IN DECEMBER 2009, a submarine plunged 2,000 meters into the Gulf of California and emerged clutching a whole new branch of life. The deep-sea craft hadn’t uncovered a new species of fish, or some hitherto unknown crustacean, but something much more profound. In one of the most alien environments on Earth, the submarine had found a group of microbes utterly distinct from all other life. In animal terms, it was like stumbling across mollusks or insects for the first time. Not just one new species but a whole swath of life had swum into focus.
This might sound momentous. It is momentous. But for Brett Baker, a microbial ecologist at the University of Texas at Austin, adding mighty branches to the tree of life is a fairly common occurrence. When he analyzes a deep-sea sample for the first time, just five out of every 200 genomes might already be known to science. In other samples taken from the ocean floor close to hydrothermal vents, he has found dozens of new microbial groups that no one has identified before. Each of them is a new piece in a puzzle of life that so far we can only see the edges of.
Baker named the group of deep-sea microbes collected in 2009 Helarchaeota—after the Norse goddess of the underworld. These microbes joined other groups named after Norse gods: Lokiarchaeota, Thorarchaeota, and Odinarchaeota. “We like these names because they’re easy to remember and they’re charismatic, right? Microbes usually aren’t charismatic, so giving them these names as it relates to their evolutionary history or their environments, it’s more fun, it’s more interesting,” says Baker.
There is just one problem. Baker’s names, well, they kinda break every rule of naming microbial species. From a certain point of view, the organisms that Baker has discovered technically don’t exist at all. They occupy a strange microbial hinterland: Species that are out there somewhere but are so strange and novel that they don’t quite fit into the scheme humans use to name microbes. Officially speaking, Helarchaeota falls into a category called Candidatus—a designation reserved for microbes that haven’t earned a proper scientific name yet.
“We are finding new kinds of life right and left,” says Karen Lloyd, a microbial ecologist at the University of Tennessee, Knoxville. But as more and more newly discovered microbes fall afoul of these naming rules, the result is a scientific snafu that is dividing microbiologists into two camps: Those who think it’s time to drag naming rules into the era of genomics and those who are worried that such a move would plunge the field into chaos. Within the small world of microbial naming, the winds of change are blowing, and not everyone is happy about it.
TO REALLY UNDERSTAND the predicament Lloyd and Baker are facing, there’s one thing you need to know about how species get their scientific names. In taxonomy—the field of biology that deals with naming and organizing life—it’s really important to be able to point to a physical specimen that represents a given species. Think you’ve seen a Carduelis carduelis (European goldfinch)? Open a dusty drawer inside the Natural History Museum’s storage facility just outside of London and you’ll find a dead bird with a tag around its ankle affirming that scientists agree that this specimen really is Carduelis carduelis. Other species are represented by fossils, or drawings, but generally to have a scientific name an animal must be represented by what zoologists call a “type”—a physical thing that is tied to that species. (The type for Homo sapiens, by the way, is the skeleton of Carl Linnaeus, the 18th-century Swedish zoologist who kicked off the whole field of taxonomy. Inconveniently, those bones are buried beneath the floor of Uppsala Cathedral in Sweden.)
The rules for naming microbes—including the ones that Baker and Lloyd work with—are surprisingly similar. To name a new species, a scientist must take a microbe and grow it in the lab. This process is called culturing. Then they must submit this culture to type collections: physical libraries of microbes that store cultures in sub-zero conditions and sell them to whichever scientist wants a copy. Once they’ve got their culture in two different collections, scientists can publish the name in a scientific journal, and the name will ascend to the List of Prokaryotic names with Standing in Nomenclature. Et voilà, a new microbial species becomes known to science.
Requiring scientists to submit their cultures to type collections is, on the face of it, a smart idea, says Brian Hedlund, a microbiologist at the University of Nevada, Las Vegas. “If I can buy that microbe, I can repeat someone else’s experiment and test their idea. That’s the central idea of the scientific method. So the reasons are very good and very noble,” he says. But it’s also nerve-racking. Carrie Brady, a microbiologist at the University of the West of England in Bristol, recently isolated a new bacteria from a Linden tree with a student; they waited months for their culture to be officially accepted into two type collections. “I’m kind of on edge now, because there are so many people describing bacteria in these species,” she says. Twice in her career she had isolated a new species only to find that someone else had snuck in there and registered a name before her. “It’s a horrible feeling to be scooped by someone else.”
