Moisture Matters for Viruses in Soil

The Science

Soil is teeming with life. Every teaspoon of soil contains billions of microorganisms, including viruses. In this study, scientists identified DNA and RNA viruses in soil from Kansas prairies using several “omics” techniques. These are techniques that examine the biological molecules associated with organisms. In this study, scientists used omics techniques to sequence the viruses’ genes and identify the viruses’ proteins. They also determined how virus activity varied under different environmental conditions. They found that the DNA viruses in the prairie soils were mainly types that attack bacteria, called bacteriophages. In contrast, the RNA viruses were mainly types that attack eukaryotic species, such as insects and fungi. The researchers found that extreme shifts in soil moisture conditions, such as those expected to occur with climate change, affected the types and activity of DNA and RNA viruses in those soils.

The Impact

Soil viruses are part of the environmental microbiome, the collection of microorganisms in soil that contributes to plant health, the movement of nutrients, and other functions. However, it is difficult to extract and decode the genetic complexity of viruses in soil, so scientists have an incomplete picture of most of these viruses. Scientists also have a limited view of how these soil viruses respond to environmental change. Scientists want to learn more about that response because climate change is shifting global precipitation patterns. Some ecosystems are experiencing increased drought, while others have increased precipitation. This study showed that extreme shifts in soil moisture have profound effects on soil DNA and RNA viruses. These effects include greater abundance of some viruses and greater activity among other viruses in moist soil. Although researchers do not know the long-term consequences of these changes, they could have sweeping effects on soil ecology.

Summary

A multi-institutional team collected native prairie soil in Kansas, which sits at the crossroads for predicted shifts in precipitation with climate change. These shifts range from increasing drought toward the southwest to increasing rainfall to the northeast. The researchers then wet the soil, air-dried it, or left it unchanged. Finally, they determined which DNA and RNA viruses were present under each condition. The scientists used a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics) to identify viral composition and activity, as well as track their responses to extremes in soil moisture. The untargeted proteomics measurements used mass spectrometry capabilities at the Environmental Molecular Sciences Laboratory, a Department of Energy (DOE) scientific user facility.

The majority of transcribed DNA viruses were bacteriophages, but some were assigned to eukaryotic hosts, mainly insects. Higher soil moisture increased transcription of a subset of DNA viruses. The soil also had a high abundance of RNA viruses, with highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in the samples, with higher amounts in wet soil. The protein data revealed that viral chaperonins, known to be essential for virion replication and assembly, were produced in soil. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. This study demonstrated that extreme shifts in soil moisture had dramatic impacts on the composition, activity, and potential functions of both DNA and RNA soil viruses.

Funding

Funding was provided by the DOE Office of Science, Biological and Environmental Research program and is a contribution of the Scientific Focus Area “Phenotypic response of the soil microbiome to environmental perturbations.” The proteomic work was funded by a DOE Early Career Research Program award to Kristin Burnum-Johnson.