A Mathematician Who Decodes the Patterns Stamped Out by Life: Corina Tarnita deciphers bizarre patterns in the soil created by competing life-forms. She’s found that they can reveal whether an ecosystem is thriving or on the verge of collapse. Quanta Magazine by Joshua Sokol
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Corina Tarnita decoded mysterious “fairy circle” patterns in the landscape. Photo by Sasha Maslov for Quanta Magazine.
When Corina Tarnita was a budding mathematician, she found her interest in mathematics flickering, about to burn out. As a girl she had stormed through Romania’s National Mathematical Olympiad — where she won a three-peat from 1999 to 2001 — then on to Harvard University as an undergraduate and straight into its graduate school to study questions in pure mathematics.
Then suddenly, around a decade ago, it wasn’t so fun anymore. “I would still get a kick out of solving a problem,” she said. “The question is whether it was just kind of an ego kick.”
Facing a crisis of faith, Tarnita felt her future narrow to just a few paths. She had been offered a cushy “quant” job working for a bank. She could take time off. And then she found in the library an intriguing book with a colorful cover called Evolutionary Dynamics: Exploring the Equations of Life. The book’s author, the mathematical biologist Martin Nowak, was, conveniently, also at Harvard. The same week she had to decide on the job, she sent him an email asking to meet.
The meeting changed her life. Tarnita turned down the job and finished her doctorate with Nowak. (She completed her Ph.D. just a year after earning her master’s degree.) She began a project with him and the legendary biologist Edward O. Wilson that led to a 2010 Nature paper on the evolution of cooperative insects like ants and termites. Since 2013, she has continued to study biology using mathematical tools as a member of the faculty at Princeton University.
Since switching fields, Tarnita has focused her work on how living things orchestrate themselves itself into patterns on different scales. Sometimes the forces of natural selection bear down on individuals. Other times, they act on a unit such as an ant colony. Other collective organisms such as slime molds must contend with evolutionary pressures both on the whole and on individuals. And in still larger systems like the African savanna, evolution shapes the component parts, but not the whole. “From the small scale to the large scale,” she wonders, “does nature use the same rules?”
Fairy circles are bare patches that dot the Namibian landscape. Photo by milehightraveler / Getty Images.
Of all the patterns Tarnita explores, one of the most enchantingly enigmatic are fairy circles: barren round patches that dot the grasslands of Namibia like pepperoni slices on a pizza. They can persist as long as 75 years, but their cause has been hotly debated. Some scientists argue that termite colonies build and maintain the bare circles, while others blame them on plants battling for water across the arid landscape. In January 2017, Tarnita and her colleagues published an article in Nature that suggested a compromise: that both processes together, acting on different scales, could imprint the observed pattern on the ecosystem.
Among her other projects, Tarnita is still working on understanding the fairy circles, which may someday allow environmental scientists to tell from satellite imagery if an ecosystem is on the verge of collapsing into a desert (or if it’s especially resilient). Quanta caught up with her to ask about her early forays into mathematics, her career arc and her current research. The interview has been condensed and edited for clarity.
You recently argued that we need to better understand how systems like multicellular organisms evolve out of individual units. What would this kind of research program look like?
If you think about any kind of system, hierarchical organization is everywhere. Similar units are somehow combined to create a new level. Whether it’s human society, ant society, zebras, primates or multicellular organisms formed of single cells, these combinations happen a lot in nature. I’m trying to understand how nature organizes simple, similar individuals into a new level that might do different things.
For example, maybe you’re a single-celled organism. You’re eaten by a predator, and that predator has a mouth as big as you but not bigger. You can’t grow too big as a single cell, so your only option is to be together with other cells. You could do that in a couple of different ways. If you find one way of doing it, does that preclude you from finding another way? If you find a simple solution to something, that might not be the best solution. Evolution is not necessarily an optimizer. It’s a tinkerer. How much of it is due to just accidents?
Tarnita in her office at Princeton University. Photo by Sasha Maslov for Quanta Magazine.
You started out as something of a prodigy. How did you get your start in math?
My mom is a professor of materials science and an engineer and is very fond of math. She always approached it as: Math is a language. Just like with any other language, the earlier you start, the better you can get at it. She started me really early. Everything we talked about — much to my frustration as a child — had some sort of math in it. But I think that really served me well.
When did you start winning Mathematical Olympiads?