The microbes that Lloyd and Baker are working with pose an even more fundamental problem. How do you culture a microbe that lives thousands of meters under the ocean next to a boiling hydrothermal vent and eats the raw materials of liquid fuel? Naming rules require the microbes to be cultured completely on their own, but many microbes can’t survive without other species right next to them. There’s no way a microbe like that can be reliably cultured in the lab, says Lloyd. “There’s this shadow world that exists of microbes,” she says. “I don’t think people really understand how vast this world of uncultured things is.”
And for the time being, uncultured means unnameable. That’s why Baker’s Helarchaeota microbes are classed as Candidatus microbes. Unless he can culture them, they’ll never get official scientific names. By some estimates, up to 99 percent of all microbes are unculturable and make up a group that some scientists refer to as microbial dark matter. And without accepted names, scientists don’t know how the microbes they’re working on relate to each other. In fact, they might double-up on the same work without realizing it. “All we need to be able to do is put it in the literature, organize it, and talk about it,” says Lloyd.
THERE'S JUST ONE thing that stands in the way of Lloyd’s vision of a more inclusive world of microbial naming: The Code. The rules around type cultures and naming are governed by the International Code of Nomenclature of Prokaryotes—but most microbiologists simply call it The Code: capital T, capital C. The Code is a long document that sets out the rules behind naming microbial species, and the task of revising and upholding The Code falls to the International Committee on Systematics of Prokaryotes, a group of 26 representatives from different microbiological societies around the globe. If the naming rules for microbes are going to change, it’ll require the acquiescence of the ICSP.
By most accounts the ICSP does a good job of shepherding the messy world of microbial naming. It publishes its minutes online, and its members regularly appear on an industry podcast to debate the future of microbial taxonomy. (Some recent episodes, ICSP members told me, are about as close to appointment TV as you can get in the world of microbial taxonomy). But it isn’t always the most progressive of organizations. “At one point the committee had been held to ransom by one cranky individual who shall remain nameless,” says Phil Hugenholtz, a microbiologist at the University of Queensland and a current member of the ICSP. “Often it’s the case that you just have to wait for people to retire or die.”
Pressure is mounting on the ICSP to update its naming conventions. Advocates for a new naming system argue that type cultures shouldn’t be the only form of evidence required to name a new species. If a species can’t be cultured, they argue that describing the genetic code of an organism should be enough to earn a name. In the last few decades, a series of new breakthroughs in genetic analysis has revealed a whole new world of microbes that are knowable only through their DNA. Baker discovered his Helarchaeota by analyzing all the microbial DNA in a sample of deep-sea sediment and using that data to piece together the genomes of certain groups of microbes. Other techniques let scientists see full genomes of individual organisms, or focus on important snippets of genetic code to discern the differences between species.
“In the realm of science that I’m in, we’re all using DNA as our evidence that an organism is there,” says Alison Murray, a microbial ecologist at the Desert Research Institute in Nevada. Murray’s search for microbial genomes has taken her as far south as the Antarctic Peninsula and as far north as the Arctic, but most of the microbes she works with have never been named. One of the most abundant organisms in the Southern Ocean—and one of Murray’s microbial best friends—is known only as 74A4. Everyone in her lab is well acquainted with 74A4, but when it comes to writing about this organism in the scientific literature, the lack of a proper scientific name makes things confusing.
For Murray, a genome should be enough to earn a species an official name. “We can use the genome to give us a blueprint of what the organism’s lifestyle is like,” she says. Genomes can tell us what a microbe eats, who it is related to, and the kinds of environments in which it thrives. In the past, scientists could use drawings of microbes as type—why not use DNA instead to paint a portrait of a species? “I can do a much better job by sequencing the genome of a microbe and telling you all about the neat things that its genome has in it,” says Murray. “I don’t really see why that should limit me from being able to name it.”
