Moisture is important for viruses in the soil

Science

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

The impact

Soil viruses are part of the environmental microbiome, the collection of microorganisms in the soil that contribute to plant health, nutrient movement, and other functions. However, extracting and decoding the genetic complexity of viruses in soil is difficult, 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 changes. Scientists want to know more about this answer because climate change is altering global precipitation patterns. Some ecosystems are experiencing increased drought, while others are experiencing increased precipitation. This study showed that extreme variations 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 far-reaching effects on soil ecology.

Summary

A multi-agency team collected soil from native grasslands in Kansas, which sits at the crossroads of projected changes in rainfall with climate change. These changes range from increased drought to the southwest to increased precipitation to the northeast. The researchers then wetted the soil, air-dried it, or left it as is. Finally, they determined which DNA and RNA viruses were present in each condition. The scientists used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to identify viral composition and activity, as well as to track their responses to soil moisture extremes. The untargeted proteomics measurements utilized the mass spectrometry capabilities of the Molecular Environmental Sciences Laboratory, a Department of Energy (DOE) science 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 showed a high abundance of RNA viruses, with the highest representation of Reoviridae. Leviviridae were the most diverse RNA viruses in samples, with higher amounts in moist soil. 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 the previously described marine viral chaperonins. This study demonstrated that extreme variations in soil moisture had significant impacts on the composition, activity and potential functions of soil DNA and RNA viruses.

Funding

Funding was provided by the DOE’s Science, Biology and Environmental Research Program and is a contribution to the Phenotypic Response of the Soil Microbiome to Environmental Disturbances Science Interest Area. The proteomics work was funded by a DOE Early Career Research Program award to Kristin Burnum-Johnson.