Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
Abstract
Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and othermore »
- Publication Date:
- Research Org.:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA Forest Service; National Science Foundation (NSF); USDOE National Nuclear Security Administration (NNSA)
- OSTI Identifier:
- 1826202
- Alternate Identifier(s):
- OSTI ID: 1830222; OSTI ID: 1844484
- Report Number(s):
- PNNL-SA-162885; LLNL-JRNL-814032
Journal ID: ISSN 2049-2618; 208; PII: 1154
- Grant/Contract Number:
- 18-ERD-041; SCW1632; AC05-76RL01830; DEB 1026415; PNW01-JV112619320-16; AC52-07NA27344
- Resource Type:
- Published Article
- Journal Name:
- Microbiome
- Additional Journal Information:
- Journal Name: Microbiome Journal Volume: 9 Journal Issue: 1; Journal ID: ISSN 2049-2618
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; soil viruses; bacteriophage; stable isotope probing; permafrost; peat; o-water; metagenomics
Citation Formats
Trubl, Gareth, Kimbrel, Jeffrey A., Liquet-Gonzalez, Jose, Nuccio, Erin E., Weber, Peter K., Pett-Ridge, Jennifer, Jansson, Janet K., Waldrop, Mark P., and Blazewicz, Steven J. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. United Kingdom: N. p., 2021.
Web. doi:10.1186/s40168-021-01154-2.
Trubl, Gareth, Kimbrel, Jeffrey A., Liquet-Gonzalez, Jose, Nuccio, Erin E., Weber, Peter K., Pett-Ridge, Jennifer, Jansson, Janet K., Waldrop, Mark P., & Blazewicz, Steven J. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. United Kingdom. https://doi.org/10.1186/s40168-021-01154-2
Trubl, Gareth, Kimbrel, Jeffrey A., Liquet-Gonzalez, Jose, Nuccio, Erin E., Weber, Peter K., Pett-Ridge, Jennifer, Jansson, Janet K., Waldrop, Mark P., and Blazewicz, Steven J. Mon .
"Active virus-host interactions at sub-freezing temperatures in Arctic peat soil". United Kingdom. https://doi.org/10.1186/s40168-021-01154-2.
@article{osti_1826202,
title = {Active virus-host interactions at sub-freezing temperatures in Arctic peat soil},
author = {Trubl, Gareth and Kimbrel, Jeffrey A. and Liquet-Gonzalez, Jose and Nuccio, Erin E. and Weber, Peter K. and Pett-Ridge, Jennifer and Jansson, Janet K. and Waldrop, Mark P. and Blazewicz, Steven J.},
abstractNote = {Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures). We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients. Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks.},
doi = {10.1186/s40168-021-01154-2},
journal = {Microbiome},
number = 1,
volume = 9,
place = {United Kingdom},
year = {Mon Oct 18 00:00:00 EDT 2021},
month = {Mon Oct 18 00:00:00 EDT 2021}
}
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