A New Way to Find the Tree of Life's Missing Branches

Scientists have devised a method to sequence more microbes, more quickly, which could lead to a better understanding of the origin of complex life.

Yellowstone's rainbow-colored Grand Prismatic Spring
Hot springs are one place where novel microbes may be found. (Jim Peaco / Yellowstone National Park )

Scientists have been been studying the DNA of microbes for a quarter-century, and in that time, they have sequenced about 2 million microbes. By one estimate, as many as 1 trillion microbial species may live on Earth.

Progress? 0.0002 percent.

Only a tiny fraction of the tree of life has been filled in. In fact, whole branches are likely still yet to be discovered: branches of microbes living in remote environments like hydrothermal vents, branches of microbes that might be the link between simple cells and the complex life that became humans. At the current rate, says Mads Albertsen, it would take thousands of years to get a complete microbial catalogue of the Earth.

So Albertsen, a microbiologist at Aalborg University, decided to do something about it. His lab has come up with a clever new way to find previously unknown microbes. In the past three years, they have catalogued about a million DNA sequences from microbes. More than half of the potential species they found were unknown to science.

Albertsen and his team looked for new species in only the most prosaic of places: water, dirt, mud, sewage, the human gut. A concerted effort to sequence all types of samples will expand the tree of life—and perhaps eventually fill in all the missing branches. “That’s really in reach now,” he says.

The new method may be particularly useful for discovering the most intriguing microbes—the ones unlike anything previously discovered and thus most difficult to identify.

Microbe species are catalogued by identifying variations in one particular gene called 16S rRNA, which is so common that it is found in all known living species. Traditional sequencing methods are usually biased toward finding microbes whose 16S rRNA gene is similar to ones previously sequenced. That’s because these methods rely on a process called polymerase chain reaction, when an enzyme makes several copies of the gene (in this case 16S rRNA), for later sequencing. The enzyme, however, needs to attach to something called a “primer” to start copying. The primer is essentially a tiny snippet of DNA designed to bind to the exact gene you want to copy and sequence. But if you’ve never sequenced it before, then you don’t know what the primer needs to bind to.

There you have the chicken-and-egg problem: “Every PCR primer is designed based on a previous sequence out there,” says Chris Miller, a microbiologist at the University of Colorado at Denver who was not involved in the study. “PCR primer bias is big.”

Albertsen’s team got around primer bias with a few clever tricks. First, they realized it’s possible to add extra letters to the ends of any microbe’s 16S rRNA gene. These extra letter, whose exact sequence they knew, could act as generic primer binding sites. So there was no need to know the underlying gene sequence, and no primer bias. They put this together with a method that allowed them to use high-throughput sequencing machines to test a lot of samples quickly and relatively cheaply. Soon, they were on their way to getting nearly 2 million 16S rRNA sequences.

Having a catalogue of microbes means that scientists can know when they’re talking about the same one. “It seems like a stupid problem, but it’s a really large problem,” says Albertsen. They’re too small to see with the naked eye, and even when you put them under a microscope, different microbes can look very similar. If Albertsen, who usually studies microbes in wastewater, sees one type of bacteria show up when, say, the pH drops, he wants to be able to talk to his collaborator in another city about whether they’re seeing the same microbe.

The most exciting new microbes they found appear to be related to the recently discovered Asgard microbes—the ones that may link simple and complex life. Thijs J. G. Ettema, a microbiologist at Uppsala University, has discovered Asgard microbes in several sites including Yellowstone National Park and deep-sea vents near a Japanese island. Albertsen’s came from the mud around Denmark. Ettema thinks that the method could help identify more environments where Asgard microbes live. “It can’t be understated that these 16S sequences are being used a lot,” he says. “This will revolutionize this field.”

Ettema has one note of caution. The method requires quite a bit of genetic material from microbes, and samples from extreme and hard-to-reach environments might not have enough material for this type of sequencing. He and other scientists will continue to use other sequencing methods to study novel microbes.

In addition, scientists how hope to sequence entire genomes rather than just the 16S rRNA gene, which would give a fuller picture of what novel microbes are actually like. Tanja Woyke, a microbiologist at the Joint Genome Institute, specializes in sequencing whole genomes from just a single microbial cell.

For now, what 16S rRNA sequencing and this novel method can do is create a roadmap for those undiscovered branches of life. It’s a relatively quick and easy way to sample a new environment. And if there’s something intriguing, scientists can swoop in with even more powerful genomics tools to study the microbes more closely. The tree of life will keep getting bigger and bigger.