So far the ICSP has resisted efforts to include genomes as type. In 2016 an ICSP member named William Whitman proposed an update to The Code that would allow DNA sequences to be used to describe a species in cases where it is impossible to culture a microbe. By January 2020 the ICSP was ready to debate the proposals. Its chair, a microbiologist called Iain Sutcliffe, invited members to submit their comments on the proposed changes by replying-all to an email thread. Microbiologists from all over the world chipped in to a thread that stretched to 71 pages. By the end of March the results were in: Every single proposal was rejected.
Henrik Christensen, a clinical microbiologist from the University of Copenhagen, was one of the scientists who criticized the new proposals up for discussion in Sutcliffe’s epic reply-all thread. One worry he has is that if scientists start naming lots of new bacterial species that are quite similar to existing disease-causing bacteria, then this could confuse clinical bacteriologists who are used to associating a disease with a specific bacterium. His other worry is just the sheer number of new names that might be submitted if genomes are accepted as type. “Without very strict control I can foresee chaos,” he says. There are a vast number of unnamed microbes out there, and sequencing their genomes is becoming easier and cheaper by the day. He fears a situation where scientists are submitting hundreds or thousands of new names every week: A frantic land-grab for scientific names.
This second point concerns Brady, too. “What worries me is that people might see it as a shortcut and not do all the things that they have to do to have species described,” she says. If the field is flooded with low-quality genomes, for example, that’ll create huge headaches for researchers that come later. Brady is part of the ICSP, but the vote on the Whitman proposal took place before she became a full member. Even today she finds it difficult to come down on one side of the debate. “I’m on the fence. I think my problem is that I can see both sides very clearly, because I have the same frustrations as other people do.”
AND LIKE A phoenix rising from the ashes of the doomed Whitman proposal, a new scheme for changing the way scientists name microbes has emerged. Shortly after the proposal was rejected, a group of microbiologists got working on their own alternative to The Code. This one—called SeqCode—would allow microbiologists to name uncultivated microbes by using their DNA sequences as type. “We would rather not have to do all this work,” says Hedlund, one of the scientists working on SeqCode. To prevent a deluge of low-quality genomes flooding the database, SeqCode stipulates that the genome needs to be over 90 percent complete and with less than 5 percent contamination to qualify for naming.
Although SeqCode exists outside the ICSP—and is anathema to some of its members—it’s not exactly the Rebel Alliance to the ICSP’s Galactic Empire. Four of the members of SeqCode’s organizing committee are also members of the ICSP, including the ICSP chair Iain Sutcliffe. Phil Hugenholtz and Alison Murray are also members of the SeqCode organizing committee. SeqCode includes all the same naming rules as The Code, so any microbe that has already been named is still valid under the SeqCode but also includes extra provisions for other microbes to be named using genomes as type. As of today, a microbiologist who wants to name a newly discovered species can decide whether they want to register their species with SeqCode or The Code.
Hedlund admits that this two-tier situation isn’t exactly the neatest solution for the quandary facing the microbiological world. “We would rather not have two systems,” he says, but he hopes that if enough people use SeqCode then the ICSP will be forced to change its rules before it becomes hopelessly out of step with the rest of the microbiological world. “We all hope that SeqCode merges with [The Code] sooner rather than later.” But in the world of microbial taxonomy, “soon” is a pretty flexible word. It took the ICSP four years to get around to debating the Whitman proposal. It might take it another 10 years to incorporate SeqCode. Or maybe it’ll never happen at all.
In the meantime, scientists keep turning up whole worlds of unculturable microbes that until very recently defied naming conventions. Now they’re caught in a tussle between two worlds. “We’re just marching and fighting and suiting up and battling and trying to get it to go in the right direction,” Hedlund says. In their laboratories, scientists like Lloyd and Baker have huge new groups of life that are just waiting to be named. In one set of deep-sea samples, Baker has 50 new phyla of microbes that haven’t been described yet. That’s more diversity than exists between humans, eels, and birds. Whole new categories of microbes are out there, just waiting to join the tree of life, if only we had the words to describe them.
