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 det...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390657/ https://www.ncbi.nlm.nih.gov/pubmed/34446837 http://dx.doi.org/10.1038/s42003-021-02514-2 |
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author | Wu, Ruonan Davison, Michelle R. Gao, Yuqian Nicora, Carrie D. Mcdermott, Jason E. Burnum-Johnson, Kristin E. Hofmockel, Kirsten S. Jansson, Janet K. |
author_facet | Wu, Ruonan Davison, Michelle R. Gao, Yuqian Nicora, Carrie D. Mcdermott, Jason E. Burnum-Johnson, Kristin E. Hofmockel, Kirsten S. Jansson, Janet K. |
author_sort | Wu, Ruonan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8390657 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-83906572021-09-22 Moisture modulates soil reservoirs of active DNA and RNA viruses Wu, Ruonan Davison, Michelle R. Gao, Yuqian Nicora, Carrie D. Mcdermott, Jason E. Burnum-Johnson, Kristin E. Hofmockel, Kirsten S. Jansson, Janet K. Commun Biol Article 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. Nature Publishing Group UK 2021-08-26 /pmc/articles/PMC8390657/ /pubmed/34446837 http://dx.doi.org/10.1038/s42003-021-02514-2 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Wu, Ruonan Davison, Michelle R. Gao, Yuqian Nicora, Carrie D. Mcdermott, Jason E. Burnum-Johnson, Kristin E. Hofmockel, Kirsten S. Jansson, Janet K. Moisture modulates soil reservoirs of active DNA and RNA viruses |
title | Moisture modulates soil reservoirs of active DNA and RNA viruses |
title_full | Moisture modulates soil reservoirs of active DNA and RNA viruses |
title_fullStr | Moisture modulates soil reservoirs of active DNA and RNA viruses |
title_full_unstemmed | Moisture modulates soil reservoirs of active DNA and RNA viruses |
title_short | Moisture modulates soil reservoirs of active DNA and RNA viruses |
title_sort | moisture modulates soil reservoirs of active dna and rna viruses |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390657/ https://www.ncbi.nlm.nih.gov/pubmed/34446837 http://dx.doi.org/10.1038/s42003-021-02514-2 |
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