In sixth grade I won, and I was very pleased. What I remember is I felt very calm about it, about doing math in general. Sixth grade made me realize this is fun, this is great; I’m going to keep doing this. Ninth grade was the time when I really had a moment of reckoning. Was I doing it because my mom had been encouraging it for so long, or is this something that really was just me? Is math going to be it? The answer was yes. The win that year meant the most.
In graduate school, you went through another moment of reckoning and then ended up working with one of the world’s most famous biologists, E.O. Wilson. What was that experience like?
I always felt blissfully unaware of the giants of a lot of the fields that I wasn’t part of. I didn’t grow up revering E.O. Wilson. It wasn’t like meeting Andrew Wiles, or any of these giants of mathematics. When I came to Princeton, I ran into John Nash, and I felt pretty much overwhelmed. It was hard for me to actually say anything to him, which was so strange. But with Ed it was like oh, he sounds amazing, I’d love to meet him, and let’s see where this goes.
But then I ended up getting a lot more from it than I would have expected originally. I had never worked with someone who was a real biologist, who had spent time in the field, who had a favorite organism. For hours he could talk about ants, and just tell the most amazing stories. He made me realize I am a biologist.
Since going to Princeton, you seem to have followed Wilson’s lead and found a social insect to keep coming back to. How did you get into termites?
I was looking at evolutionary questions, like the evolution of social behavior and of cooperation. I moved to Princeton, and I realized you need to understand ecology to understand behavior. That’s how I started to get interested in the termites, and their way of spatially organizing themselves.
Termites break down dead matter. They release all these nutrients into the system, and they do so on their mounds, so vegetation grows much better. There are more lizards there, there are more spiders, there are more grasshoppers.
One of my closest collaborators, Rob Pringle, had shown that in a system where we work in Kenya, termite mounds are evenly spaced. The fact that termite mounds are equally distributed like that throughout the savanna enhanced the productivity of the system more than any other random distribution of those mounds.
This could be interesting: How could a tiny termite create this amazing spatial patterning that could go for hundreds and sometimes thousands of kilometers, that can be seen from space? What drives that? The system doesn’t evolve. It’s not like a multicellular organism.
So how do they do it?
They space each other out because of really strong competition for resources. If two different colonies run into each other, they will fight to the death. They like to be separated from each other, and so they create this hexagonal, honeycomb-type pattern.
Photo by Sasha Maslov for Quanta Magazine.
With Pringle in Science in 2015, and again with him in the Annual Review of Entomology this year, you argue that it’s crucial to separate this kind of pattern of green islands caused by termite mounds — which signify a healthy ecosystem — from similar-looking patterns that would mean an ecosystem is failing. Can you walk me through this second kind of pattern?
Do you know about Alan Turing? Turing was obsessed with morphological patterns. Why do tigers have stripes, why do leopards have spots, and so on. He created what’s called an activator-inhibitor system, and it’s a very elegant system that people had employed for vegetation as well.
The Turing-type pattern says that when I have a lot of rainfall, the world should look like my well-watered lawn. As I start to lose precipitation I start to lose biomass, but the way I lose biomass is in a very predictable manner. The first thing I should see is something that looks like regular gaps of vegetation. As you keep decreasing the precipitation, those gaps start to form this maze-like pattern that looks like a beautiful labyrinth. As you keep decreasing the precipitation even further, those gaps stretch even more into spots.
And immediately after you’ve gotten to the spots-like stage, if you keep losing precipitation, the very next thing you should see is desert. You have what’s called catastrophic collapse. You just immediately lose everything.
I wondered: If I compared this pattern with the healthy patterns formed by termite mounds, would they look the same to me? We can’t just look at photos of patterns and say which shape is going to be bad or not.
Both termites and vegetation can create green spots in places like your site in Kenya. These same two factors are viewed as the big competing theories for Namibia’s mysterious fairy circles. But it seems like the fairy circles are almost the opposite: just bare patches in grassland. How can you move from one system to the other?
Termites create a lot of different mound types. We thought you don’t always expect them to look like islands of vegetation. Sometimes you expect them to look like castles, and therefore from photos they will probably look like bare patches.
What our framework has said is that when you have termites and vegetation in the same system, they both might be organizing. Both are processes that should in principle occur simultaneously. So what we asked is: What if these two processes actually happen on two very different scales? That would be great.
