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<sub>4</sub> but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH<sub>4</sub>-C m<sup>−2</sup> day<sup>−1</sup> w...
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MDPI AG
2020-12-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/12/2047 |
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| 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 |
| collection | DOAJ |
| description | Upland soils of tundra function as a constant sink for atmospheric CH<sub>4</sub> but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH<sub>4</sub>-C m<sup>−2</sup> day<sup>−1</sup> 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<sub>4</sub> oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the <i>pmoA</i> gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these <i>pmoA</i> gene fragments by means of specific qPCR assay detected ~10<sup>7</sup><i>pmoA</i> gene copies g<sup>−1</sup> dry soil. The <i>pmoA</i> diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to <i>pmoA</i> of <i>Candidatus</i> Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order <i>Methylococcales</i> and the family <i>Methylocystaceae</i>. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated <i>Beijerinckiaceae</i> bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of <i>Candidatus</i> Methyloaffinis lahnbergensis and “<i>Methylocapsa gorgona”</i> 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. |
| first_indexed | 2024-03-10T13:53:34Z |
| format | Article |
| id | doaj.art-87bb55b5f07948d5b544a6e0f36d03d3 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T13:53:34Z |
| publishDate | 2020-12-01 |
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| spelling | doaj.art-87bb55b5f07948d5b544a6e0f36d03d32023-11-21T01:51:30ZengMDPI AGMicroorganisms2076-26072020-12-01812204710.3390/microorganisms8122047Methane-Oxidizing Communities in Lichen-Dominated Forested Tundra Are Composed Exclusively of High-Affinity USCα MethanotrophsSvetlana E. Belova0Olga V. Danilova1Anastasia A. Ivanova2Alexander Y. Merkel3Svetlana N. Dedysh4Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, RussiaWinogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, RussiaWinogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, RussiaWinogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, RussiaWinogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, RussiaUpland soils of tundra function as a constant sink for atmospheric CH<sub>4</sub> but the identity of methane oxidizers in these soils remains poorly understood. Methane uptake rates of −0.4 to −0.6 mg CH<sub>4</sub>-C m<sup>−2</sup> day<sup>−1</sup> 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<sub>4</sub> oxidation activity was localized in an organic surface soil layer underlying the lichen cover. Molecular identification of methanotrophic bacteria based on retrieval of the <i>pmoA</i> gene revealed Upland Soil Cluster Alpha (USCα) as the only detectable methanotroph group. Quantification of these <i>pmoA</i> gene fragments by means of specific qPCR assay detected ~10<sup>7</sup><i>pmoA</i> gene copies g<sup>−1</sup> dry soil. The <i>pmoA</i> diversity was represented by seven closely related phylotypes; the most abundant phylotype displayed 97.5% identity to <i>pmoA</i> of <i>Candidatus</i> Methyloaffinis lahnbergensis. Further analysis of prokaryote diversity in this soil did not reveal 16S rRNA gene fragments from well-studied methanotrophs of the order <i>Methylococcales</i> and the family <i>Methylocystaceae</i>. The largest group of reads (~4% of all bacterial 16S rRNA gene fragments) that could potentially belong to methanotrophs was classified as uncultivated <i>Beijerinckiaceae</i> bacteria. These reads displayed 96–100 and 95–98% sequence similarity to 16S rRNA gene of <i>Candidatus</i> Methyloaffinis lahnbergensis and “<i>Methylocapsa gorgona”</i> 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.https://www.mdpi.com/2076-2607/8/12/2047atmospheric methane oxidationforested tundraacidic soilsmethanotrophic bacteriaUSCα group<i>pmoA</i> gene |
| spellingShingle | 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 Microorganisms atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group <i>pmoA</i> gene |
| 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 | atmospheric methane oxidation forested tundra acidic soils methanotrophic bacteria USCα group <i>pmoA</i> gene |
| url | https://www.mdpi.com/2076-2607/8/12/2047 |
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