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.”