Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs
Upland soils of tundra function as a constant sink for atmospheric CH 4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH 4 -C m −2 day −1 were determined by the static chamber method in a mildly acidic upland soil of the liche...
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MDPI AG
2020
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Online Access: | https://doi.org/10.3390/microorganisms8122047 https://doaj.org/article/87bb55b5f07948d5b544a6e0f36d03d3 |
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ftdoajarticles:oai:doaj.org/article:87bb55b5f07948d5b544a6e0f36d03d3 2023-05-15T18:28:34+02:00 Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs Svetlana E. Belova Olga V. Danilova Anastasia A. Ivanova Alexander Y. Merkel Svetlana N. Dedysh 2020-12-01T00:00:00Z https://doi.org/10.3390/microorganisms8122047 https://doaj.org/article/87bb55b5f07948d5b544a6e0f36d03d3 EN eng MDPI AG https://www.mdpi.com/2076-2607/8/12/2047 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms8122047 2076-2607 https://doaj.org/article/87bb55b5f07948d5b544a6e0f36d03d3 Microorganisms, Vol 8, Iss 2047, p 2047 (2020) atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group pmoA gene Biology (General) QH301-705.5 article 2020 ftdoajarticles https://doi.org/10.3390/microorganisms8122047 2022-12-31T06:07:02Z Upland soils of tundra function as a constant sink for atmospheric CH 4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH 4 -C m −2 day −1 were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH 4 oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~10 7 pmoA gene copies g −1 dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae . The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and “ Methylocapsa gorgona” MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs. Article in Journal/Newspaper Subarctic Tundra Siberia Directory of Open Access Journals: DOAJ Articles Microorganisms 8 12 2047 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group pmoA gene Biology (General) QH301-705.5 |
spellingShingle |
atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group pmoA gene Biology (General) QH301-705.5 Svetlana E. Belova Olga V. Danilova Anastasia A. Ivanova Alexander Y. Merkel Svetlana N. Dedysh Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
topic_facet |
atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group pmoA gene Biology (General) QH301-705.5 |
description |
Upland soils of tundra function as a constant sink for atmospheric CH 4 but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH 4 -C m −2 day −1 were determined by the static chamber method in a mildly acidic upland soil of the lichen-dominated forested tundra, North Siberia, Russia. The maximal CH 4 oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the pmoA gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these pmoA gene fragments by means of specific qPCR assay detected ~10 7 pmoA gene copies g −1 dry soil. The pmoA diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to pmoA of Candidatus Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order Methylococcales and the family Methylocystaceae . The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated Beijerinckiaceae bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of Candidatus Methyloaffinis lahnbergensis and “ Methylocapsa gorgona” MG08, respectively, and were represented by eight species-level operational taxonomic units (OTUs), two of which were highly abundant. These identification results characterize subarctic upland soils, which are exposed to atmospheric methane concentrations only, as a unique habitat colonized mostly by USCα methanotrophs. |
format |
Article in Journal/Newspaper |
author |
Svetlana E. Belova Olga V. Danilova Anastasia A. Ivanova Alexander Y. Merkel Svetlana N. Dedysh |
author_facet |
Svetlana E. Belova Olga V. Danilova Anastasia A. Ivanova Alexander Y. Merkel Svetlana N. Dedysh |
author_sort |
Svetlana E. Belova |
title |
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
title_short |
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
title_full |
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
title_fullStr |
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
title_full_unstemmed |
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs |
title_sort |
methane-oxidizing communities in lichen-dominated forested tundra are composed exclusively of high-affinity uscα methanotrophs |
publisher |
MDPI AG |
publishDate |
2020 |
url |
https://doi.org/10.3390/microorganisms8122047 https://doaj.org/article/87bb55b5f07948d5b544a6e0f36d03d3 |
genre |
Subarctic Tundra Siberia |
genre_facet |
Subarctic Tundra Siberia |
op_source |
Microorganisms, Vol 8, Iss 2047, p 2047 (2020) |
op_relation |
https://www.mdpi.com/2076-2607/8/12/2047 https://doaj.org/toc/2076-2607 doi:10.3390/microorganisms8122047 2076-2607 https://doaj.org/article/87bb55b5f07948d5b544a6e0f36d03d3 |
op_doi |
https://doi.org/10.3390/microorganisms8122047 |
container_title |
Microorganisms |
container_volume |
8 |
container_issue |
12 |
container_start_page |
2047 |
_version_ |
1766211088466051072 |