The newly discovered single-celled archaea was discovered in hot spring sediments by scientists.
A previously unknown group of archaea has been discovered in Earth’s hot springs and hydrothermal vents. Researchers report in Nature Communications on April 23 that these archaea, unlike related small, single-celled organisms that live deep in sediments and eat rotting plant matter, do not emit the climate-warming gas methane.
“Microorganisms are the most diverse and abundant form of life on Earth, and we just know 1 percent of them,” says Valerie De Anda, an environmental microbiologist at the University of Texas at Austin. “Our information is biased toward the organisms that affect humans. But there are a lot of organisms that drive the main chemical cycles on Earth that we just don’t know.”
The Archaea are a highly enigmatic species. They weren’t accepted as a separate realm of life from bacteria and eukaryotes until the late 1970s (which include everything else, from fungi to animals to plants).
Archaea is believed to only occur in the most intense conditions on Earth, such as hot springs, for many years. However, archaea are found all over the world, and these microbes may have a significant impact on how carbon and nitrogen are cycled between the soil, oceans, and atmosphere. According to De Anda, one group of archaea, Thaumarchaeota, is the most abundant microbe in the ocean.
Cows’ stomachs contain methane-producing archaea, which causes them to burp huge quantities of the gas into the atmosphere.
De Anda and her collaborators have now discovered an entirely new phylum, archaea, which is a vast branch of similar species on the tree of life. The first evidence of these new species was found in sediments from seven Chinese hot springs as well as deep-sea hydrothermal vents in the Gulf of California’s Guaymas Basin. The team discovered bits of DNA in these sediments, which they carefully assembled into the genetic blueprints, or genomes, of 15 different archaea.
The scientists then compared the genomes’ genetic details to that of thousands of previously known microbe genomes listed in publicly accessible databases. But, as De Anda points out, “these sequences were totally different from everything we knew.”
Brockarchaeota was named after Thomas Brock, a microbiologist who was the first to develop archaea in the lab and died in April. Brock’s discovery led to the creation of polymerase chain reaction, or PCR, a Nobel Prize–winning technique for copying tiny bits of DNA that is now used in COVID-19 experiments.
Brockarchaeota, it turns out, are found all over the world, but they have gone unnoticed, undescribed, and unnamed until now. De Anda and her team discovered that bits of these previously unknown species had been detected in hot springs, geothermal and hydrothermal vent sediments from South Africa to Indonesia to Rwanda after piecing together the latest genomes and searching for them in public databases.
The team also looked for genes linked to the microbes’ metabolism, such as what nutrients they eat and what waste they generate, in the new genomes.
Initially, the researchers assumed that, like other archaea previously discovered in similar conditions, these archaea would contain methane. They eat the same things as methane-producing archaea: one-carbon compounds such as methanol or methylsulfide.
“But we couldn’t identify the genes that produce methane,” De Anda says. “They are not present in Brockarchaeota.”
That means these archaea must have a previously unknown metabolism that allows them to recycle carbon without creating methane, such as in seafloor sediments. And, considering their widespread distribution, these species may be playing a previously unknown but important role in Earth’s carbon cycle, according to De Anda.
“It’s twofold interesting — it’s a new phylum and a new metabolism,” says Luke McKay, a microbial ecologist of extreme environments at Montana State University in Bozeman. The fact that this entire group could have remained under the radar for so long, he adds, “is an indication of where we are in the state of microbiology.”
But, as McKay points out, the finding also demonstrates the power of metagenomics, a technique that allows researchers to painstakingly separate individual genomes from a massive mash-up of microbes in a sample of water or sediments. Researchers are discovering more and more parts of the previously unknown microbial environment thanks to this technique.
“There’s so much out there,” De Anda says. And “every time you sequence more DNA, you start to realize that there’s more out there that you weren’t able to see the first time.”