Eukaryotes—fungi, plants, us—are complex. Our large cells are characterized by their different compartments, many of which are neatly enclosed within a boundary of membrane. These compartments contain complex molecular machines that perform equally complex metabolic tasks: they degrade proteins, they splice RNA molecules, they engulf foreign bodies.

Prokaryotes, on the other hand—one celled organisms like bacteria—are simple, with a notable lack of internal membrane enclosed structures (i.e., nuclei) in their one and only cell. It has been assumed that eukaryotes must have somehow evolved from prokaryotes, but it has not been at all clear how that may have happened.

A clue came in 1977, when another branch type of prokaryotic life was discovered: archaea. They are single-celled organisms that lack nuclei and other structures, just like bacteria. But from an evolutionary standpoint, they are about as distant from bacteria as they are from eukaryotes. As soon as archaea were recognized, people started speculating that eukaryotes may have originated within the archaeal branch of life rather than the bacterial branch, or that eukaryotes and archaea might share a common ancestor.

One particular group of archaea has a number of proteins that were part of the eukaryotic signature, suggesting that there might be a missing link between prokaryotes and eukaryotes—an archaea that is more complex than the ones we have thus far identified. But finding that organism had to wait until the technology existed to generate and analyze genome data from entire populations of organisms. And now we can.

While tooling around near the Arctic Mid-Ocean Ridge, between Greenland and Siberia, a bunch of biologists dredged up some microbes near a vent on the ocean floor. They found a group of archaea that are among the most widely distributed and abundant in the deep marine biosphere—but they had never been cultivated in a lab or had their genome sequenced. The latter issue was quickly corrected.

When the biologists examined the genome of these archaea, they found that 175 proteins, about three percent of the total, were most similar to eukaryotic (as opposed to bacterial or archaeal) proteins. These archaea were initially identified near the vent known as Loki's castle—you know how that Loki was always stirring up trouble—so the researchers named them Lokiarchaeota. The researchers also found Lokiarchaeota in another sediment core sample from the ocean floor near Japan. Their discovery is reported in Nature.

Phylogenic analysis suggested that Lokiarchaeota and eukaryotes share a common ancestor. Lokiarchaeota have genes similar to eukaryotic actins, cytoskeletal proteins that help the eukaryotic cell maintain its three-dimensional shape and provide the scaffolding for cell division, cell movements, the shuffling of cargo within a cell, and the ingestion of material in the environment, a process called phagocytosis.

The organisms also have a large collection of Ras-superfamily GTPases, which comprise about two percent of their genome; this percentage is much more similar to that seen in eukaryotic cells than the number found in bacterial or even archaeal cells. These GTPases, like actins, are involved in cytoskeletal and cellular transport processes. And they have other eukaryotic signature proteins involved in protein degradation and membrane budding.

If Lokiarchaeota and eukaryotes do in fact share a common ancestor, as this work suggests, then many of the eukaryotic cells' complexities—notably a cytoskeleton and the ability to form membrane-bound vesicles—may have been in place before eukaryotes split off from archaea, roughly two billion years ago.

The defining moment in eukaryogenesis is thought to be when one primordial cell engulfed a bacterial neighbor, then kept that neighbor sequestered inside where it eventually became a power-generating organelle called a mitochondrion—considered a universal feature of eukaryotes. But that primordial cell would need to have the ability to swallow its neighbor, meaning phagocytosis. Lokiarchaeota has genes that might give it just those phagocytic abilities.

This new group is only one of the first of a vast population of uncultivatable archaea to be examined. It provides a candidate for a primordial, almost-but-not-yet-quite eukaryotic cell—one potential missing link. But its full significance will probably only become clear once we obtain the genomes of more of its relatives.

Nature, 2015. DOI: 10.1038/nature14447 (About DOIs).

Nature, 2015. DOI: 10.1038/nature14522 (About DOIs).