On one scale you should get a very large pattern that’s dominated by termites. But then if we really zoomed in and started to look in between the circles, we should see a smaller-scale pattern predicted by the Turing models. We sent students to Namibia, and they took photos of the vegetation, and they loved it. (They will be very happy if we do the most exotic projects in the most exotic places.) We found two patterns: Termites basically drive the big pattern of the fairy circles, but vegetation is also self-organizing, and it couldn’t be creating the large circles because it’s creating smaller spots. We want to now start setting up experiments there to really clinch this.
Once you understand what causes the different spotty patterns more generally, is the idea to diagnose from above how ecosystems are faring in the face of climate change?
We’re not kidding ourselves into thinking that this will be the answer to everything. We’d like to understand this because we would love to be able to use this in some way for conservation reasons. Then there’s the broader sense that this is just remarkable.
What we want are some predictive tools. Patterns, for us, are a little bit of a hopeful inroad into a complicated system. Who would expect that an African savanna, with all of its complexities, might show such amazingly regular patterns? Just to find such amazing symmetry in something that is so messy and has so many dimensions and elements is already an incredible surprise. We’re hoping that symmetry might teach us something about how things work in that system. Not everything, but some things.
Joshua Sokol is a freelance science journalist in Boston.
How a Guy From a Montana Trailer Park Overturned 150 Years of Biology
Biology textbooks tell us that lichens are alliances between two organisms—a fungus and an alga. They are wrong.
- Ed Yong
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I’m lichen your style. Photo by Conor Lawless / Flickr.
In 1995, if you had told Toby Spribille that he’d eventually overthrow a scientific idea that’s been the stuff of textbooks for 150 years, he would have laughed at you. Back then, his life seemed constrained to a very different path. He was raised in a Montana trailer park, and home-schooled by what he now describes as a “fundamentalist cult.” At a young age, he fell in love with science, but had no way of feeding that love. He longed to break away from his roots and get a proper education.
At 19, he got a job at a local forestry service. Within a few years, he had earned enough to leave home. His meager savings and non-existent grades meant that no American university would take him, so Spribille looked to Europe.
Thanks to his family background, he could speak German, and he had heard that many universities there charged no tuition fees. His missing qualifications were still a problem, but one that the University of Gottingen decided to overlook. “They said that under exceptional circumstances, they could enroll a few people every year without transcripts,” says Spribille. “That was the bottleneck of my life.”
Throughout his undergraduate and postgraduate work, Spribille became an expert on the organisms that had grabbed his attention during his time in the Montana forests—lichens.
You’ve seen lichens before, but unlike Spribille, you may have ignored them. They grow on logs, cling to bark, smother stones. At first glance, they look messy and undeserving of attention. On closer inspection, they are astonishingly beautiful. They can look like flecks of peeling paint, or coralline branches, or dustings of powder, or lettuce-like fronds, or wriggling worms, or cups that a pixie might drink from. They’re also extremely tough. They grow in the most inhospitable parts of the planet, where no plant or animal can survive.
Lichens have an important place in biology. In the 1860s, scientists thought that they were plants. But in 1868, a Swiss botanist named Simon Schwendener revealed that they’re composite organisms, consisting of fungi that live in partnership with microscopic algae. This “dual hypothesis” was met with indignation: it went against the impetus to put living things in clear and discrete buckets. The backlash only collapsed when Schwendener and others, with good microscopes and careful hands, managed to tease the two partners apart.
Schwendener wrongly thought that the fungus had “enslaved” the alga, but others showed that the two cooperate. The alga uses sunlight to make nutrients for the fungus, while the fungus provides minerals, water, and shelter. This kind of mutually beneficial relationship was unheard of, and required a new word. Two Germans, Albert Frank and Anton de Bary, provided the perfect one—symbiosis, from the Greek for ‘together’ and ‘living’.
When we think about the microbes that influence the health of humans and other animals, the algae that provide coral reefs with energy, the mitochondria that power our cells, the gut bacteria that allow cows to digest their food, or the probiotic products that line supermarket shelves—all of that can be traced to the birth of the symbiosis as a concept. And symbiosis, in turn, began with lichens.
In the 150 years since Schwendener, biologists have tried in vain to grow lichens in laboratories. Whenever they artificially united the fungus and the alga, the two partners would never fully recreate their natural structures. It was as if something was missing—and Spribille might have discovered it.
