The microbe was collected from deep sea sediments The Asahi Shimbun / Getty Images

A single-celled organism found off the coast of Japan could offer us a glimpse of one of our most distant ancestors. The microbe may explain one of the great mysteries of evolutionary history: the origin of the complex cells that make up organisms like plants and humans.

“This is a very influential and monumental paper,” says Thijs Ettema of Wageningen University in the Netherlands.

For much of Earth’s history, the only living things were single-celled organisms like bacteria. However, today the planet is also home to much larger organisms like trees and elephants. These more complex “eukaryotes” differ from their simpler ancestors at the cellular level. While bacterial cells have little internal structure, eukaryotic cells are more intricate. In particular, they contain sausage-shaped structures called mitochondria that supply them with energy.


Most biologists are now convinced that eukaryotes emerged when one cell swallowed another. The mitochondria packed into your cells are all descended from a bacterium that was engulfed by another cell and then set up home there.

The question is: who did the swallowing?

Loki of Asgard

Clues to a possible answer started to emerge in 2010, when researchers drilled a core of sediment from the bottom of the Arctic Ocean, near a set of hydrothermal vents called Loki’s Castle, named after the Norse god of mischief. Five years later, Ettema’s team found DNA from an unknown microorganism lurking in the mud.

It was an archaean, a simple cell from an ancient group of organisms that split from bacteria early in the history of life. But it had genes that were supposedly unique to the more advanced eukaryotes – including some that are used to deform the outer membranes of cells, hinting at an ability to swallow smaller objects. The team called the organism Lokiarchaeota.

Several related archaea have since been identified from their DNA. In keeping with the theme of Norse mythology, the group is now called the Asgard archaea, after the realm of the Norse gods.

Researchers like Ettema believe the Asgard archaea hint at the origin of eukaryotes. An Asgard-like archaean that lived billions of years ago could have swallowed a bacterium to become the first eukaryote – setting evolution on the path towards humanity.

However, nobody has ever seen a living Asgard archaean. All the studies were based on DNA collected from the environment and then sequenced and analysed in the laboratory – until now.

A world first

In 2006, before anyone had heard of Asgard archaea, a Japanese team collected a sediment core from an area of seabed, 2,533 metres down in the Nankai Trough off Japan’s southern coast. Later that year, Hiroyuki Imachi of the Japan Agency for Marine-Earth Science and Technology and his colleagues began trying to grow microorganisms from the sample in an incubator.

After hearing Ettema talk about Asgard archaea at a conference in 2014, Imachi worked with colleagues to devise a special mixture of nutrients and other chemicals that have now finally enabled an Asgard archaean to be grown and studied in a lab for the first time.

The team have imaged the archaean organism using electron microscopes Hiroyuki Imachi / SUGAR/X-star/JAMSTEC

Imachi calls the new microbe Prometheoarchaeum syntrophicum, and the team has photographed the microbes and studied their behaviour.

“Several groups worldwide are trying this, including my lab,” says Ettema. “They’ve beat us to it.”

Living with neighbours

Two features of Prometheoarchaeum leap out as significant.

The first is that it does not live on its own. Imachi’s team could only grow it alongside at least one other microbe, and preferably two: another archaean called Methanogenium and a bacterium called Halodesulfovibrio.

Experiments indicate that Prometheoarchaeum breaks down amino acids into simpler chemicals, including hydrogen, which the other microbes then eat. Organisms that eat one another’s wastes are called syntrophs. Close partnerships like these could have been a stepping stone for Asgard archaea towards swallowing cooperative microbes into their cells.

Asgard archaea were always likely to be syntrophs, because they live in mud where organic matter is breaking down, with little oxygen, says Purificación López-García of the National Centre for Scientific Research in Orsay, France. “These are very complex communities with very different members.”

Many-armed microbe

Secondly, Prometheoarchaeum is an unusual shape for an archaean. It has long arms, a bit like the tentacles of an octopus, and its microbial partners nestle within these.

Imachi suggests that these arms explain how complex cells originated. If an Asgard archaean had bacteria in its arms, and the arms fused into a single lump, the bacterium would have ended up inside the Asgard archaean.

It’s possible, says Ettema, but we don’t yet know if all Asgard archaea have these arms. “It will be very exciting if we can cultivate other Asgard members to see if they have similar types of protrusions,” he says. “Only then will we be able to infer the ancestral characteristics of the Asgard cell from which eukaryotes evolved.”

Glimpse into the unknown

Growing other Asgard archaea like Prometheoarchaeum could help resolve many outstanding puzzles about the origin of eukaryotes.

For example, several lines of evidence suggest the host cell was an archaean, which swallowed a bacterium. But there is a big problem with that, says López-García. “Eukaryotes have bacteria-like membranes,” she says. If the host was an archaean, it somehow lost its distinctive outer membrane and replaced it with a bacterial one. “That is a very radical difference,” she says: nobody has explained why it would happen or if it is even possible.

López-García suggests the explanation could mean a more complex story: instead of just two cells being involved, perhaps there were three or more. She points out that Prometheoarchaeum preferred to live with two partners in the experiment, and in the wild it may well co-exist with more. Two cells may be a simpler story, she says, but that doesn’t make it right.

We still don’t know why complex cells evolved. There is evidence that they can generate much more energy than bacteria or archaea, giving them an advantage, but it is unclear whether that was true from the start. Taking on an oxygen-capable bacterium may have allowed the first Asgardian eukaryotes to survive as oxygen levels rose, suggests Ettema. “One way or another, oxygen has been a big factor in the origin of eukaryotes,” he says.

Finally, there is the question of whether the origin of eukaryotes was a fluke, something that happened despite astronomical odds, as many have suggested, or whether it happened more than once. “All the eukaryotes we see today, they all have a single origin,” says Ettema. We know this from DNA analysis.

But if Asgard archaea were primed to engulf other cells, perhaps it happened more than once but only one lineage survived. If the first eukaryotic cell had a big advantage, Ettema suggests, perhaps “it outcompeted any other cells that tried to do the same”.

Reference: bioRxiv

We corrected the nature of the organism that was imaged