Interactive by Emily Fuhrman and artwork by MRK for Quanta Magazine, with art direction by Olena Shmahalo/Quanta Magazine

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Life’s Secrets Sought in a Snowflake

Clever geometry illuminates how single cell organisms can band together to form cooperative multicellular entities.

Chapter 1: Complex Cells

Mongrel Microbe Tests Story of Complex Life

A newly discovered class of microbe could help to resolve one of the biggest and most controversial mysteries in evolution — how simple microbes transformed into the complex cells that produced animals, plants and fungi.


In September 2014, Christa Schleper embarked on an unusual hunting expedition in Slovenia. Instead of seeking the standard quarry of deer or wild boar, Schleper was in search of Lokiarchaeota, or Loki, a newly discovered group of organisms first identified near deep-sea vents off the coast of Norway. The simple, single-celled creatures have captured scientists’ interest because they are unlike any other organism known to science. They belong to an ancient group of creatures known as archaea, but they seem to share some features with more complex life-forms, including us.

Though little is known about Loki, scientists hope that it will help to resolve one of biology’s biggest mysteries: how life transformed from simple single-celled organisms to the menagerie of complex life known as eukaryotes — a category that includes everything from yeast to azaleas to elephants. “Next to the origins of life, there’s probably no bigger mystery in the history of life,” said John Archibald, an evolutionary biologist at Dalhousie University in Nova Scotia.

The jump from single cells to complex creatures is so puzzling because it represents an enormous evolutionary gulf. “How do you make a eukaryote, that’s a big question,” said Schleper, a microbiologist at the University of Vienna in Austria. “It’s a huge transition.”

Though single-celled organisms blanket the Earth and are capable of impressive biochemistry — some can eat nuclear waste, for example — their structure and shape remain simple. Cells from animals, plants and fungi, which make up the eukaryotes, are much more sophisticated. They possess a suite of features lacking in their simpler brethren: a nucleus that houses DNA; an energy-producing device known as the mitochondrion; and molecular architecture, known as the cytoskeleton, that controls cell shape and movement.

Most biologists agree that at some point around two billion years ago, one featureless cell swallowed another, and the two began to work together as one. But the details of this process — whether this symbiosis jump-started an evolutionary process, or whether it happened midway along the path to eukaryotes — continue to drive huge disputes in the field. One group theorizes that eukaryotes emerged in a rapid burst, driven by the acquisition of the cellular energy factories known as mitochondria. Others propose a slower, stepwise process. They say that mitochondria couldn’t have developed in simple cells; some level of complexity must have evolved before mitochondria came onboard. The debate has grown so heated that members of each camp no longer attend the other’s conference sessions.

University of Bergen, Norway

Lokiarchaeota were first discovered off the coast of Norway, 15 kilometers from deep sea vents known as Loki’s castle, shown here.

Since biologists can’t travel back in time, they search surviving life-forms for clues. But no detectable intermediates between ancient, single-celled life and early eukaryotes exist, making it nearly impossible to reconstruct the order of evolutionary events. “When something only happens once, it’s hard to grapple with the problem,” Archibald said. “We’re left studying the DNA sequence of modern organisms and trying to piece it together.”

Enter Loki, which some scientists have dubbed a microbial missing link. It is descended from an ancient lineage and is a simple organism with patches of apparent complexity. Genetic analysis places Loki squarely within the single-celled archaea. But it possesses an intriguing collection of genes that look as though they would be more at home in eukaryotes, rather like modern words dotting a medieval manuscript. In fact, Loki’s genetic machinery suggests that the organism might be able to engulf other cells, the first step in the creation of mitochondria. “These genes could have provided a starter kit for eukaryogenesis, the emergence of eukaryotes,” said Thijs Ettema, a microbiologist at Uppsala University in Sweden who first described Loki in collaboration with Schleper in Nature last May.

Loki thus outlines a new potential origin story for eukaryotes, one that walks a middle path between the two extremes. Mitochondria may have been born early in the evolution of eukaryotes. But that first mitochondrial host may have already possessed some sophisticated features, most notably the ability to engulf other cells. “It hints that [the Loki] are stepping-stones to eukaryotic complexity,” Archibald said.