He has shown that largest and most species-rich group of lichens are not alliances between two organisms, as every scientist since Schwendener has claimed. Instead, they’re alliances between three. All this time, a second type of fungus has been hiding in plain view.
“There’s been over 140 years of microscopy,” says Spribille. “The idea that there’s something so fundamental that people have been missing is stunning.”
The path to this discovery began in 2011, when Spribille, now armed with a doctorate, returned to Montana. He joined the lab of symbiosis specialist John McCutcheon, who convinced him to supplement his formidable natural history skills with some know-how in modern genetics.
The duo started studying two local lichens that are common in local forests and hang from branches like unruly wigs. One is yellow because it makes a strong poison called vulpinic acid; the other lacks this toxin and is dark brown. They clearly look different, and had been classified as separate species for almost a century. But recent studies had suggested that they’re actually the same fungus, partnered with the same alga. So why are they different?
To find out, Spribille analyzed which genes the two lichens were activating. He found no differences. Then, he realized that he was searching too narrowly. Lichenologists all thought that the fungi in the partnership belonged to a group called the ascomycetes—so Spribille had only searched for ascomycete genes. Almost on a whim, he broadened his search to the entire fungal kingdom, and found something bizarre. A lot of the genes that were activated in the lichens belonged to a fungus from an entirely different group—the basidiomycetes. “That didn’t look right,” says McCutcheon. “It took a lot of time to figure out.”
At first, the duo figured that a basidiomycete fungus was growing on the lichens. Perhaps it was just a contaminant, a speck of microbial fluff that had landed on the specimens. Or it might have been a pathogen, a fungus that was infecting the lichens and causing disease. It might simply have been a false alarm. (Such things happen: genetic algorithms have misidentified plague bacteria on the New York subway, platypuses in Virginia tomato fields, and seals in Vietnamese forests.)
But when Spribille removed all the basidiomycete genes from his data, everything that related to the presence of vulpinic acid also disappeared. “That was the eureka moment,” he says. “That’s when I leaned back in my chair.” That’s when he began to suspect that the basidiomycete was actually part of the lichens—present in both types, but especially abundant in the yellow toxic one.
And not just in these two types, either. Throughout his career, Spribille had collected some 45,000 samples of lichens. He began screening these, from many different lineages and continents. And in almost all the macrolichens—the world’s most species-rich group—he found the genes of basidiomycete fungi. They were everywhere. Now, he needed to see them with his own eyes.
Down a microscope, a lichen looks like a loaf of ciabatta: it has a stiff, dense crust surrounding a spongy, loose interior. The alga is embedded in the thick crust. The familiar ascomycete fungus is there too, but it branches inwards, creating the spongy interior. And the basidiomycetes? They’re in the outermost part of the crust, surrounding the other two partners. “They’re everywhere in that outer layer,” says Spribille.
Despite their seemingly obvious location, it took around five years to find them. They’re embedded in a matrix of sugars, as if someone had plastered over them. To see them, Spribille bought laundry detergent from Wal-Mart and used it to very carefully strip that matrix away.
And even when the basidiomycetes were exposed, they weren’t easy to identify. They look exactly like a cross-section from one of the ascomycete branches. Unless you know what you’re looking for, there’s no reason why you’d think there are two fungi there, rather than one—which is why no one realised for 150 years. Spribille only worked out what was happening by labeling each of the three partners with different fluorescent molecules, which glowed red, green, and blue respectively. Only then did the trinity become clear.
“The findings overthrow the two-organism paradigm,” says Sarah Watkinson from the University of Oxford. “Textbook definitions of lichens may have to be revised.”
“It makes lichens all the more remarkable,” adds Nick Talbot from the University of Exeter. “We now see that they require two different kinds of fungi and an algal species. If the right combination meet together on a rock or twig, then a lichen will form, and this will result in the large and complex plant-like organisms that we see on trees and rocks very commonly. The mechanism by which this symbiotic association occurs is completely unknown and remains a real mystery.”
Based on the locations of the two fungi, it’s possible that the basidiomycete influences the growth of the other fungus, inducing it to create the lichen’s stiff crust. Perhaps by using all three partners, lichenologists will finally be able to grow these organisms in the lab.
