Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for...
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Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/ http://www.ncbi.nlm.nih.gov/pubmed/35064149 https://doi.org/10.1038/s41598-021-04486-z |
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ftpubmed:oai:pubmedcentral.nih.gov:8782848 2023-05-15T14:31:47+02:00 Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning Altshuler, Ianina Raymond-Bouchard, Isabelle Magnuson, Elisse Tremblay, Julien Greer, Charles W. Whyte, Lyle G. 2022-01-21 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/ http://www.ncbi.nlm.nih.gov/pubmed/35064149 https://doi.org/10.1038/s41598-021-04486-z en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/ http://www.ncbi.nlm.nih.gov/pubmed/35064149 http://dx.doi.org/10.1038/s41598-021-04486-z © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) . CC-BY Sci Rep Article Text 2022 ftpubmed https://doi.org/10.1038/s41598-021-04486-z 2022-01-30T01:33:37Z Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy (13)CH(4) (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH(4) metabolism in these high Arctic cryosols. Sequencing of (13)C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-(13)C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and ... Text arctic methane Arctic permafrost PubMed Central (PMC) Arctic Scientific Reports 12 1 |
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Article Altshuler, Ianina Raymond-Bouchard, Isabelle Magnuson, Elisse Tremblay, Julien Greer, Charles W. Whyte, Lyle G. Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
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Article |
description |
Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy (13)CH(4) (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH(4) metabolism in these high Arctic cryosols. Sequencing of (13)C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-(13)C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and ... |
format |
Text |
author |
Altshuler, Ianina Raymond-Bouchard, Isabelle Magnuson, Elisse Tremblay, Julien Greer, Charles W. Whyte, Lyle G. |
author_facet |
Altshuler, Ianina Raymond-Bouchard, Isabelle Magnuson, Elisse Tremblay, Julien Greer, Charles W. Whyte, Lyle G. |
author_sort |
Altshuler, Ianina |
title |
Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
title_short |
Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
title_full |
Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
title_fullStr |
Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
title_full_unstemmed |
Unique high Arctic methane metabolizing community revealed through in situ (13)CH(4)-DNA-SIP enrichment in concert with genome binning |
title_sort |
unique high arctic methane metabolizing community revealed through in situ (13)ch(4)-dna-sip enrichment in concert with genome binning |
publisher |
Nature Publishing Group UK |
publishDate |
2022 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/ http://www.ncbi.nlm.nih.gov/pubmed/35064149 https://doi.org/10.1038/s41598-021-04486-z |
geographic |
Arctic |
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Arctic |
genre |
arctic methane Arctic permafrost |
genre_facet |
arctic methane Arctic permafrost |
op_source |
Sci Rep |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782848/ http://www.ncbi.nlm.nih.gov/pubmed/35064149 http://dx.doi.org/10.1038/s41598-021-04486-z |
op_rights |
© The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This 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/) . |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41598-021-04486-z |
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