Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment
This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln<sup>3+</sup>)-rich underground mine environment using a metagenomic and metapr...
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MDPI AG
2022-04-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/7/3947 |
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| author | Agnieszka Daszczyńska Tomasz Krucoń Robert Stasiuk Marta Koblowska Renata Matlakowska |
| author_facet | Agnieszka Daszczyńska Tomasz Krucoń Robert Stasiuk Marta Koblowska Renata Matlakowska |
| author_sort | Agnieszka Daszczyńska |
| collection | DOAJ |
| description | This study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln<sup>3+</sup>)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by <i>Alpha</i>-, <i>Beta</i>-, and <i>Gammaproteobacteria</i> represented by the four orders <i>Methylococcales</i>, <i>Nitrosomonadales</i>, <i>Rhizobiales</i>, and <i>Xanthomonadales</i>. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with <i>Nitrosomonadales</i> and <i>Rhizobiales</i>, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment. |
| first_indexed | 2024-03-09T11:44:15Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T11:44:15Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2634e68f3f0e49ec937037f5936e75832023-11-30T23:24:25ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-04-01237394710.3390/ijms23073947Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep EnvironmentAgnieszka Daszczyńska0Tomasz Krucoń1Robert Stasiuk2Marta Koblowska3Renata Matlakowska4Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandDepartment of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandDepartment of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandLaboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, PolandDepartment of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, PolandThis study investigated the occurrence and diversity of proteobacterial XoxF-type methanol dehydrogenases (MDHs) in the microbial community that inhabits a fossil organic matter- and sedimentary lanthanide (Ln<sup>3+</sup>)-rich underground mine environment using a metagenomic and metaproteomic approach. A total of 8 XoxF-encoding genes (XoxF-EGs) and 14 protein sequences matching XoxF were identified. XoxF-type MDHs were produced by <i>Alpha</i>-, <i>Beta</i>-, and <i>Gammaproteobacteria</i> represented by the four orders <i>Methylococcales</i>, <i>Nitrosomonadales</i>, <i>Rhizobiales</i>, and <i>Xanthomonadales</i>. The highest number of XoxF-EG- and XoxF-matching protein sequences were affiliated with <i>Nitrosomonadales</i> and <i>Rhizobiales</i>, respectively. Among the identified XoxF-EGs, two belonged to the XoxF1 clade, five to the XoxF4 clade, and one to the XoxF5 clade, while seven of the identified XoxF proteins belonged to the XoxF1 clade, four to the XoxF4 clade, and three to the XoxF5 clade. Moreover, the accumulation of light lanthanides and the presence of methanol in the microbial mat were confirmed. This study is the first to show the occurrence of XoxF in the metagenome and metaproteome of a deep microbial community colonizing a fossil organic matter- and light lanthanide-rich sedimentary environment. The presented results broaden our knowledge of the ecology of XoxF-producing bacteria as well as of the distribution and diversity of these enzymes in the natural environment.https://www.mdpi.com/1422-0067/23/7/3947methanolXoxFlanthanidesblack shalemetagenomemetaproteome |
| spellingShingle | Agnieszka Daszczyńska Tomasz Krucoń Robert Stasiuk Marta Koblowska Renata Matlakowska Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment International Journal of Molecular Sciences methanol XoxF lanthanides black shale metagenome metaproteome |
| title | Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment |
| title_full | Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment |
| title_fullStr | Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment |
| title_full_unstemmed | Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment |
| title_short | Lanthanide-Dependent Methanol Metabolism of a <i>Proteobacteria</i>-Dominated Community in a Light Lanthanide-Rich Deep Environment |
| title_sort | lanthanide dependent methanol metabolism of a i proteobacteria i dominated community in a light lanthanide rich deep environment |
| topic | methanol XoxF lanthanides black shale metagenome metaproteome |
| url | https://www.mdpi.com/1422-0067/23/7/3947 |
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