In the Montana lichens that Spribille studied, the basidiomycete obviously goes hand-in-hand with vulpinic acid. But is it eating the acid, manufacturing it, or unlocking the ability to make it in the other fungus? If it’s the latter, “the implications go beyond lichenology,” says Watkinson. Lichens are alluring targets for ‘bioprospectors’, who scour nature for substances that might be medically useful to us. And new basidiomycetes are part of an entirely new group, separated from their closest known relatives by 200 million years ago. All kinds of beneficial chemicals might lie within their cells.
“But really, we don’t know what they do,” says McCutcheon. “And given their existence, we don’t really know what the ascomycetes do, either.” Everything that’s been attributed to them might actually be due to the other fungus. Many of the fundamentals of lichenology will need to be checked, and perhaps re-written. “Toby took huge risks for many years,” says McCutcheon. “And he changed the field.”
But he didn’t work alone, Watkinson notes. His discovery wouldn’t have been possible without the entire team, who combined their individual expertise in natural history, genomics, microscopy, and more. That’s a theme that resonates throughout the history of symbiosis research—it takes an alliance of researchers to uncover nature’s most intimate partnerships.Ed Yong is a staff writer at The Atlantic, where he covers science.
**
Some ate woolly rhinos; some were vegetarians. ED YONG MARCH 8, 2017
Neanderthal dental plaque is a precious commodity, so it’s a little embarrassing when you’re trying to dislodge a piece and it goes flying across the room. “We just stood still, and everyone’s like: Where is it? Where is it?” recalls Laura Weyrich from the University of Adelaide. “Usually, we try to wrap the skull in foil and work underneath it, but that time, the foil didn’t happen to cover a small area.”
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Weyrich and her team of unorthodox dentists eventually found the wayward plaque, and recovered similar samples from the skulls of five Neanderthals. Each was once a colony of microbes, growing on a tooth. But over tens of thousands of years, they had hardened into small, brittle pieces of rock. Still, each nugget contained DNA—from the microbes, and also from whatever the Neanderthals had eaten.
By harvesting and sequencing that DNA, Weyrich has shown that there was no such thing as a typical Neanderthal diet. One individual from Spy cave in Belgium mostly ate meat like woolly rhinoceros and wild sheep, as well as some edible mushrooms. But two individuals who lived in El Sidrón cave in Spain seemed to be entirely vegetarian. The team couldn’t find any traces of meat in their diet, which consisted of mushrooms, pine nuts, tree bark, and moss. The Belgian Neanderthals hunted; the Spanish ones foraged.
“When people talk about the Paleo diet, that’s not paleo, that’s just non-carb,” Weyrich says. “The true paleo diet is eating whatever’s out there in the environment.”
One of the El Sidron Neanderthals even seemed to be self-medicating with edible plants. One of his teeth had an abscess, and his plaque contained a parasite that causes diarrhea. But the plaque also contained Penicillium, the mould that produces the antibiotic penicillin, and poplar bark, a natural source of the aspirin-like painkiller, salicylic acid. The Neanderthal’s medical history—both diseases and treatments—were written in his plaque.
Neanderthals were our closest relatives, who lived in Europe before they went extinct 40,000 years ago. They left their DNA behind in people of Eurasian descent, and their bones in various European caves. By analyzing the chemical content of those bones, some scientists concluded that they were apex carnivores, much like polar bears or wolves. But other teams, who looked at the erosion patterns on Neanderthal teeth or plant matter stuck in their plaque, argued that they occasionally ate a lot of plants.
Weyrich’s results matches all of these earlier ones, and portrays Neanderthals as adaptable and versatile. “Those that occupied southern regions with relatively warm climates, consumed different types of foods, including meat and vegetables,” says Luca Fiorenza from Monash University, who was not involved in the study. “But Neanderthals that lived in very harsh conditions, such as northern Europe, were forced to rely on the limited sources available—meat.”
“We need to revamp the view of Neanderthals as these meat-eating, club-toting cavemen,” adds Weyrich. “They had a very good understanding of what foods were available to them.”
“It’s nice that the different types of data appear to match,” says Anne Stone from Arizona State University. And that’s important because “I don’t think we really understand how dietary DNA is incorporated into plaque.” Do some types of food get incorporated more than others, or is it random? How much do you need to eat of something before it shows up? “We don’t know if we’re looking at their last meal or random food debris from the last ten years,” Weyrich admits.
