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Meet Loki, your closest-known prokaryote relative

It may not look like it, but these deep-sea critters are our closest known (prokaryote) relative

Deep in hydrothermal vents beneath the Arctic Ocean, scientists have discovered an organism that sheds fresh light on the evolutionary link between simple and complex cellular life.

The microbe and its relatives known as Lokiarchaeota, described in the journal Nature, are single-celled critters with a strange mix of traits connecting them to eukaryotes -- the group that includes all complex cellular life on Earth, including animals, plants and fungi (and, yes, humans).

The composite genome of one such microbe, Lokiarchaeum, represents our closest-known simple-celled relative, according to the work led by Anja Spang of Uppsala University in Sweden. 

“This technically outstanding paper has far-reaching implications for how we view early eukaryotic evolution, including our own deep ancestry,” T. Martin Embley and Tom A. Williams at Newcastle University in England wrote in a commentary on the study.

Cellular life on Earth is descended from two groups of humble organisms: prokaryotes (which include bacteria and archaea) and eukaryotes (which includes every complex living thing you can see with your naked eye, humans included). The eukaryotic cell stands out from its two prokaryote peers in many ways. Among them: It has a nucleus filled with its DNA, mitochondria to produce energy and many other membrane-enclosed organelles.

(Mitochondria, by the way, probably originated as free-living bacteria that ended up getting swallowed by other cells, becoming a symbiotic partner. The mitochondria maintains its own DNA, which is why it can be used to trace back maternal lineages.)

Figuring out how eukaryotes emerged from prokaryotes has been something of a mystery, because there don’t seem to be a lot of organisms alive today whose lineages help fill in that evolutionary chain of events. So researchers have debated whether eukaryotes are a separate group of organisms that share a common ancestor with archaea, or whether they’re actually a subgroup of archaea.

“The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology,” the study authors wrote.

Lokiarchaeum (or Loki for short) was found in 7.5 grams of sediment taken from a 2-meter-long core pulled out of an active venting site along the Arctic Mid-Ocean Ridge 10,771 feet below sea level, near a site called Loki’s Castle.

After carefully analyzing the DNA in this tiny sample, the researchers discovered evidence of an archaean prokaryote – but one whose genes revealed a number of shared characteristics with eukaryotes, including a dynamic protein cytoskeleton and the ability to engulf and consume other cells – an ability that could have allowed them to capture the ancestor of mitochondria.

“Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor,” the authors wrote. “This provided the host with a rich genomic ‘starter-kit’ to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.”

The find raises hopes that perhaps other living examples of microbes that are descended from microbes along the prokaryote-eukaryote transition may still be just waiting to be found, the study authors said.

“The gap between prokaryotes and eukaryotes might, to some extent, be a result of poor sampling of the existing archaeal diversity,” they wrote. “Environmental surveys have revealed the existence of a plethora of uncultured archaeal lineages, and some of these likely represent even closer relatives of eukaryotes.”

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