DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes
Abstract
Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism andmore »
- Authors:
-
[1];
[1];
[2];
[1];
[3];
[4];
[1]
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Washington State Univ., Pullman, WA (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Oregon Health & Science University, Portland, OR (United States)
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Iowa State Univ., Ames, IA (United States)
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1830372
- Report Number(s):
- PNNL-SA-166275
Journal ID: ISSN 2150-7511
- Grant/Contract Number:
- AC05-76RL01830
- Resource Type:
- Accepted Manuscript
- Journal Name:
- mBio (Online)
- Additional Journal Information:
- Journal Name: mBio (Online); Journal Volume: 12; Journal Issue: 6; Journal ID: ISSN 2150-7511
- Publisher:
- American Society for Microbiology (ASM)
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; soil virus; soild bacteriophage; auxiliary metabolic genes; lysogeny; grassland soil; metagenome
Citation Formats
Wu, Ruonan, Davison, Michelle R., Nelson, William C., Graham, Emily B., Fansler, Sarah J., Farris, Yuliya, Bell, Sheryl L., Godinez, Iobani G., McDermott, Jason E., Hofmockel, Kirsten S., and Jansson, Janet K. DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. United States: N. p., 2021.
Web. doi:10.1128/mbio.02595-21.
Wu, Ruonan, Davison, Michelle R., Nelson, William C., Graham, Emily B., Fansler, Sarah J., Farris, Yuliya, Bell, Sheryl L., Godinez, Iobani G., McDermott, Jason E., Hofmockel, Kirsten S., & Jansson, Janet K. DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes. United States. https://doi.org/10.1128/mbio.02595-21
Wu, Ruonan, Davison, Michelle R., Nelson, William C., Graham, Emily B., Fansler, Sarah J., Farris, Yuliya, Bell, Sheryl L., Godinez, Iobani G., McDermott, Jason E., Hofmockel, Kirsten S., and Jansson, Janet K. Tue .
"DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes". United States. https://doi.org/10.1128/mbio.02595-21. https://www.osti.gov/servlets/purl/1830372.
@article{osti_1830372,
title = {DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes},
author = {Wu, Ruonan and Davison, Michelle R. and Nelson, William C. and Graham, Emily B. and Fansler, Sarah J. and Farris, Yuliya and Bell, Sheryl L. and Godinez, Iobani G. and McDermott, Jason E. and Hofmockel, Kirsten S. and Jansson, Janet K.},
abstractNote = {Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.},
doi = {10.1128/mbio.02595-21},
journal = {mBio (Online)},
number = 6,
volume = 12,
place = {United States},
year = {Tue Nov 02 00:00:00 EDT 2021},
month = {Tue Nov 02 00:00:00 EDT 2021}
}
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