She didn’t actually set out to study Neanderthal diets. She was more interested in the microbes within the plaque. In an earlier study led by Alan Cooper, she and her colleagues looked at plaque from European hunter-gatherers, who lived between 5,450 and 7,500 years ago, and showed that they carried more diverse range of mouth microbes than people in industrialized societies. That discovery pushed them to look at even older samples. As DNA ages, it degrades and shatters, so the team had to invent new methods to recover microbial DNA from their Neanderthals, and to exclude contaminating modern microbes. Their payoff: the very first microbiomes from extinct hominids.
The mouth microbiomes of the various Neanderthals were as different as their diets. Those form the largely vegetarian individuals from El Sidron were closer to the microbial communities in chimps and Stone Age human gatherers. Those of the Spy Neanderthal clustered with other humans who eat more meat, including European hunter-gatherers and African cattle-farmers. These results suggest that you can use the microbes preserved within fossilized plaque to work out what their long-dead owners may have eaten.
Weyrich’s team also managed to completely sequence one particular microbe called Methanobrevibacter oralis. At 48,000 years old, it’s the oldest microbial genome around. Compared to modern counterparts, which still live in human mouths, it lacks genes for resisting antiseptics and digesting maltose, which suggests that this microbe has adapted to hygiene and changing human diets.
Christina Warriner from the Max Planck Institute for the Science of Human History, who also studies ancient microbiomes, has consistently found that Methanobrevibacter was more common in the human microbiomes of old. “But we know very little about its diversity or function, either today or in the past,” she says. “It is an important reminder of how we’re really just scratched the surface of the human microbiome, and how much work there is to do to understand the evolution of this fundamental part of our human biology.”
The microbe might even have something to say about Neanderthal behavior. Weyrich’s team calculated that the Neanderthal strain split apart from those found in modern humans between 112,000 and 143,000 years ago. That’s well after Neanderthals and modern humans themselves split apart, which suggests that the two groups were trading Methanobrevibacter—likely when they had sex, Weyrich speculates. “When you think about swapping oral microbiomes, there are just three ways that’s known to happen—kissing, food sharing, or parental care,” she says. “It suggests that those interactions between modern humans and Neanderthals were more friendly than they have been painted in the past.”
But after the paper was published, and several publications noted Weyrich’s suggestion about kissing in their headlines, Jonathan Eisen from the University of California, Davis, expressed skepticism about the claim. “Maybe the M. oralis comes from food,” he wrote in a blog post. It could have been picked up independently from the environment, or from water contaminated with feces, or from other kinds of sexual contact. A kissing route “it is just one of many and it relies upon a lot of conclusions for which the evidence is tenuous at best,” Eisen said.
ED YONG is a staff writer at The Atlantic, where he covers science.
visible organisms should be the small wedge. We’re latecomers to Earth’s story, and represent the smallest sliver of life’s diversity. Bacteria are the true lords of the world. They’ve been on the planet for billions of years and have irrevocably changed it, while diversifying into endless forms most wonderful and most beautiful. Many of these forms have never been seen, but we know they exist because of their genes. Using techniques that can extract DNA from environmental samples—scoops of mud or swabs of saliva—scientists have been able to piece together the full genomes of organisms whose existence is otherwise a mystery.
Using 1,011 of these genomes, Laura Hug, now at the University of Waterloo, and Jillian Banfield at the University of California, Berkeley have sketched out a radically different tree of life. All the creatures we’re familiar with—the animals, plants, and fungi—are crowded on one thin branch. The rest are largely filled with bacteria.
And around half of these bacterial branches belong to a supergroup, which was discovered very recently and still lacks a formal name. Informally, it’s known as the Candidate Phyla Radiation. Within its lineages, evolution has gone to town, producing countless species that we’re almost completely ignorant about. With a single exception, they’ve never been isolated or grown in a lab. In fact, this supergroup and “other lineages that lack isolated representatives clearly comprise the majority of life’s current diversity,” wrote Hug and Banfield.
“This is humbling,” says Jonathan Eisen from the University of California, Davis, “because holy **#$@#!, we know virtually nothing right now about the biology of most of the tree of life.”
Our ignorance is understandable. Ever since Antony van Leeuwenhoek became the first human to see bacteria in 1675, scientists have studied these organisms by growing them in beakers and Petri dishes. But most species simply won’t grow in a lab. This “uncultured majority” remained a mystery until the 1980s, when Norm Pace and others developed ways of sequencing microbial genes straight from environmental samples.
