You and I are eukaryotes. So are tulips, armadillos, and blue whales. We’re different from bacteria (prokaryotes) because our cells are more complex. But where did all of us eukaryotes ultimately come from?
Evidence about our common ancestor — the ancestor of all animals and all plants, the Big Kahuna — has been mounting over the last 5 years or so. There was tantalizing DNA evidence out there that made it look like we were on the right track, but we hadn’t isolated any real living thing to talk about.
But after 12 years of trying, a group of government and academic collaborators in Japan look like they’ve nailed it. The pictures you see above are our first glimpse of Lokiarchaeota, a type of one-celled creature that has some eerie similarities to you and me. No one had ever cultured it before, or even seen it.
Their paper just came out a few days ago, though it has not yet been formally reviewed. But let’s peek at what some experts are saying about it to the leading science journals of our day:
Science:
“This is the work that many people in the field have been waiting for,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands. The finding has not yet been published in a peer-reviewed journal, but on Twitter, other scientists reviewing a preprint on it have already hailed it as the “paper of the year” and the “moon landing for microbial ecology.” [...]
“It was really a gargantuan task,” says David Baum, an evolutionary biologist at the University of Wisconsin in Madison, who was not involved with the work. [...]
Willem van Schaik, a microbiologist at the University of Birmingham in the United Kingdom [said], “It feels like this will go into microbial textbooks immediately.”
Nature:
“This is a monumental paper that reflects a tremendous amount of work and perseverance,” says Thijs Ettema, an evolutionary microbiologist at Wageningen University in the Netherlands. “It’s a major step forward in understanding this important lineage. … I don’t think anyone predicted that it would look like this. It’s sort of an organism from outer space.” [...]
“The whole field has been waiting for this moment for a long time,” says Simonetta Gribaldo, an evolutionary microbiologist at the Pasteur Institute in Paris. “It’s a tremendous effort. … Halfway through their experiment they must’ve realized they had gold in their hands.”
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One of the main things our cells have that bacteria don’t are organelles, or large structures inside the cell that do specific things. One of those is the nucleus, where all the DNA is kept. Another is the mitochondrion (plural: mitochondria), which generates energy, especially when oxygen is available. Mitochondria are really critical; malfunctions there can lead to diabetes mellitus, hearing loss, seizures, dementia, chronic fatigue, and a host of other issues.
It’s been clear for a long time that mitochondria used to be bacteria. They apparently got swallowed up by some other kind of cell that eventually became us, eukaryotes. There’s a ton of circumstantial evidence for it: Mitochondria have their own DNA, they divide like bacteria do, and their genes look an awful lot like bacterial genes. Their DNA is most similar to a kind of bacteria called Rickettsia that can invade animal cells and live within them, just like mitochondria do!
I’m taking care of my friends’ cats this week while they’re away (bear with me here), and when I went over there the other day, I saw, on the kitchen floor, an open box of Nilla Wafers, a phone case that had been up on the counter where the cabinet is, two whole Nilla Wafers, and a fair number of Nilla crumbs. You don’t need a biological expert to figure out what happened there. The circumstantial evidence for mitochondria once being bacteria is up there in the Nilla Wafers tier.
But what about the other part? What swallowed up those bacteria? Who was the culprit that is our distant ancestor? Until recently, it wasn’t very clear.
in 2015, a Swedish group had done some sampling from a deep-sea place called Loki’s Castle between Greenland and Scandinavia. You might remember the “Dumbo” creature that was discovered there:
This group found evidence — but only DNA evidence — that a simple bacterium-like creature called an archaeon was living there, and that it was more similar to us eukaryotes than any other bacterium or archaeon ever found. They said it amounted to a sort of genetic ‘starter kit’ for eukaryotes. Despite its apparent simplicity, it had primitive versions of a lot of machinery that eukaryotes have and bacteria don’t. They were really excited by their find, but a little disappointed they didn’t have any real organism to look at.
Enter our Japanese group, who had been doing a lot of deep-sea sampling in the Nankai Trough, more than 8,000 feet beneath the surface:
They didn’t know exactly what they were looking for when they started. They just wanted to know what was down there. They had been busy for five years already trying to grow organisms from this trough in a reactor that they were bubbling methane through, because that’s the kind of environment these organisms would be used to.
They spent another year splitting up the contents of their reactor into little tubes, each of which was fed different things. After about a year, ONE tube out of what must have been a hundred tubes finally showed a teeny bit of growth. And when they looked at the DNA, some of it was Lokiarchaeota DNA, and they actually use the word “excitingly” in their paper when they describe that. By then they knew what the Swedish group had found.
They figured out what the Lokiarchaeota were eating (amino acids) and so fed them more of that. It turned out that Lokiarchaeota can’t grow by themselves; they need a partner to eat the hydrogen they make. Their partner uses that hydrogen as fuel in order to make some other molecules to feed back to the Lokiarchaeota. So they have to work as a team.
They also found out that these guys grow REALLY slowly. It takes them about three weeks to divide once! It doesn’t matter what you feed them or how nice you are to them. Compare that to bacteria, some of whom can divide in 20 minutes! So it took them a LONG time to enrich the culture for Lokiarchaeota.
Finally, after a total of (gulp) twelve years, our intrepid researchers arrived at a pure culture of Lokiarchaeota and their hydrogen-eating partner.
Our long-lost ancestor!
This is like Henry Louis Gates Jr. showing us our family tree on PBS!
We can’t really go back in time and visit our true ancestor, of course, but here’s the most likely scenario of what happened:
Two billion years ago or so, we had the Great Oxidation Event, when oxygen levels started building up in the atmosphere. If you were deep in the mud, that didn’t matter much.
But if you wanted to compete with other organisms in the open, you’d need to figure out how to use oxygen. If you can respire (basically breathe oxygen), there’s way more energy to be had. You could wait millions of years to evolve the necessary genes, or you could find someone that had them already and borrow them somehow.
So we — and I can say “we” now, can’t I? This is my people! — had to figure out what to do.
We already had bacteria among us, and those little buggers had figured out how to use oxygen. But we were resourceful: we had complicated machinery — and tentacles! It seems we used our noodly appendages to grasp onto these oxygen-using bacteria to “Entangle-Engulf-Enslave” them! (The Japanese group coined that trifecta.) Can we just say we “cuddled” them?
The bacterium would ultimately become the mitochondrion, while the bulb (the blue part), containing all the DNA and a nice membrane structure around it, would become the nucleus. And those are two of the main things that distinguish our cells from bacterial cells.
There are a few other types of similar archaea (named after other Norse gods and collectively called the Asgard archaea) that remain to be cultured, and isolating those will help fill in the picture more completely. But twelve years of hard work by some pioneers in Japan has led the way.
A “monumental” paper, indeed.