This virus self-mutates to infect in extreme places

This schematic shows viruses attempting to dock on a microbial host using the tips of their tail fiber appendages. Tail fibers of this sort are one target of self-mutation identified in this study. (Credit: Blair Paul/UC Santa Barbara)

Until recently, archaea took the prize for the oddest organisms to live in the sea.

The primitive single-celled, bacteria-like microorganisms go to great lengths—eating methane or breathing sulfur or metal instead of oxygen—to thrive in the most extreme environments on the planet.

But researchers believe they may have found something odder still: a virus that not only seemingly infects archaea, but also selectively targets one of its own genes for mutation.

submergence vehicle Alvin
Deep submergence vehicle Alvin, shown here onboard R/V Atlantis, was deployed to a depth of 800 meters to retrieve sediment samples. (Credit: David Valentine/UC Santa Barbara)

Into the deep

“Our study illustrates that self-guided mutation is relevant to life within the Earth’s subsurface and uncovers mechanisms by which viruses and archaea can adapt in this hostile environment,” says David Valentine, professor in the Earth science department at University of California, Santa Barbara.

“These findings raise exciting new questions about the evolution and interaction of the microbes that call Earth’s interior home.”

Using the submarine Alvin, researchers collected samples from a deep-ocean methane seep by pushing tubes into the ocean floor and retrieving sediments. The contents were brought back to the lab and fed methane gas, which helped the archaea in the samples grow.

When the team assayed the samples for viral infection, they discovered a new virus with a distinctive genetic fingerprint that suggested its likely host was methane-eating archaea.

“It’s now thought that there’s more biomass inside the Earth than anywhere else, just living very, very slowly in this dark, energy-limited, starved environment,” says coauthor Sarah Bagby, a postdoctoral scholar in Valentine’s lab.

For the study, published in Nature Communications, the researchers also used the genetic sequence of the new virus to chart other occurrences in global databases.

“We found a partial genetic match from methane seeps in Norway and California,” says lead author Blair Paul, a postdoctoral scholar in the Valentine lab. “The evidence suggests this viral type is distributed around the globe in deep ocean methane seeps.”

Molecular arms race

Further investigation revealed another unexpected finding: a diversity-generating retroelement that greatly accelerates mutation of a specific section of the viral genome.

Such small genetic elements had previously been identified in bacteria and their viruses, but never among archaea or the viruses that infect them. While the self-guided mutation element in the archaeal virus clearly resembles the known bacterial elements in many respects, researchers discovered it has a divergent evolutionary history.

“The target of guided mutation—the tips of the virus that make first contact when infecting a cell—was similar,” Paul says. “The ability to mutate those tips is an offensive countermeasure against the cell’s defenses—a move that resembles a molecular arms race.”

Having found guided mutation in a virus infecting archaea, the scientists reasoned that archaea themselves might use the same mechanism for genetic adaptation. In an exhaustive search, they identified parallel features in the genomes of a more mysterious subterranean group of archaea known as nanoarchaea.

Four firing at once

Unlike the deep-ocean virus that uses guided mutation to alter a single gene, nanoarchaea target at least four distinct genes.


“This is a new record,” Bagby says. “Previously, a few bacteria had been observed to target two genes with this mechanism. That may not seem like a huge difference, but targeting four is extraordinary. If they’re all firing at once, suddenly the number of combinations of protein variants in play is really massive.”

The genetic mutation that engenders these potential variations may be a key element to survival of archaea beneath the Earth’s surface, Valentine says.

“The cell is choosing to modify certain proteins. It’s doing its own protein engineering internally. While we don’t know what those proteins are being used for, I think learning about the process can tell us something about the environment in which these organisms thrive. Right now, we know so little about life in that environment.”

The National Science Foundation supported the work. Viral DNA sequencing was provided through a Gordon and Betty Moore Foundation grant to the Broad Institute. Researchers from University of California, Los Angeles, University of California, San Diego, and the Department of Energy’s Joint Genome Institute contributed to the study.

Source: UC Santa Barbara

“The target of guided mutation—the tips of the virus that make first contact when infecting a cell—was similar,” says Blair Paul. “The ability to mutate those tips is an offensive countermeasure against the cell’s defenses—a move that resembles a molecular arms race.”  (Credit: