sea level in the Nankai Trough off Japan. There, methane seeps on the flat plain of the seabed feed a community of unusual microorganisms.

Imachi, of the Japan Agency for Marine-Earth Science and Technology in Yokosuka, had relatively modest ambitions. He hoped to identify and culture the microbes and learn how they survived in this peculiar environment. Using the submersible’s robotic arm, the crew collected a cylinder of sediments from the seabed. They were mostly gray, with some black dots.

Imachi spent years figuring out how to grow the microbes from the sediments in a reactor in his lab. It was slow work, because the microbes lived slow lives, doubling in number over 14 to 25 days. He had previously worked on biological treatment of wastewater, and he stuck with the methods he knew. Instead of trying to grow isolated strains in test tubes and glass plates, he used a continuous-flow bioreactor to replicate the environment of the deep-sea methane seep, trickling in methane and sulfate to feed the microbes living inside.

With biologist Masaru Nobu and other colleagues, Imachi had analyzed the genome of the microbes, and the pair was planning a paper about their ecology. Then Imachi saw Spang’s supervisor Thijs Ettema give a presentation about Lokiarchaeota, not long before Spang’s 2015 Nature paper was published. Imachi realized he was growing what would soon become known as an Asgard archaean — and he was the only person on the planet who had worked out how to do so.

Imachi and Nobu were shocked. “Neither of us had a background in evolutionary biology,” Nobu says, and they certainly hadn’t been working on the origins of eukaryotes. But they had stumbled onto a huge discovery. Instead of their planned ecology paper, they would “go all the way,” Nobu says, and propose a new theory for how archaea evolved towards eukaryotes using the Asgard archaea that Imachi had cultured.

First, they had to take a proper look at their microbes, which they were calling strain MK-D1. The team managed to identify individual MK-D1 cells in the culture and examined them using an array of methods, including electron microscopy. The cells proved to be small and spherical, about 550 nanometers across: not unusual for an archaean, and much smaller than a eukaryote. They showed no sign of the kinds of internal structures found in eukaryotes, such as a nucleus.

What they did have was tentacles. Long tendrils extended from the cell body, often dividing into multiple branches. When Imachi first saw them, he thought he must have contaminated the culture, ruining years of work. “But then, as we looked at it closely together, we realized that these filamentous structures were growing from the spherical cells that we’re familiar with,” Nobu says. In the electron microscope images, each cell looked rather like a squashed mosquito.

The team called their archaean Candidatus Prometheoarchaeum syntrophicum — breaking with the Norse theme by naming it after the Greek mythological hero who stole fire from the gods. The team published their findings on bioRxiv.org in 2019, and it appeared in Nature the following year.

Crucially, Prometheoarchaeum could not grow in isolation. It exists in a special kind of symbiosis in which it can feed only in partnership; in the culture it grew only with another archaean called Methanogenium. The partner produces amino acids and vitamins that Prometheoarchaeum cannot make, and in return Methanogenium receives essential chemicals in the form of hydrogen and formate.

Putting all this together, Imachi, Nobu and their colleagues proposed a significantly different scenario for the formation of the first eukaryotic cell. The Asgard archaean was the host, but it did not capture its partner using phagocytosis. Instead, it had a bacterial feeding partner. The Asgard archaean’s tendrils gripped this partner, holding it close. As the two cells became more interdependent, the tendrils slowly fused around the partner — until it was entirely enclosed.

For many researchers, including Spang, this now seems like a far more plausible scenario than phagocytosis. Although the Asgard archaean that merged with a bacterium billions of years ago had some of the genes required, “I don’t think it had a fully fledged phagocytosis machinery,” Spang says. In contrast, subsequent studies have shown that other Asgard archaea live with a feeding partner.

In April 2019, Schleper collected sediments from a shallow, brackish canal near Piran, Slovenia. Three years later, she and her colleagues reported that they had successfully cultured a second Asgard archaean, Candidatus Lokiarchaeum ossiferum. Like Prometheoarchaeum, it had long tendrils. Within the cells, the team identified a protein called actin, which in eukaryotes is a major component of the internal scaffolding called the cytoskeleton.

