A nucleus is one of many membrane-bound compartments that distinguishes our eukaryotic cells from the prokaryotic cells of microorganisms like bacteria. Eukaryotic cells also possess energy-producing compartments we call mitochondria.

Because mitochondria look like prokaryotes, it's long been assumed that eukaryotic cells came into existence when one prokaryote swallowed another prokaryote. The subsumed prokaryote then set up shop inside the host prokaryote and evolved into a mitochondrion. A problem with this idea is that prokaryotic cells lack the ability to phagocytose—to swallow other cells. Eukaryotic cells can, but every eukaryote we know about has mitochondria. It's not clear which came first: the ability to swallow other cells, or the mitochondria.

But over time, researchers have made the case that the ancestor of all eukaryotes belonged to a group of organisms called archaea. And now, one team says it can point the finger at a specific organism.

The first clue about our ancestry came with the discovery of archaea in the 1970s. This third branch of life is unicellular and lacks a nucleus, like bacteria and other prokaryotes. But the genetics, biochemistry, and metabolism of archaea are as distinct from prokaryotes as they are from eukaryotes like us. Archaea seemed like a good place to look for the first host cell to subsume and transform a bacterium into a mitochondrion—a microbial missing link, if you will.

According to a paper recently published in Nature, researchers now think they've homed in on the particular species of archaea that may have done it: Lokiarchaea, initially described last year. These critters got their ominous name because they were found at Loki’s Castle, a hydrothermal vent under the Arctic.

Metagenomics! Lokiarchaea were identified via metagenomics, a process that deserves a tangential paragraph or two. Lokiarchaea were identified via metagenomics, a process that deserves a tangential paragraph or two. In a metagenomic analysis, molecular biologists scoop up a complex mixture of many types of microorganisms—in this case, sediment off the ocean floor near the Bering Strait—and obtain DNA sequences from it. From these sequences, we can parse out all the different species mixed in there. This is a far cry from how scientists used to study genes by growing a single species in the lab in order to sequence its purified DNA. Because metagenomics allows us to examine the DNA of organisms that cannot be cultivated in a lab, the number and types of organisms now available for scrutiny has exploded.

Because they possess a number of enzymes and metabolic capabilities that prokaryotes don’t, Lokiarchaea are already kind of like proto-eukaryotes. They don’t phagocytose, but a new analysis of their genome shows that they have qualities consistent with an alternate proposal about mitochondrion-acquisition: the hydrogen hypothesis.

The idea is that the host that first acquired the mitochondrion was autotrophic (able to live off simple chemicals), anaerobic (does not require oxygen), and hydrogen dependent. An organism that is autotrophic can generate whatever organic compounds it needs (proteins, fats, sugars) from simple inorganic compounds in its environment as long as it has energy (plants can do this, but we can’t). Instead of using oxygen to generate ATP, the molecule that provides energy to drive metabolism, our hypothetical ancestor used hydrogen instead.

Conveniently, the bacterium that was engulfed by a host to become a mitochondrion almost certainly generated hydrogen as a waste product of its own metabolism.

Lokiarchaea meets all three conditions. And, in contrast to the theory of acquisition that relied on one cell swallowing the other, the hydrogen hypothesis does not need the host to have already evolved a nucleus or other complicated cellular structures.

Once it became apparent that eukaryotes did not arise from bacteria, it's still unclear if they arose from archaea or if archaea and eukaryotes shared a common ancestor before splitting off from each other. By fitting very neatly into the existing hydrogen hypothesis, Lokiarchaea suggest the former scenario: a hydrogen-dependent archaea merged with a hydrogen-producing prokaryote to form the first eukaryotic cell.

Nature Microbiology, 2016. DOI: 10.1038/nmicrobiol.2016.34 (About DOIs).

Nature, 2016. DOI: 10.1038/32096 (About DOIs).