New soil virus database reveals unknown diversity

Soil scientists including researchers from Washington State University recently published a new Global Soil Virus Atlas online in the journal "Nature Microbiology." The team, led by the Department of Energy's Pacific Northwest National Laboratory (PNNL), is now investigating whether these soil viruses have a long-overlooked impact on the climate and soil health. They hope to utilize the new database as a starting point for further research.

"We found a wealth of diversity among soil viruses-so much that our finding challenged the traditional ways of analyzing such data," said Emily Graham, an adjoint-faculty member of the WSU School of Biological Sciences who also serves as a quantitative ecosystem ecologist for the Microbial System Dynamics Team at PNNL. "We need to understand how this amazing diversity of viruses beneath our feet affects processes like plant productivity and carbon sequestration."

The atlas is the cumulative effort of dozens of scientists from around the globe and includes nearly 3,000 soil samples from six continents. From these thousands of samples, more than 600,000 distinct fragments of viral DNA were found intermixed with rocks, dirt, bacteria, and other soil components. These fragments are considered "viral dark matter" that have no known function or connection to a specific host, a key component of survival in all viruses.

Researchers have estimated that every gram of soil holds millions of viruses, but the scientific community has generally investigated soil bacteria instead due to the difficulty of detecting and measuring the much smaller genetic information housed by viruses. Scientists have known that bacteria are crucial in helping process greenhouse gases, but the role of viruses stored in the Earth's vast soil reservoir is less understood and scientists are curious about just how the underground virosphere affects the climate.

One thing is for certain from the new analysis: the underground viral world is diverse and full of surprises. The research team identified more than 1.4 million viral genes within the samples, comprising over 616,000 likely viruses. Researchers then sorted those viruses into over 38,000 groups known as operational taxonomic units, a term used similarly to species when describing other organisms.

The study suggests an unprecedented diversity in the underground virosphere. About 90% of the operational taxonomic units had never been observed before, and 86% of the units were found only once in the 2,953 samples. In fact, many soil samples bore little resemblance to one another. The research team found that in soil samples taken near one another, even just 30 feet apart, the viral units and populations were very different comparatively. That contrasts starkly with bacterial soil surveys, which typically present more uniformity when in the same ecosystem.

"We've found a community of viruses with a diversity beyond anything we've seen in bacteria," said Graham. "We're hoping the (Global Soil Virus Atlas) spurs technology development and becomes a launching point for others to generate specific hypotheses so that we can understand the soil virosphere more fully."

The work was funded by the Department of Energy's (DOE) Office of Science. Authors of the study are from WSU, PNNL, JGI, Kyoto University in Japan and a newly established Soil Virosphere Consortium that includes authors from around the globe. Of the 2,953 soil samples analyzed in the study, nearly half were provided through the Integrated Microbial Genomes & Microbiomes data portal compiled and maintained by the DOE Joint Genome Institute, a DOE Office of Science user facility.