We’ve finally gotten a look at the microbe that might have been our ancestor

The cells of all animals, plants, and fungi have an impressive complexity, with a variety of compartments specialized in various tasks, like generating energy, digesting proteins, or holding DNA. If you look at bacteria or archaea, however, their interiors are essentially featureless. How did this cellular complexity come about?

A key thing that has limited our understanding here is that we've never gotten a sense of what the ancestors of complex cells looked like. Over the last several years, we've found increasing genetic evidence of the existence of modern descendants of these organisms, but we've never been able to grow them to have a look at them. On Tuesday, however, a paper reports on the success of a decade-long attempt to get one of these to survive in culture. And the resulting microbes look very weird—but weird in a way that hints at how complex cells evolved.

Welcome to Asgard

Complex cells, called eukaryotes, carry a mixture of three types of genes. Some come from the bacteria that were incorporated as mitochondria and chloroplasts. Others seem to have evolved after the origin of complex cells. And yet others seem to have originated in archaea, a distinct type of simple, single-celled organisms that were once classified as bacteria. This provided key support to the idea that complex cells originated when archaea somehow swallowed bacteria and started using them to produce energy.

A careful comparison of the genes found in eukaryotes to bacteria, along with a consideration of the mitochondria's metabolism, has pointed to a specific type of bacteria as the ancestor of the mitochondria. A similar sort of analysis of the archaeal gene contribution, however, wasn't quite as definitive. Although it identified a couple of branches of archaea as relatively close to eukaryotes, the match wasn't especially good.

That situation changed with the advent of large-scale DNA sequencing, which enabled us to start looking at the DNA of organisms that couldn't otherwise be grown in sufficient quantities to characterize. In 2010, sequencing of environmental samples revealed the existence of the Asgard archaea (including Lokiarchaeota, Thorarchaeota, Odinarchaeota, and Heimdallarchaeota). Based on the genome reconstructions, these organisms appear to have relatives of some genes that had only been seen previously in eukaryotes and are used for organizing the inside of cells. Various studies of their DNA placed them as eukaryotes' closest living relatives—in fact, all eukaryotes can be considered a single branch of the Asgard archaea.

There was just one problem: we had no idea what they looked like. That means we couldn't possibly determine what these genes were doing inside their cells. It's possible that the Asgard archaea had already evolved some degree of complexity before swallowing bacteria. At the same time, because we couldn't definitively show that these genes came from an archaeal cell, questions were raised about whether Asgard archaea really existed and had the genes we thought they had.

Patience was a virtue

Assuming it holds up to peer review, a paper posted on the bioRxiv on Tuesday should end the debate. A group in Japan has finally cultivated a strain of Lokiarchaeota it is calling Candidatus Prometheoarchaeum syntrophicum strain MK-D1 (we'll just be casual about it and go with MK-D1). Part of the story is what this tells us about the origin of complex cells. But another part is the phenomenal patience the researchers demonstrated in getting this work done.

It all started with a sample of the sorts of sediments where Asgard archaea had been found previously, placed in a bioreactor that continued to feed its contents the nutrients found in the sediment. This was allowed to run for over five years before the researchers started taking samples out of it and trying to grow individual microbial strains. They did this by sealing small samples from the bioreactor in glass tubes with some minimal nutrients and letting them sit at room temperature. Amazingly, they did not give up as the months rolled by and nothing grew. It took an entire year for one of the tubes to show some of the faint cloudiness caused by microbial growth.

Several rounds of regrowth and purification followed, each of which took about three months for growth to get going (the team estimates that the microbes need two to three weeks to do a single cell division). Eventually, the researchers were left with a culture that had just a single bacterial species and MK-D1 growing in it, but the process took a dozen years—longer than we'd known that Asgard archaea existed.

The bacteria and MK-D1 grew together because they apparently had a symbiotic relationship of sorts. MK-D1 was able to break down a number of different amino acids to obtain energy, and it produced hydrogen as a byproduct. But allowing hydrogen to build up caused this metabolism to slow down dramatically, so the archaeal cells would hand off the hydrogen to the bacteria, which consumed that as fuel.

Building complexity

That tight association provides an obvious route to internalizing the bacteria and generating mitochondria. There was just one small problem with the idea: the MK-D1 cells were really small; they didn't seem to be capable of doing anything like swallowing bacteria. In fact, the cells had no detectable internal structure at all, making the idea that the Asgard archaea had been complex prior to forming eukaryotes unlikely.

What they did have, however, was external complexity. Under some circumstances, the cells would form lots of membrane protrusions that jutted out from their surface. Under others, they would stretch out long filaments that formed complex branching patterns. Thus, rather than building structures inside the cells, it seems that many of the genes shared by us and MK-D1 are used to organize their membranes to form external structures.

The research team suggests that these protrusions normally interact with the symbiotic bacteria, increasing the ability to shuttle hydrogen out of cells and have it metabolized away. And, the researchers argue, this provides a clear model for how complex cells came about. By continuing to elaborate these contacts, a cell like MK-D1 could eventually engulf its bacterial partner. And should the process proceed in an uncontrolled manner, it could potentially swallow the archaeal cell itself, which would explain how the cells' genetic material ended up encased in a distinct membrane compartment.

While there are still some hypotheticals to this model, it does explain two of the most important features of eukaryotic cells. And even if the model needs revision, the ability to cultivate Asgard archaea has already answered two of the most critical questions about them: they're real, and they don't seem to have any internal complexity. The next important step will be to try to shift these cells back to something like a sterile version of their native environment to ensure that the strange features of MK-D1 are its normal state and not just a response to the culture conditions.

bioRxiv. Abstract number: 10.1101/726976v1  (About the arXiv).