Schleper, Ettema and others are now searching for new varieties of Loki, hoping to find some that are even closer to eukaryotes on the evolutionary tree. Schleper’s expedition to Slovenia was part of this ongoing hunt. The trip was successful, though she is reluctant to reveal the details for fear of being scooped. Like a prospector for gold, she has her own secret methods for figuring out the most promising sites for finding Loki. Yet her discoveries are even more precious — they promise to illuminate the mystery of how complex life began.

Mitochondrial Merger

Eukaryotes have a number of innovations compared to their more primitive archaeon ancestors. Most notable among them are the nucleus, which houses vastly more DNA than bacteria and archaea can accommodate, and the mitochondrion, which provides the energy to manufacture the many proteins produced by that genome.

Both the nucleus and the mitochondrion reflect a remarkable merger that took place early in eukaryotic life. At some point, an archaeon or a primitive eukaryote engulfed a bacterium, developing a symbiotic relationship. Against all odds, the two organisms became irreversibly intertwined. The resident bacterium became more and more dependent on its host cell, surrendering the vast majority of its genes, some of which ended up in the nucleus. The result was a singular development in the history of evolution that birthed the mitochondrion.

Video: An amoeba consumes two paramecia. A similar event among two much simpler organisms two billion years ago led to cells with complex internal features.

“A single event in four billion years of evolution sculpted the whole future evolution of eukaryotes — that’s kind of freaky,” said Nick Lane, a biochemist at University College London. “Chances are that it would go wrong, because the two organisms have to figure out how to get along and to synchronize their life cycles.”

Exactly how and when mitochondria came onboard is one the biggest controversies surrounding the origin of eukaryotes. Did mitochondria emerge early on, or did eukaryotes develop gradually over time, acquiring mitochondria somewhere along the way?

“The field really is hung up over the question of whether the bulk of eukaryotic cellular complexity arose before, during or after the evolution of mitochondria,” Archibald said. The debate is so intense that when Ettema began to explore this question, colleagues told him it would be career suicide.

Christa Schleper

In search of new varieties of Lokiarchaeota, a student collects water samples from salt flats in Slovenia.

The first option, called the big-bang or mitochondria-early theory, predicts that a primitive archaeon engulfed a bacterium, an event that drove the development of eukaryotes. But it’s unclear how the archaeon could have picked up that bacterium. Scientists know of only two cases where bacteria live within other bacteria. (Eukaryotes, on the other hand, frequently harbor symbiotic bacteria.) “That’s one of the biggest hurdles faced by the mitochondria-first scenario,” said Eugene Koonin, an evolutionary biologist at the National Center for Biotechnology Information in Bethesda, Md.

The second option, sometimes called the slow-drip or mitochondria-late theory, posits that proto-eukaryotes had already begun to develop complex features — particularly the ability to engulf prey — when the mitochondria came onboard. According to this theory, the most ancient eukaryotes should lack mitochondria.

Evidence once seemed to point toward this option. For example, a number of parasites, such as giardia, are missing mitochondria. Scientists initially thought that these parasites never had the organelle. But in recent years, it’s become clear that these organisms simply lost their mitochondria over the course of evolution.

The discovery of Loki opens a sort of middle ground between the two groups. Here is a relatively simple cell that might have the machinery for engulfing bacteria, the first step in the creation of mitochondria. Loki has a number of genes typically found in eukaryotes, including genes linked to the dynamic, shape-shifting cytoskeleton. In eukaryotes, these genes enable the cell membrane to change shape. Amoebas, for example, change shape both to move and to engulf prey. “This is a very eukaryotic-specific process, and for the first time, we found them in an archaeon,” Ettema said. “This was very exciting.”

“An archaea with these features, such as a cytoskeleton, certainly makes [the mitochondria-early] scenario more palatable than it was before,” Koonin said.

Sight Unseen

Two-Pronged Tree

Archaea are a relatively new addition to the tree of life, first discovered in the 1970s in the famed hot springs of Yellowstone National Park. Though they outwardly resemble bacteria, on a genetic level archaea are as different from bacteria as we are.

Based on their RNA, the biologist Carl Woese proposed that archaea represent a third domain of life, requiring a reconfiguration of the basic tree. The classic five-kingdom version that many of us learned in elementary school was eventually replaced by a simpler structure with just three main branches: eukaryotes, bacteria and archaea.

But the tree of life is in a constant state of revision. Lokiarchaeota and other newly discovered archaea are the closest living relatives to eukaryotes found to date and share a smattering of eukaryotic features. This suggests that eukaryotes grew out of archaea rather than in parallel. We are a daughter to archaea, not a sibling.

