"Moisture modulates soil reservoirs of active DNA and RNA viruses"
Soil is known to harbor viruses, but the majority are uncharacterized and their responses to environmental changes are unknown. Here, we used a multi-omics approach (metagenomics, metatranscriptomics and metaproteomics) to detect active DNA viruses and RNA viruses in a native prairie soil and to determine their responses to extremes in soil moisture. The majority of transcribed DNA viruses were bacteriophage, but some were assigned to eukaryotic hosts, mainly insects. We also demonstrated that higher soil moisture increased transcription of a subset of DNA viruses. Metaproteome data validated that the specific viral transcripts were translated into proteins, including chaperonins known to be essential for virion replication and assembly. The soil viral chaperonins were phylogenetically distinct from previously described marine viral chaperonins. 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. This study demonstrates that extreme shifts in soil moisture have dramatic impacts on the composition, activity and potential functions of both DNA and RNA soil viruses.
Linked Experimental Data
- NCBI BioProject Accession: PRJNA744880 (DNA/RNA viral sequence data)
- MassIVE Accession: MSV000086114| ftp://massive.ucsd.edu/MSV000086144/ (proteomics data)
- Zenodo DOI: 10.5281/zenodo.5081148 (R code and source data used for figure generation and curation of databases)
- OSF Accession: 10.17605/OSF.IO/4UVJ7 (KPBS soil metatranscriptome + 16S rRNA sequence data) - Chowdhury et al. 2019
- SRA Accession: SRP075174 (KPBS soil long-read sequence data) - Chowdhury et al. 2019
- GenBank Accession(s): KX239231-KX239311, KX239037-KX239230 (KPBS soil moleculo-only 16S rRNA sequence data) - White et al. 2016
KEYWORDS: Functional modules, microbiome, reduced complexity, soil metatranscriptome, soil microbiome
Wu, R., Davison, M.R., Gao, Y. et al. Moisture modulates soil reservoirs of active DNA and RNA viruses. Commun Biol 4, 992 (2021). https://doi.org/10.1038/s42003-021-02514-2
Projects (1)
The Phenotypic Response of the Soil Microbiome to Environmental Perturbations Project (Soil Microbiome SFA) at Pacific Northwest National Laboratory is a Genomic Sciences Program Science Focus Area (SFA) Project operating under the Environmental Microbiome Science Research Area. The Soil Microbiome...
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