Scientists Find First Direct Evidence of How Complex Cells May Have Evolved

Stromatolites — dense, layered microbial communities that can look like little more than dark rocks — helped release some of Earth's earliest oxygen into the atmosphere billions of years ago, before animals or plants existed. A study published in Current Biology suggests these "living fossils," which still form today at Shark Bay, a World Heritage-listed site in Western Australia, may also preserve clues to a separate milestone in evolution: how complex life first emerged.

A team led by Associate Professor Brendan Burns, an evolutionary microbiologist at UNSW Sydney, working with researchers from the University of Technology Sydney and the University of Melbourne, isolated a previously unknown microbe from Shark Bay samples. It belongs to the Asgard archaea, an unusual group of microbes believed to be closely related to the ancestors of eukaryotes — the type of cell that makes up all plants and animals, including humans. One long-standing theory holds that the first eukaryotic cell arose when an ancient archaeon and a bacterium formed an intimate partnership, with one organism eventually engulfing the other to produce mitochondria, the energy-producing structures inside complex cells. Until now, scientists lacked direct evidence of what such a partnership actually looked like.

Using electron cryotomography, a high-resolution 3D imaging method capable of revealing structures at the scale of a millionth of a millimeter, the researchers captured the first visual evidence of an Asgard archaeon physically connected to a bacterium through extremely thin, tube-like structures called nanotubes. The archaeon also produced chains of budded vesicles and other elaborate tube-like structures. The two microbes appeared to complement each other chemically, each producing compounds — including vitamins, nutrients and hydrogen — that the other could use. "This could be a little model for how these kinds of partnerships started and ultimately formed eukaryotes," Burns said.

Growing the elusive microbe in the laboratory took four to five years, Burns said, partly because Asgard archaea are notoriously difficult to cultivate away from their natural habitat; the researchers could never grow the organism in pure culture, which Burns said may itself show it depends on other organisms to survive. The team also used deep learning, a type of machine learning, to predict the microbes' protein structures, said coauthor Kate Mitchie of UNSW. The newly identified archaeon has been named Nerearchaeum marumarumayae, combining Nereus, the ancient Greek sea god, with a Malgana word meaning "ancient home" — honoring the Malgana people, the traditional custodians of the Shark Bay region.