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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 li...

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Autores principales: Belova, Svetlana E., Danilova, Olga V., Ivanova, Anastasia A., Merkel, Alexander Y., Dedysh, Svetlana N.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766663/
https://www.ncbi.nlm.nih.gov/pubmed/33371270
http://dx.doi.org/10.3390/microorganisms8122047
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author Belova, Svetlana E.
Danilova, Olga V.
Ivanova, Anastasia A.
Merkel, Alexander Y.
Dedysh, Svetlana N.
author_facet Belova, Svetlana E.
Danilova, Olga V.
Ivanova, Anastasia A.
Merkel, Alexander Y.
Dedysh, Svetlana N.
author_sort Belova, Svetlana E.
collection PubMed
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.
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spelling pubmed-77666632020-12-28 Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs Belova, Svetlana E. Danilova, Olga V. Ivanova, Anastasia A. Merkel, Alexander Y. Dedysh, Svetlana N. Microorganisms Article 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. MDPI 2020-12-21 /pmc/articles/PMC7766663/ /pubmed/33371270 http://dx.doi.org/10.3390/microorganisms8122047 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Belova, Svetlana E.
Danilova, Olga V.
Ivanova, Anastasia A.
Merkel, Alexander Y.
Dedysh, Svetlana N.
Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα Methanotrophs
title 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_short 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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7766663/
https://www.ncbi.nlm.nih.gov/pubmed/33371270
http://dx.doi.org/10.3390/microorganisms8122047
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