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Scientists glimpse oddball microbe that could help explain rise of complex life

‘Lokiarchaea’, previously known only from DNA, is isolated and grown in culture.

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Iron and silica rich chimneys on the summit of Giggenbach underwater volcano

Archaea are often found in extreme environments, such as these chimneys on the summit of Giggenbach underwater volcano, off New Zealand.Credit: New Zealand-American Submarine Ring of Fire 2005 Exploration, NOAA Vents Program

Biologists have for the first time captured and grown an elusive type of microbe that is similar to those that might have given rise to all complex life on Earth.

In a preprint posted to the bioRxiv repository1, scientists in Japan report that they have isolated and grown microbes from an ancient lineage of archaea — single-celled microbes that look, superficially, like bacteria but are quite distinct — that was previously known only from genomic sequences.

It took the researchers 12 years to cultivate pure laboratory cultures of these microbes from deep-sea mud. The effort gives scientists their first look at the kind of organisms that could have made the jump from simple, bacteria-like cells to eukaryotes — the group of organisms whose cells have nuclei and other structures, and which includes plants, fungi, and humans and other animals.

“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. “It’s a major step forward in understanding this important lineage.”

Muddy origins

The mysterious group, called Lokiarchaea, rose to prominence from microbial muck dredged up not far from Loki’s Castle, a sea-floor hydrothermal vent field off the coast of Greenland. In 2015, Ettema and his colleagues sequenced genetic fragments from the mishmash of microbes in the sediment and assembled them into fuller genomes of individual species2, a method called metagenomics.

One genome stood out. It was clearly a member of the archaea. But dotted throughout this genome were eukaryotic-like genes, suggesting to Ettema that this oddball could help to bridge the evolutionary gap between simpler microbes and eukaryotes. The researchers called it Lokiarchaea, after Loki, the trickster of Norse mythology.

Soon, other labs found additional Loki-like archaea, and together these formed the Asgard archaea, named after a mythological region inhabited by Norse gods. Although the organisms’ precise place in the tree of life remains contentious, many analyses pair Asgards and eukaryotes together, which could mean that some distant Asgard-like ancestor gave rise to all eukaryotes — everything from panda bears to portabello mushrooms.

Two become one

Proponents of this view think that, some 2 billion years ago, an Asgard-like archaeon gobbled up a bacterium. Instead of providing a meal, the ingestion sparked a mutually beneficial relationship, a phenomenon known as endosymbiosis. Eventually, according to this hypothesis, the bacterium evolved into mitochondria, the ‘powerhouse’ organelles of the cell that helped to fuel eukaryotes’ rise. A similar merger could have led to the first nucleated cells.

Not all researchers agree that Asgards made this jump. Some have argued that the eukaryotic-like genes that make Asgards special are just contamination from other sediment microbes. And without an actual organism to study in the lab, it was hard to know what the eukaryotic-like genes actually do, or begin to understand how endosymbiosis might have progressed. “We’ve learnt a lot from the genome, but without a lab culture, we can only learn so much,” says Ettema.

Because Asgards hail from extreme environments and have very slow growth rates, no one has previously succeeded in growing them in the lab. “The whole field has been waiting for this moment for a long time,” says Simonetta Gribaldo, an evolutionary microbiologist at the Pasteur Institute in Paris.

Twelve years of work

Years before anyone knew Asgard archaea even existed, Hiroyuki Imachi, a microbiologist at the Japan Agency for Marine-Earth Science and Technology in Yokosuka and his collaborators began the painstaking work that would eventually bring Asgards to the lab.

To cultivate microbes from deep-sea sediments, Imachi and his colleagues built a bioreactor that mimicked the conditions of a deep-sea methane vent. Over the course of 5 years, the researchers waited for the slow-growing microbes in the reactor to multiply.

They then took samples from the reactor and placed these, along with nutrients, in glass tubes, which sat for another year before showing any signs of life. Genetic analysis revealed a barely perceptible population of Lokiarchaea. The researchers patiently coaxed the Lokiarchaea — which took 2–3 weeks to undergo cell division — into higher abundance and purified the samples. “It’s one of the slowest-dividing organisms I know of,” says Ettema.

Finally, after 12 years of work, the researchers produced a stable lab culture containing only this new Lokiarchaeon and a different methane-producing archaeon. Together, the two microbes formed a symbiotic relationship (similar colonies of bacteria and archaea have been observed before). The scientists named the cultured Lokiarchaeon Prometheoarchaeum syntrophicum. The authors declined requests for interviews from Nature's news team while their paper was under review at a journal.

“It’s a tremendous effort,” says Gribaldo. “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.”

‘An organism from outer space’

Under the microscope, that gold took the form of round cells less than one micrometre wide. Like other archaea and bacteria, they have relatively simple interiors, but their external surface can produce wisp-like protrusions that extend from their bodies. “I don’t think anyone predicted that it would look like this,” says Ettema. “It’s sort of an organism from outer space.”

Scanning electron micrographs of archaeon Candidatus 41 Prometheoarchaeum syntrophicum strain MK-D1

The proposed new organism, Prometheoarchaeum syntrophicum, puts out unusual protrusions, seen here in scanning electron micrographs.Credit: H. Imachi et al.

The researchers report that the cultured Lokiarchaeon produces energy by breaking down amino acids and that it can exchange molecules used to carry energy with symbiotic partners. Ettema says the Asgard genomes hinted at these capabilities, but without a lab culture they weren’t confirmed.

Finally, because the researchers could extract and sequence DNA from a pure sample, rather than sediment containing a multitude of organisms, their findings would confirm that Lokiarchaea do, in fact, contain numerous eukaryote-like genes. “It puts to rest any concerns about contamination,” says Gribaldo.

Ettema says this research opens the door to the next stage of Asgard research, although he stresses that many more Asgards will need to be cultured for researchers to work out whether, and how, Asgard-like archaea gave rise to eukaryotes.

Scanning electron micrographs of archaeon Candidatus 41 Prometheoarchaeum syntrophicum strain MK-D1

More scanning electron micrographs of P. syntrophicum.Credit: H. Imachi et al.

“We can’t just go back in time and observe what happened,” says Ettema. The Asgards we see today are not the same as the microbe that gave rise to eukaryotes. But he says that culturing more Asgards and studying what their eukaryotic-like genes actually do will give a fuller picture of the evolutionary tree, and help researchers to better infer how simple, single-celled organisms made the first giant leap towards complexity.

Nature 572, 294 (2019)

doi: 10.1038/d41586-019-02430-w

References

  1. 1.

    Imachi, H. et al. Preprint at https://doi.org/10.1101/726976 (2019).

  2. 2.

    Spang, A. et al. Nature 521, 173–179 (2015).

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