“The discovery of the Loki certainly adds huge weight to the archaeal origin of eukaryotes,” said Mark Field, a biologist at the University of Dundee in Scotland. That means that Woese’s three-domain tree has been stripped to just two basic branches: bacteria and archaea.

The Loki discovery comes with one major caveat: So far, no one has ever seen one. Scientists can’t yet grow them in the lab. All they can do is isolate their DNA and try to infer what it does. “We have to be clear, we don’t know what it looks like,” Archibald said. “Their biology is being pieced together from genomic data.”

In the world of microbiology, that’s not unusual. The vast majority of microbes can’t be grown on demand, so scientists study them by analyzing and comparing their DNA. “That’s what we do in microbiology, we make predictions from genomes,” Schleper said. “[The Loki] for sure have something very special in their membranes.”

The precise nature of that special something is still unclear. Archibald and others caution that though Loki has genes that are involved in membrane remodeling in other organisms, no one knows for sure that they perform the same function in Loki. Perhaps they do something different in these simpler organisms, and membrane remodeling evolved later.

Lane, for one, is unconvinced that Loki can engulf other microbes — without a mitochondrion, he says, it simply lacks the power. “It costs a lot of energy to become large, to move around and engulf and digest cells,” Lane said. In modern cells, that process involves 1,000 genes, all of which cost a lot of energy to produce, he said.

Schleper and Ettema are working hard on growing Loki in the lab, but culturing it has proved extremely difficult. The original samples were excavated from the deep sea, where oxygen is scarce and the organisms’ metabolism is extremely slow. Some estimates predict that the creatures that live there divide only once every 10 years. Moreover, these sediment-dwelling Loki are adapted to the extreme environment at the bottom of the ocean, so bringing them to the surface is likely a death sentence. To get them to survive, “you have to be very careful and lucky,” Ettema said.

Fortunately, the researchers have discovered that Loki also inhabits less alien environments, and they expect samples from those sources to prove easier to grow. Since their initial discovery, Schleper and Ettema have found that Loki are more common than anyone expected. They have since identified new variants in a number of environments: hot springs, shallow marine sediments, rivers, even the permafrost. “It’s like an Easter egg,” Ettema said. “We don’t know what we’re going to find, but every new genome has something in it.”

Part of the challenge in finding Loki samples is that they tend to be few in number, a rare figure in local microbial ecosystems. That might explain why they remained undetected for so long. Moreover, Schleper said, the methods used to survey microbial diversity aren’t well suited to detecting archaea in general.

Ettema is optimistic that they will figure out how to grow Loki in the lab. But he cautions that observing live Loki might not resolve questions about its ancestral abilities. Present-day Loki may be very different from the ancient versions that gave rise to eukaryotes. Even if modern Loki can engulf bacteria, that doesn’t prove that ancient ones did. It has had 2 billion years to evolve — a length of time that saw the emergence of humans from single-celled organisms. “People overstate a bit what we’ll know from culturing it,” Ettema said.

Even if Loki doesn’t solve the mystery of our ancient origins, its discovery shows just how much biological diversity remains to be unearthed. Perhaps the next discovery will be a eukaryote with no history of possessing mitochondria. Or perhaps it will be an archaeon with signs of a symbiotic bacterium living within. “It emphasizes just how much novelty we can find by sequencing the genomes of organisms that can’t be grown in the lab,” Koonin said. “Chances are that more is going to be discovered, discoveries that can be dramatic and crucial for our understanding of biology.”

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  • Quote: "Though single-celled organisms blanket the Earth and are capable of impressive biochemistry — some can eat nuclear waste, for example — …"

    Not sure if eating it the right word for it, but … to extend on it a bit to limit the possible wrong conclusion it might trigger:

    Quote[1]: "It is reported that, Shewanella putrefaciens CN32 can change toxic and water soluble uranium (VI) to the less soluble, stationary and therefore less harmful uranium (IV) as part of their normal growth. Actually, radioactivity is not removed, but uranium is no longer chemically available to be absorbed by organisms that might be harmed by them.


