Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
Abstract 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 v...
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ftdoajarticles:oai:doaj.org/article:513bf342f8ab4d30987693416c182276 2023-05-15T15:02:16+02:00 Active virus-host interactions at sub-freezing temperatures in Arctic peat soil Gareth Trubl Jeffrey A. Kimbrel Jose Liquet-Gonzalez Erin E. Nuccio Peter K. Weber Jennifer Pett-Ridge Janet K. Jansson Mark P. Waldrop Steven J. Blazewicz 2021-10-01T00:00:00Z https://doi.org/10.1186/s40168-021-01154-2 https://doaj.org/article/513bf342f8ab4d30987693416c182276 EN eng BMC https://doi.org/10.1186/s40168-021-01154-2 https://doaj.org/toc/2049-2618 doi:10.1186/s40168-021-01154-2 2049-2618 https://doaj.org/article/513bf342f8ab4d30987693416c182276 Microbiome, Vol 9, Iss 1, Pp 1-15 (2021) Soil viruses Bacteriophage Stable isotope probing Permafrost Peat 18O-water Microbial ecology QR100-130 article 2021 ftdoajarticles https://doi.org/10.1186/s40168-021-01154-2 2022-12-31T15:22:22Z Abstract 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 H2 18O 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. 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 ... Article in Journal/Newspaper Arctic permafrost Alaska Directory of Open Access Journals: DOAJ Articles Arctic Bonanza ENVELOPE(-119.820,-119.820,55.917,55.917) Microbiome 9 1 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Soil viruses Bacteriophage Stable isotope probing Permafrost Peat 18O-water Microbial ecology QR100-130 |
spellingShingle |
Soil viruses Bacteriophage Stable isotope probing Permafrost Peat 18O-water Microbial ecology QR100-130 Gareth Trubl Jeffrey A. Kimbrel Jose Liquet-Gonzalez Erin E. Nuccio Peter K. Weber Jennifer Pett-Ridge Janet K. Jansson Mark P. Waldrop Steven J. Blazewicz Active virus-host interactions at sub-freezing temperatures in Arctic peat soil |
topic_facet |
Soil viruses Bacteriophage Stable isotope probing Permafrost Peat 18O-water Microbial ecology QR100-130 |
description |
Abstract 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 H2 18O 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. 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 |
Article in Journal/Newspaper |
author |
Gareth Trubl Jeffrey A. Kimbrel Jose Liquet-Gonzalez Erin E. Nuccio Peter K. Weber Jennifer Pett-Ridge Janet K. Jansson Mark P. Waldrop Steven J. Blazewicz |
author_facet |
Gareth Trubl Jeffrey A. Kimbrel Jose Liquet-Gonzalez Erin E. Nuccio Peter K. Weber Jennifer Pett-Ridge Janet K. Jansson Mark P. Waldrop Steven J. Blazewicz |
author_sort |
Gareth Trubl |
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 |
BMC |
publishDate |
2021 |
url |
https://doi.org/10.1186/s40168-021-01154-2 https://doaj.org/article/513bf342f8ab4d30987693416c182276 |
long_lat |
ENVELOPE(-119.820,-119.820,55.917,55.917) |
geographic |
Arctic Bonanza |
geographic_facet |
Arctic Bonanza |
genre |
Arctic permafrost Alaska |
genre_facet |
Arctic permafrost Alaska |
op_source |
Microbiome, Vol 9, Iss 1, Pp 1-15 (2021) |
op_relation |
https://doi.org/10.1186/s40168-021-01154-2 https://doaj.org/toc/2049-2618 doi:10.1186/s40168-021-01154-2 2049-2618 https://doaj.org/article/513bf342f8ab4d30987693416c182276 |
op_doi |
https://doi.org/10.1186/s40168-021-01154-2 |
container_title |
Microbiome |
container_volume |
9 |
container_issue |
1 |
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1766334232602345472 |