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There are giant viruses lurking in the woods

"The fact that we found all these giant virus genomes in soil was especially intriguing, as most of the previously described giant viruses were discovered in aquatic habitats," said researcher Frederik Schulz.

By Brooks Hays
Soil samples collected in Massachusetts' Harvard Forest revealed 16 new giant virus species. Photo by UMass Amherst
Soil samples collected in Massachusetts' Harvard Forest revealed 16 new giant virus species. Photo by UMass Amherst

Nov. 19 (UPI) -- There are more than just bears and cougars to worry about when hiking through the woods. As a team of researchers recently discovered, there are giant viruses living in the forest soil.

The discovery, described Monday in the journal Nature Communications, was unintentional.

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"We were not looking for giant viruses," Jeff Blanchard, a biologist at the University of Massachusetts, Amherst, said in a news release. "Our goal was to isolate bacteria directly from the environment to understand how microbial communities are changing in response to soil warming."

Scientists discovered the massive viruses using the same method used for observing bacterial cells.

First, researchers suspended microbial cells collected from the soil in a detergent solution. Next, a non-toxic DNA-binding dye is added, and a fluorescence-activated cell sorting technique is used to isolate individual cells.

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The method illuminated the cells of giant viruses, some several hundreds of times larger than other viruses.

Before sequencing the viral genomes, scientists dipped the virus cells into small pools -- a method called mini-metagenomics. The technique allowed scientists to record the DNA of more than 2,000 individual cells. Inside the pools, scientists identified 16 new giant virus species.

"The fact that we found all these giant virus genomes in soil was especially intriguing, as most of the previously described giant viruses were discovered in aquatic habitats," said Frederik Schulz, a bioinformaticist at the Department of Energy's Joint Genome Institute. "The metagenomic data generated here from a single sampling site contained far more new giant virus genomes than any other data set I have seen to date."

Scientists say their findings only scratch the surface -- literally and figuratively. An expanded search would surely return other never-before-seen giant virus species.

"If we sample more at the same site this number would easily double, triple or even quadruple," Schulz said.

Researchers usually collect and study viruses by cultivating a protist or amoeba that viruses infect. In other words, scientists fish for viruses with bait. But the technique is labor intensive and their haul is limited. Only a small percentage of viruses in the soil may be interested in the host.

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The new discovery technique, involving isolating cells in a solution and employing mini-metagenomics, could be used to reveal previously unknown viral communities.

But while the new technique can more easily reveal the DNA of giant virus species in a soil sample, the methodology doesn't allow scientists to see the virus in action. Imaging an intact virus is labor intensive project.

Last year, scientists imaged the world's largest virus -- an extraordinary feat.

Imaged or not, the new viruses offer further evidence that the world of giant viruses is much more complex and omnipresent than previously thought.

"To me, the most intriguing and eye-opening part of the study was the high number and diversity of major capsid proteins, which is like a barcode for giant viruses, found in the unassembled bulk soil metagenome," said Tanja Woyke, senior scientist at JGI. "Deep sequencing of soil metagenomes is revolutionizing our understanding of this very important terrestrial ecosystems with many exciting soil microbiome initiatives ongoing, yet our data emphasizes that still many missing pieces to the puzzle remain."

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