“This actin is really interesting because it is found in all Asgard archaea,” Schleper says, suggesting it was present in the earliest members of its group. It may be the key to the cells’ ability to form long, branching tendrils.

What the Asgard archaea mean for aliens

The question of exactly what structures and abilities Asgard archaea possess is crucial to understanding how endosymbiosis could have happened. But there are uncertainties about even basic biological traits. One big example: Do Asgard archaea have internal structures similar to those of eukaryotes, or are they internally simple like other archaea and bacteria?

The initial DNA study suggested they were capable of remodeling their membranes, which hinted at complex structures. Avcı and colleagues gathered sediments containing Asgard archaea from Denmark’s Aarhus Bay. They found that the archaea’s DNA appeared to be separated from the machinery for making proteins. This could suggest that the cells store their DNA in a nucleus, with the protein-making machinery elsewhere, like eukaryotes.

However, Schleper says the existing data don’t show this. “I don’t think they have ever seen a membrane, so I don’t think we have a nucleus here,” she says, adding that other archaea do separate DNA and ribosomes, the cellular machinery that forms proteins.

More evidence of a simple internal structure, typical of archaeans, emerged in a study posted in February 2025 by Imachi, Nobu and their colleagues. They reported culturing two more Asgard archaeans, in a group called Hodarchaeales, named for Hodr, the blind son of Odin in Norse mythology. Both had similar shapes and lifestyles as Prometheoarchaeum, and no sign of internal structures like nuclei.

However, two months later Avcı and his colleagues reported that they had imaged archaea closely related to Hodarchaeales, again gathered from Aarhus Bay. The cells were very different. For starters, they were around 3 micrometers across, several times the size of Prometheoarchaeum. They were shaped like stubby sausages, with a swollen “bulb” at one end containing dense DNA.

“It is most likely we see the first form of the nucleus organized in Asgard archaea,” Avcı says.

Avcı notes that the Asgard archaea are already a highly diverse group, and scientists have barely scratched the surface. The first ones cultured might not be representative of their ranks.

The debate is likely to grind on for some time, if only because it takes so long to culture a new strain. But as more Asgardians are identified, researchers are trying to discover the group that gave rise to eukaryotes. A 2023 analysis highlighted the Heimdallarchaeia as the most promising subgroup. For the first time, scientists have something that looks like the host cell that became a eukaryote. “That makes it more graspable,” Schleper says.

Plus, the mere discovery of Asgard archaea carries exciting implications for extraterrestrial life.

The more we understand about Asgard archaea, with their tentacles and their close partnerships with other microbes, the more the birth of eukaryotes seems almost inevitable. That calls into question the long-standing assumption that the rise of eukaryotes was an astronomically rare event that happened only once in Earth’s history.

“This is just my own intuition,” Spang says, but “it happened more than once.” She suggests that multiple groups of Asgard archaea took in symbionts, “but one lineage somehow really made it to the stop where it became an integrated cell over time.”

If eukaryotes really arose more than once, then we will have to rethink a key idea about evolutionary history — and our expectations for the kinds of life that might exist on other planets. In a study published in February 2025 in Science Advances, Mills and colleagues reconsidered whether the origin of eukaryotes, and other supposed “hard steps” in the evolution of complex life, are really that hard. The birth of eukaryotes looks like a singular event because all modern eukaryotes are descended from one shared ancestor. But there are other explanations.

“It could be that … a eukaryotic organization evolved many times, and all these other examples have gone extinct,” Mills says. Or it may be that the first group to become true eukaryotes was so successful that they prevented other Asgard archaea from following suit, effectively “pulling up the ladder” behind them.

If the origin of eukaryotes was truly unlikely, we might never find plants and animals anywhere else, just worlds covered in unicellular slime. However, if one of the alternative explanations Mills highlighted is the truth, then we might expect to find complex life on other Earthlike planets where it has had time to evolve.

One day in the far future, a space probe may gaze down on an exoplanet with liquid water and a thick atmosphere. If the planet has been around for a few billion years, perhaps we’ll find alien eukaryotes. Maybe there’ll even be complex animals wondering about the strange new star in the sky.