They discovered that the majority of species in hot springs, oceanic water, and human mouths, were totally unknown. The bacterial part of the tree of life quickly sprouted new branches, twigs, and leaves. In the 1980s, all known bacteria fit nicely into a dozen major groups, or phyla. When I spoke to Pace last June for my book, he told me that we now are up to 100. A month later, Jill Banfield discovered around 35 more.
Banfield is a pioneer in the art of sequencing environmental microbes. Since 1995, she has been studying the denizens of Iron Mountain Mine in Northern California, a hellish place with some of the most acidic water on the planet. More recently, her team catalogued the microbes in the sediments of an aquifer flowing past Rifle, Colorado. That’s where they first found the members of the Candidate Phyla Radiation—a group of over 35 phyla that account for at least 15 percent of the full diversity of bacteria.
“We didn’t even have the faintest inkling that they were out there,” says Banfield. “And once we realized that these things were there, we wanted to put them into context.” So, her team reached out to colleagues who were sequencing samples from different environments, including an underground research site in Japan, the salty earth of Chile’s Atacama Desert, a meadow in northern California, and the mouths of two dolphins.
From every organism in these samples, the team analyzed sixteen proteins that form part of the ribosome—a universal machine that’s found in all living things and that makes other proteins. Every organism has its own version of these proteins, and as new species diverge from each other, their versions become increasingly different. So by comparing these sixteen proteins, Hug and Banfield could work out how closely related their various microbes were, and draw their tree of life.
It has two main trunks—one full of bacteria and another comprised of archaea, a dynasty of single-celled microbes that look superficially similar but run on very different biochemistry. The eukaryotes—the domain that includes all animals and plants—are but a thin branch coming off the archaeal trunk. (This hints at a much broader debate about the origin of eukaryotes, which Banfield is staying out of; for more on that, see this piece I wrote for Nautilus in 2014.)
The bacterial trunk is much thicker than the archaeal one, reflecting their greater prominence and diversity. And the enigmatic Candidate Phyla Radiation (CPR) is clearly a huge part of the bacteria. Banfield and others have named many of its newly discovered lineages after pioneering microbiologists—Woesebacteria, Pacebacteria, Falkowbacteria.
Beyond that, we know that they’re really small, both in physical size and in terms of their genomes. Indeed, Banfield’s team originally discovered them by passing water from the Colorado aquifer through filters with extremely small pores. Such filters are used to sterilize water on the assumption that nothing could get through. And yet, lots of things were getting through.
Many of these mystery microbes are missing supposedly essential genes. “They don’t have the resources they need to manufacture what organisms need to live,” says Banfield. “They’re clearly dependent on other organisms.”
You see this pattern in bacteria that end up inside insect cells—their genomes tend to shrink and they lose genes that are important for a free-living existence. Similarly, the CPR bacteria might survive by forming partnerships with other microbes. Indeed, one of them has been seen sitting on the surface of another bacterium, like a remora on a shark, or a louse on a human. Perhaps it’s a parasite. Perhaps it’s a beneficial partner. Either way, it can’t live alone. That may explain why it and its relatives have been so hard to grow in a lab. You can’t culture any of them alone; you need the full partnership.
Banfield hopes that the genomes of these bacteria will hold clues about how to grow them, and thus study them. And she expects more new branches of the tree of life to reveal themselves, as scientists look to more new habitats. “We decided to stop because we were starting to find the same phyla in new environments,” she says. “The fact that they were turning up over and over again suggested that maybe we were approaching saturation for the major trunks of the tree. But it’s clear that new lineages will appear as we do more sequencing.”
Why does this matter? There’s a practical answer: almost all of our antibiotics come from the Actinobacteria, just one of the many branches that populate Hug and Banfield’s tree. Imagine what chemical and pharmaceutical riches lie in the other branches.
There’s also a grander answer: we are the first and only organisms in Earth’s history with the capacity to find and understand the others. We’ve done a reasonable job with the tools we have, but it’s clear that our understanding of life is so unfinished that it makes iceberg tips look complete. If we care about knowing our world, and our place in it, then our work is just starting.
ED YONG is a staff writer at The Atlantic, where he covers science.
