Elusive Asgard Archaea Finally Cultured in Lab
Elusive Asgard Archaea Finally Cultured in Lab

Elusive Asgard Archaea Finally Cultured in Lab

The 12-year-long endeavor reveals Prometheoarchaeum as a tentacled cell, living in a symbiotic relationship with methane-producing microbes.

Aug 12, 2019
Nicoletta Lanese

ABOVE: Scientists collected deep-sea mud from Omine Ridge off the Japanese coast using the manned submersible Shinkai 6500.
OAR/NATIONAL UNDERSEA RESEARCH PROGRAM (NURP), JAMSTEC

An elusive marine microbe, once known only by its DNA, has finally been cultured in the lab and could grant hints as to how eukaryotic life originated, researchers reported August 8 in a preprint posted to bioRxiv. The single-cell organism grows branching appendages and contains eukaryote-like genes, though it belongs to the domain Archaea.

“This is a monumental paper that reflects a tremendous amount of work and perseverance,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands who was not involved in this study, in an interview with Nature. “We’ve learnt a lot from the genome, but without a lab culture, we can only learn so much.”  

In 2015, Ettema and his colleagues spotted samples of the mysterious microbes in mud collected near Loki’s Castle, a sea-floor hydrothermal vent field off the Greenland coast. They recovered an archaean genome speckled with eukaryote-like genes, and soon were followed by other labs that uncovered similar archaea. Many scientists now believe that an ancestor of these Asgard archaea, as they’re collectively known, gave rise to eukaryotic life. They propose that, about 2 billion years ago, an Asgard relative enveloped a passing bacterium that later evolved into a mitochondrion, according to Nature

See “Archaea Family Tree Blossoms, Thanks to Genomics

Until now, scientists have pieced together this narrative from isolated genetic fragments of the Asgard lineage. The new study from Japan began long before the ancient archaea captured everyone’s attention, in 2006, and represents a new chapter in the study of these organisms’ evolution, being the first time they have been cultured. 

“It’s a tremendous effort, and it’s a really nice story because they started out before the Asgard frenzy even started. Halfway through their experiment they must’ve realized they had gold in their hands,” Simonetta Gribaldo, an evolutionary microbiologist at the Pasteur Institute in Paris, tells Nature.

The strange organism was first plucked from the 2,500-meter-deep Omine Ridge off the coast of Japan, where it was buried in deep-sea mud, according to Science. To mimic the harsh conditions of the seabed, microbiologist Hiroyuki Imachi of the Japan Agency for Marine-Earth Science and Technology and his colleagues built a bioreactor to contain the seafloor muck and continually bathe it in methane gas. Five years later, they scraped samples into glass tubes filled with various nutrients and waited. 

A year later, they detected microbes growing in one of the samples that resembled bacteria, superficially, but were genetically distinct. These were the Asgard archaea they had hoped for. Over the next six years, they worked to isolate and culture pure samples of the organism, which they found takes between 14 and 25 days to double its cells in culture. In comparison, most bacteria double in under an hour. 

Finally, the researchers produced a pure sample of Prometheoarchaeum syntrophicum, which they named for the Greek god Prometheus who sculpted humans from mud. Although not yet published in a peer-reviewed journal, the paper has already earned praise from prominent leaders in the field.

“It’s one of the slowest-dividing organisms I know of,” says Ettema. Ettema also shared his excitement over the groundbreaking experiment on Twitter and unpacked the significance of the study. 

With the cultured microbe in hand, the researchers sequenced its full genome and confirmed the existence of eukaryote-like genes. They also observed that the microbe usually grows in tandem with a second, methane-producing archaeon, with whom it fosters a symbiotic relationship. Prometheoarchaeum breaks down amino acids and supplies its partner with energy in the form of hydrogen, which might otherwise impede the Asgard’s growth, according to Science

Images captured with an electron microscope revealed that Prometheoarchaeum develops lengthy appendages with multiple branches, according to Nature. The authors suggest the microbe may have used the tentacles to grab hold of oxygen-producing organisms.      

“This is exactly what we predicted,” says David Baum, an evolutionary biologist at the University of Wisconsin-Madison, in an interview with Science. In 2014, Baum and a colleague proposed an “inside-out origin” of eukaryotic evolution: internal organelles did not evolve from components drawn into simpler cells, but rather from extensions of the cell membrane that latched onto beneficial partners.

Ettema notes that other known archaea more closely resemble eukaryotes than Prometheoarchaeum, so it remains unclear which stood as the immediate precursor to complex life as we know it. But he expects follow-up studies should now be much easier to pursue. “I’m sure it will not take 12 years to get the next Asgard into culture,” he tells Science.

The preprint authors declined requests for interviews with Nature while their paper is being reviewed by a journal. 

Opinion: Archaea Is Our Evolutionary Sister, Not Mother

Nicoletta Lanese is an intern at The Scientist. Email her at nlanese@the-scientist.com.

Correction (August 26): Scientists propose that an Asgard relative enveloped a bacterium that evolved into a mitochondrion about 2 billion years ago, not 2 million as previously stated. The Scientist regrets the error.