PNNL

The Science

RNA viruses represent a critical component of the soil microbiome due to their impact on reshaping host phenotypes (e.g., metabolic function and pathogenicity) in response to the changing environment. Yet, little is known about how environmental factors individually and interactively influence these viral communities. By analyzing viral sequences in total RNA collected from a 5-year-old grassland experiment, researchers found more identifiable RNA viruses with eukaryotic hosts (i.e., plants and fungi) than prokaryotic hosts (i.e., bacteria). Soil water content, plant presence, and type of plant cultivar all individually promoted greater diversity of eukaryotic RNA viruses, while depth in the soil negatively impacted these communities. These results reveal how biological and environmental factors may shape the soil RNA viral communities.

The Impact

Climate change has been reshaping the soil environment as well as the residing microbiome. This study provides field-relevant information on how plants, water, and microbial community factors collectively shape soil RNA communities in surface and deep soils. Understanding the effects of soil moisture, crop choice, and host diversity contributes to the ecological understanding of virus-host relationships in soil and RNA viral survival under various environmental conditions. This knowledge is important for understanding the viral responses to climate change and the potential emergence of biothreats.

Summary

Despite the widespread presence of RNA viruses in soils, little is known about the relative contributions and interactions of biological and environmental factors shaping the composition of soil RNA viral communities. We evaluated the direct and indirect effects of environmental factors (high and low irrigation practices across planted and unplanted plots with two genotypes of perennial tall wheatgrass) on soil containing RNA viral communities recovered from metatranscriptomes (microbial RNA sequenced by the DOE-Joint Genome Institute). Our analyses revealed RNA viruses in these grassland soils were mostly eukaryotic RNA viruses with fungi as their natural hosts (average relative abundance of 72.4 percent). Network analysis and structural equation modeling suggested that land use and agricultural practices such as irrigation, plant presence, and type of cultivar directly benefit the composition and associated genetic diversity of soil RNA viral communities and indirectly influence viral communities through structuring the host communities. This study demonstrates how metatranscriptomic data from an established field experiment can advance the understanding of the complex interactions of environmental factors on soil RNA viral communities and the potential for irrigation and cultivar choice to influence RNA viral communities and their host populations.

PNNL Contacts

Kirsten S Hofmockel, Pacific Northwest National Laboratory, kirsten.hofmockel@pnnl.gov
Ruonan Wu, Pacific Northwest National Laboratory, ruonan.wu@pnnl.gov

Funding

This program is supported by the Department of Energy (DOE), Office of Science, through the Genomic Science program, Biological and Environmental Research program. Metatranscriptomic data was generated under the Facilities Integrating Collaborations for User Science (FICUS) project and used resources at the DOE Joint Genome Institute. PNNL is a multiprogram national laboratory operated by Battelle for DOE.