  • What is referred to as "bulk of eukaryotic cellular complexity" includes the nucleus. Although the mitochondria are integral to understanding eukaryotic biology, the nucleus is the largest unknown. There is no precedent in bacteria or archea for most of the nuclear characteristics. No theory of endosymbiosis explains the nucleus from present observations. One idea is that the nucleus came from megaviruses, but that is still speculation. I question whether Loki will answer this question, but it is nonetheless, a very interesting scientific endeavor.

  • Every time I try to wrap my mind around this it seems like no matter what the original nucleus was … it was completely in control of the eventual creation of eukaryotes.

    I can comprehend a megavirus, early Achaean, or something else figuring out how to set up shop inside another cell and hijack its host.

    I hear about 'symbiosis' a lot, but other than 'being a really good host with good genetic code to utilize' I don't see any real mechanisms for the host to have any influence over what the proto-nucleus does with it once it decides to divide. I could even see how the original nucleus had all the machinery needed to take advantage of any other nifty toys it came across (like the mitochondria), though I see a huge analog scale between 'extra-powerful-hijacker' and 'regular hijacker with an optimal host'

    I'm an amateur, of course, but are there any theorized mechanisms by which host cell could make sure the nucleus includes it when it divides? Maybe some odd three-entity process where a virus is used by the host or something?

  • “How do you make a eukaryote, that’s a big question,”

    Are you serious? Lynn Margulis (aka Lynn Sagan) solved this problem 50 years ago in her now classic paper the Origins of Mitosing Cells.

    And in the subsequent years a huge body of research has accumulated to show that her theory of symbiogenesis makes accurate predictions. As for the origins of multi-cellularity their have been a raft of papers recently on communication between bacterial cells living in colonies. Or we could look to the slime moulds. It seems to me that the author of the article is rather confused about what the scientists are looking for in Loki – it is nothing to do with multi-cellularity for example. That's a red herring.

    I agree previous comments that the big question is regarding the nucleus. Although it remains unclear where the nucleus comes from (except for mitotic spindles which clearly are bacterial) there is at least no observation which says it could not have emerged through endosymbiosis.

    The article only seemed to inquire into "engulfing", but parasitic organisms don't wait to be invited in. There is also the fact that in theory any bacteria can share genetic material with any other bacteria. So the original endosymbiotes need not have physically entered the host cell as long as their genes/genome got inside! And since viruses also evolved from bacteria this is not so hard to imagine.

    So many possibilities exist that are not even hinted at here.

  • Very informative on the extended research and ecology of Lokiarchaeota!

    The mitochondria-late theory is supported by the latest and most elaborated mitochondrial phylogeny, where the introduction of a proto-mitochondria node allow for resolving the pre-mitochondrial ancestor as splitting from within the parasitic <i>Rickettsiales</i>. The ancestor was an ATP importing parasite, only later evolving (co-opting) the crucial endosymbiont ATP-exporter. [ ] E.g. it was a slow symbiosis that could have been attempted any number of times during the free-living parasitic, later endo-parasitic stages. [See below for recent tests of such a gradual evolution, i.e. when folding the nucleus into the evolutionary events of the lineage.]

    "Lane, for one, is unconvinced that Loki can engulf other microbes — without a mitochondrion, he says, it simply lacks the power. “It costs a lot of energy to become large, to move around and engulf and digest cells,” Lane said. In modern cells, that process involves 1,000 genes, all of which cost a lot of energy to produce, he said."

    I used to embrace Valentine's ecological energy theory on archaea (low leakage membrane energy specialists) and Lane's ecological energy theory on eukaryotes (mitochondria high energy density specialists). But they are both arguable in the light of later evidence. Metabolic rates simply scale with cell sizes, consistent with how they scale with multicellular organism sizes. [ ; ]

    Finally, notably a long series of comments speculate that the nucleus evolution can't be explained by the mitochondrial endosymbiosis [Steve Hedrick, Jayarava] and/or that it is the result of a similar endosymbiosis event [Will Holz].

    It is well known, if not consensus accepted as base for evolutionary phylogenies, that the nucleus membrane topology of a double membrane with folded nuclear pore complex openings instead of membrane channel inserts is incompatible with a separate endosymbiosis event.

    The recent inside-out model for evolution of the nucleus is compatible with both the Lokiarchaeota and the mitochondrial phylogenies, "driven primarily by selection for an increasingly intimate mutualistic association between an archaeal host cell and alpha-proteobacteria (proto-mitochondria), which initially lived on the host cell surface (Figure 1)." [ ]

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