While analyzing the genomes of single-celled microbes, a team of researchers made a startling discovery: Thousands of previously unknown viruses were "hidden" within the microbes' DNA.

The researchers found DNA from more than 30,000 viruses built into genomes of various single-celled microbes, they report in a new study. They explain that viral DNA might enable a host cell to replicate complete, functional viruses.

"We were very surprised by how many viruses we found through this analysis," says lead author Christopher Bellas, an ecologist who studies viruses at the University of Innsbruck in Austria. "In some cases, up to 10 percent of a microbe's DNA turned out to consist of hidden viruses."

These viruses don't seem to sicken their hosts, the researchers say, and they might be beneficial. Some of the new viruses resemble virophages, a type of virus that infects other pathogenic viruses attempting to infect its host cell.

"Why so many viruses are found in the genomes of microbes is not yet clear," Bellas says. "Our strongest hypothesis is that they protect the cell from infection by dangerous viruses."

Living on Earth means contending with viruses, the planet's most abundant biological entities, collectively infecting every type of life form. They're highly diverse, using many different tactics to exploit their cellular hosts.

Regardless of semantic debates about whether viruses are alive, they certainly insert themselves into the lives of other living things. Some even replicate by adding their DNA to a host cell and becoming part of its genome.

When that happens in a germ cell, it can lead to endogenous viral elements (EVEs), or viral DNA passed on from one generation to the next in a host species.

Scientists have found EVEs in a wide range of organisms, including animals, plants, and fungi. Mammals carry a variety of viral fragments in their DNA, for example, and about 8 percent of the human genome consists of DNA from ancient viral infections.

The study's authors explain that most of these are no longer functional and are considered "genomic fossils." Research suggests EVEs can be adaptive in humans and other organisms, though, possibly helping fend off modern viruses.

That's true for many single-celled eukaryotes, the researchers point out, noting these microbes are commonly infected and killed by giant viruses.

If a virophage already inhabits a host cell, it can reprogram a giant virus to build virophages instead of replicating itself, potentially saving the host.

According to the new study, DNA from the newly discovered viruses is similar to virophage DNA, suggesting microbes may enjoy some protection from giant viruses thanks to the "built-in" viruses residing in their genomes.

The study of EVEs so far has focused mainly on animals and plants, the researchers write, with little attention to protists – any eukaryotic organisms that aren't animals, plants, or fungi – even though they represent the majority of eukaryotic biodiversity on Earth.

Discovering thousands of new viruses hidden in microbe DNA wasn't the original goal for Bellas and his colleagues, who planned to study a new group of viruses they had found in the waters of Gossenköllesee, an alpine lake in the Austrian state of Tyrol.

"Initially, we wanted to find the origin of the new 'Polinton-like viruses' with our study," Bellas says.

"However, we did not know which organisms are usually infected by these viruses. That's why we conducted a large-scale study to test all microbes whose DNA sequences are known."

To do that, they enlisted help from "Leo," a high-performance computer cluster at the University of Innsbruck that can efficiently analyze vast amounts of data.

Noticing genes from virophages and other viruses in many of the microbe genomes, the researchers decided to investigate further, using Leo to systemically analyze all publicly available draft genome assemblies of protists.

They found EVEs "hidden throughout repetitive, difficult-to-assemble regions of unicellular eukaryotic genomes," they write, noting that thousands of integrated viruses in some species suggest viruses make up a significant, previously unrecognized swath of protist genomes.

The study also found evidence that many protist EVEs are not just genomic fossils but functional viruses, the researchers write, "which suggests that diverse arrays of these elements may be part of a host antivirus system."

The study was published in the Proceedings of the National Academy of Sciences.