Most of the Tree of Life is a Complete Mystery

In 1837, Charles Darwin sketched a simple tree in one of his notebooks. Above it, he scrawled “I think.” That iconic image perfectly encapsulated Darwin’s big idea: that all living things share a common ancestor. Ever since then, scientists have been adding names to the tree of life. Last year, for example, one group compiled what they billed as a “comprehensive tree,” a garguantuan geneaology of some 2.3 million species that “encompasses all of life.”

Impressive work, but they should probably have said “all the life we have sequenced so far.” Existing genetic studies have been heavily biased towards the branches of life that we’re most familiar with, especially those we can see and study. It’s no coincidence that animals made up half of the “comprehensive tree of life,” and fungi, plants, and algae took up another third, and microscopic bacteria filled just a small wedge.

That’s not what the real tree of life looks like.

We 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.