Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil
Abstract
Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilizemore »
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
- OSTI Identifier:
- 1575852
- Alternate Identifier(s):
- OSTI ID: 1591839; OSTI ID: 1661044
- Report Number(s):
- LLNL-JRNL-772064
Journal ID: ISSN 0027-8424
- Grant/Contract Number:
- AC52-07NA27344; AC02-05CH11231; SC0010570; SC0016247; SC0010566; SCW1589; SCW1632; EAR-1331940; 1487; 1472
- Resource Type:
- Published Article
- Journal Name:
- Proceedings of the National Academy of Sciences of the United States of America
- Additional Journal Information:
- Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 116 Journal Issue: 51; Journal ID: ISSN 0027-8424
- Publisher:
- National Academy of Sciences
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; virus; phage; soil; rhizosphere; metatransciptome
Citation Formats
Starr, Evan P., Nuccio, Erin E., Pett-Ridge, Jennifer, Banfield, Jillian F., and Firestone, Mary K. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. United States: N. p., 2019.
Web. doi:10.1073/pnas.1908291116.
Starr, Evan P., Nuccio, Erin E., Pett-Ridge, Jennifer, Banfield, Jillian F., & Firestone, Mary K. Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil. United States. https://doi.org/10.1073/pnas.1908291116
Starr, Evan P., Nuccio, Erin E., Pett-Ridge, Jennifer, Banfield, Jillian F., and Firestone, Mary K. Tue .
"Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil". United States. https://doi.org/10.1073/pnas.1908291116.
@article{osti_1575852,
title = {Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil},
author = {Starr, Evan P. and Nuccio, Erin E. and Pett-Ridge, Jennifer and Banfield, Jillian F. and Firestone, Mary K.},
abstractNote = {Viruses impact nearly all organisms on Earth, with ripples of influence in agriculture, health, and biogeochemical processes. However, very little is known about RNA viruses in an environmental context, and even less is known about their diversity and ecology in soil, 1 of the most complex microbial systems. Here, we assembled 48 individual metatranscriptomes from 4 habitats within a planted soil sampled over a 22-d time series: Rhizosphere alone, detritosphere alone, rhizosphere with added root detritus, and unamended soil (4 time points and 3 biological replicates). We resolved the RNA viral community, uncovering a high diversity of viral sequences. We also investigated possible host organisms by analyzing metatranscriptome marker genes. Based on viral phylogeny, much of the diversity was Narnaviridae that may parasitize fungi or Leviviridae, which may infect Proteobacteria. Both host and viral communities appear to be highly dynamic, and rapidly diverged depending on experimental conditions. The viral and host communities were structured based on the presence of root litter. Clear temporal dynamics by Leviviridae and their hosts indicated that viruses were replicating. With this time-resolved analysis, we show that RNA viruses are diverse, abundant, and active in soil. When viral infection causes host cell death, it may mobilize cell carbon in a process that may represent an overlooked component of soil carbon cycling.},
doi = {10.1073/pnas.1908291116},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 51,
volume = 116,
place = {United States},
year = {2019},
month = {11}
}
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