Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
BACKGROUND: 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 a...
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ftpubmed:oai:pubmedcentral.nih.gov:8522061 2023-05-15T15:02:07+02:00 Active virus-host interactions at sub-freezing temperatures in Arctic peat soil 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. 2021-10-18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522061/ https://doi.org/10.1186/s40168-021-01154-2 en eng BioMed Central http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522061/ http://dx.doi.org/10.1186/s40168-021-01154-2 © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. CC0 PDM CC-BY Microbiome Research Text 2021 ftpubmed https://doi.org/10.1186/s40168-021-01154-2 2021-10-24T00:39:46Z BACKGROUND: 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). RESULTS: 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 H(2)(18)O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO(2)) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up (18)O in soil and respired CO(2) 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. CONCLUSIONS: 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 ... Text Arctic Alaska PubMed Central (PMC) Arctic Bonanza ENVELOPE(-119.820,-119.820,55.917,55.917) Microbiome 9 1 |
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PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Research |
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Research 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 |
topic_facet |
Research |
description |
BACKGROUND: 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). RESULTS: 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 H(2)(18)O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO(2)) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up (18)O in soil and respired CO(2) 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. CONCLUSIONS: 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 ... |
format |
Text |
author |
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. |
author_facet |
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. |
author_sort |
Trubl, Gareth |
title |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
title_short |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
title_full |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
title_fullStr |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
title_full_unstemmed |
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
title_sort |
active virus-host interactions at sub-freezing temperatures in arctic peat soil |
publisher |
BioMed Central |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522061/ https://doi.org/10.1186/s40168-021-01154-2 |
long_lat |
ENVELOPE(-119.820,-119.820,55.917,55.917) |
geographic |
Arctic Bonanza |
geographic_facet |
Arctic Bonanza |
genre |
Arctic Alaska |
genre_facet |
Arctic Alaska |
op_source |
Microbiome |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522061/ http://dx.doi.org/10.1186/s40168-021-01154-2 |
op_rights |
© The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
op_rightsnorm |
CC0 PDM CC-BY |
op_doi |
https://doi.org/10.1186/s40168-021-01154-2 |
container_title |
Microbiome |
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9 |
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1 |
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1766334099727843328 |