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.”