Microbes in Yellowstone pools add new branch to the tree of life

JACKSON — It’s not often that scientists get to discover a new form of life, but a team of researchers from the University of Texas at Austin have recently found not just one new species, but a whole group of novel organisms, some of which can be found in Jackson Hole’s backyard.

“It’s basically adding more diversity to the tree of life,” said Valerie De Anda, a postdoctoral research associate at the University of Texas Marine Science Institute. “We’re starting to scratch the surface of the iceberg in terms of diversity.”

Already world famous for its geysers, landscapes and geothermal features, Yellowstone National Park and its hot springs played a role in this new scientific discovery.

Yellowstone boasts more than 100 thermal areas, many of which host their own microbial communities, according to Jeff Hungerford, a park geologist. These microorganisms, called extremophiles, thrive in the extreme conditions of the thermal pools.

“They’re profoundly abundant,” Hungerford said.

Research on the park’s extremophiles started in the 1960s, when Dr. Thomas Brock discovered bacteria living in hot spring pools in Yellowstone’s Great Fountain area. Brock named this bacteria Thermus aquaticus.

Brock’s discoveries led to great progress in the fields of science and medicine. In fact, Brock was instrumental in pioneering PCR technology which has been used extensively to identify and track COVID-19 infections during the global pandemic.

Astonishingly, even with such an abundance of recorded microbial life, scientists are still finding new microorganisms.

The new microbes recently found by Brett Baker and his team from the University of Texas belong to a new proposed group by the name Brockarchaeota (after Dr. Brock himself), and they might be the key to helping scientists understand the Earth’s carbon cycles, which could be invaluable to researchers designing climate change models.

“They are completely different from all of the Archaea that we know so far,” De Anda said.

Brett Baker, an associate professor at the University of Texas at Austin, told Wyoming Public Radio that his team in the Marine Sciences Department discovered Brockarchaeota by accident when conducting a study in the Gulf of California.

After the discovery, Baker’s team suspected they had found a new branch on the tree of life and decided to conduct a study to prove their microbe was something unique by comparing its DNA to the DNA of other microorganisms stored in online databases.

“The study was originally to gather evidence within the genomes that it was a unique phylum,” De Anda said.

Sure enough, the research team found that other similar unidentified microbes had been collected by other researchers around the world, including in Yellowstone. Copies of their DNA had been uploaded to online databases for other researchers to use.

“At the beginning we had only eight genomes,” De Anda said. “Then collaborators gave us more genomes that they also isolated from other hot springs in China.”

While the environments look very different at first glance — the sea floor, hot springs in China, and thermal pools and bacterial mats in Yellowstone don’t seem to have much in common — they share several common characteristics that support Brockarchaeota species.

Each of the environments are anoxic, meaning there is little to no oxygen present, and all areas are geothermally active, providing heat and nutrients for the microbes.

Part of the identification and classification process was to determine whether the new microbes belonged to the domain Archaea or Bacteria (the tree of life encompasses every living species and puts them into three broad categories known as domains: Archaea, Bacteria and Eukarya).

To decide which domain the new microbes belong to, scientists analyzed their 16S protein, a genetic protein that is common across all life forms and is used to identify Bacteria and Archaea at the species level and to differentiate between closely related species.

By comparing their genes with other known genomes, the team determined that its mystery organism was in fact part of the domain Archaea. Within Archaea, De Anda, and the other researchers propose that these microorganisms should be classified as their own new phylum because of their unique qualities.

Using genetics, biological functions and ecological roles, scientists separate organisms into distinct groups or lineages based on shared characteristics that differentiate them from other similar groups. This is how they decide where organisms fit on the tree of life, otherwise known as a phylogenetic tree.

Phylogenetic trees allow scientists to examine the evolutionary relationships among species and individuals and to classify them with the most closely related organisms. These classifications go from broad to specific: domain, kingdom, phylum, class, order, family, genus and finally the individual species.

When it comes to Brockarchaeota, figuring out where it belongs on the tree can be painstaking and slow.

“It’s more important to kind of predict and understand their ecological roles because you can be stuck in taxonomy for years,” De Anda said. “The ecological role is everything. It’s inferred based on the genomes, based on the predicted role of each of the proteins.”

What researchers found was that the protein sequences in the genes of Brockarchaeota species suggested a unique metabolism and function within their ecosystems.

Analysis of their genetics and respiratory pathways told researchers these microbes consume carbon compounds, like decaying plant matter, but don’t produce methane like scientists expect in carbon reducing organisms.

“It was not anything similar to any other known Archaea,” De Anda said. “It was more similar to other organisms that live in anoxic environments, like sulfate-reducing organisms.”

In anoxic environments, specialized microorganisms can cycle carbon compounds to yield energy in a process called fermentation. During this process, compounds like carbon dioxide are converted to gasses like methane.

However, there are species of Bacteria and Archaea that are able to thrive on other elements like sulfur and do not produce methane. According to De Anda, before the discovery of Brockarchaeota, only three types of microorganisms (methylated, methylotrophic and methanogenic archaea) had been documented to possess this capability.

The fact that Brockarchaeota species consume carbon compounds but don’t produce methane made it clear to scientists that they had discovered something new. It also told scientists that these species play a key role in anaerobic carbon cycling on the planet (the processes of carbon conversion that occur in environments without oxygen).

Scientists are particularly interested in studying the potential impacts Brockarchaeota might have on climate change because the marine sediments where the microbes were found are the largest reservoir of organic carbon on Earth, and Brockarchaeota are uniquely capable of recycling this carbon in anoxic environments without producing more greenhouse gases.

While these microbes likely aren’t the answer to the climate crisis, future research into their biology and environmental impact could provide insight into how microbial communities are involved in and affect the planet’s carbon cycles. And that insight could help improve climate change models.

While there is still a lot of research to be done, De Anda hopes that with time and research the scientific community will be better able to understand the complexities of Brockarchaeota and discover more members of the unique group.

Hungerford agrees.

“We need to work together as geologists and microbiologists,” Hungerford said. “To actually understand these systems better.”