Mysterious DNA sequences, known as ‘Borgs,’ recovered from California mud

But Graham Hatfull, a microbiologist at the University of Pittsburgh, wonders whether there couldn’t be other large viruses, similar to the bacteria-invading viruses that he helped discover, that infect archaea.

Jill Banfield

In the TV series Star Trek, the Borg are cybernetic aliens that assimilate humans and other creatures as a means of achieving perfection. So when Jill Banfield, a geomicrobiologist at the University of California, Berkeley, sifted through DNA in the mud of her backyard and discovered a strange linear chromosome that included genes from a variety of microbes, her Trekkie son proposed naming it after the sci-fi aliens. The new type of genetic material was a mystery. Maybe it was part of a viral genome. Maybe it was a strange bacterium. Or maybe it was just an independent piece of DNA existing outside of cells. Whatever it is, it’s “pretty exciting,” says W. Ford Doolittle, an evolutionary biologist at Dalhousie University who was not involved with the work.

Researchers have found many examples of DNA floating independently outside the chromosome or chromosomes that make up an organism’s standard genome. Small loops called plasmids, for example, exist inside microbes and ferry genes for thwarting antibiotics among different kinds of bacteria.

But Banfield wasn’t looking for DNA that could move between organisms. Instead, she and graduate student Basem Al-Shayeb were searching for viruses that infect archaea, a type of microbe often found in places devoid of oxygen. They would dig 1 meter or more below the surface and collect mud samples that might harbor archaea and their viruses. Next, they would sequence every stretch of DNA in the samples and use sophisticated computer programs to scan for sequences that signified a virus, rather than any other organism.

“We started off with a piece of mud and 10 trillion pieces of DNA,” Banfield says. One sample, taken from the mud on her property, contained a gene-filled stretch of DNA almost 1 million bases long—and more than half the genes were novel. This linear stretch of DNA also had a particular pattern of bases at its beginning and end, distinct stretches of repetitive DNA between its genes, and two places along the sequence where DNA duplication could begin—which indicated the Borg could make copies of itself. Together, this suggested it was not just a random concoction of genes.

After they identified the first Borg sequence, the researchers began to scan microbial DNA in public databases to see whether they could find anything similar. They found a few variations in groundwater from Colorado—there, the first purported Borg showed up about 1 meter deep and got more abundant deeper down. Other versions showed up in DNA from the discharge of an abandoned mercury mine in Napa, California, and from a shallow riverbed of the East River in Colorado.

Altogether, the researchers isolated 23 sequences they think may be Borgs—and 19 they have identified as having all the characteristics of the first Borg they discovered, they write this week on the preprint server bioRxiv. Some are almost 1 million bases long. “I don’t think anything else that’s been discovered is as big as these guys are,” among previously known extrachromosomal DNA elements, Doolittle says.

In every place, copies of the Borg co-occurred with DNA linked to a methane-oxidizing archaeon called Methanoperedens. That suggests the Borgs may exist inside the microbe, the researchers say. But because Methanoperedens can’t be grown in a lab, the team hasn’t been able to confirm this suspicion. Meanwhile, team members have ruled out the possibility that the Borg came from another microbe, as they lack many necessary genes for life, or a virus, which typically have shorter chromosomes.

But Graham Hatfull, a microbiologist at the University of Pittsburgh, wonders whether there could be other large viruses, similar to the bacteria-invading viruses that he helped discover, that infect archaea. Could the Borg be a part of such viruses? Demonstrating that will be challenging, he admits. “If you want to know about [Borg] biology, it’s experimentally really tough.” One thing the find reinforces, he says, is the idea that many genetic elements can hop between an organism’s chromosomes or between organisms, making it easier for creatures to acquire new genes to adapt to changes in their environment.

Each Borg—which are now named after colors such as “olive” and “lilac”—includes not just novel genes, but recognizable ones whose functions scientists already know. For example, a few contain genes important for processing methane; such genes seem to have been acquired from specific microbes, such as Methanoperedens. Because methane is a greenhouse gas that many microbes either break down or produce, the researchers suggest Borgs may influence that cycling by boosting its host’s ability to process methane.

Banfield says she and her colleagues don’t really know how Borgs arose, but they suspect that at one time, the DNA sequences were the genomes of a close relative of Methanoperedens that got scooped up and began living inside the archaeon. Eventually only the DNA, now much modified, remains inside the microbe, but apart from its own chromosome.

Banfield hopes her team’s discovery will lead other researchers to look for Borgs in their favorite microbes, particularly those in environments with little to no oxygen. And Hatfull predicts there will be new ones found in microbes other than Methanoperedens. In the meantime, he and other researchers are eagerly awaiting the peer-reviewed version of Banfield’s paper—and confirmatory experimental work on the Borgs. “What are they?” Doolittle asks. “It’s an interesting question that demands to be answered.”