Methanotrophy by a Mycobacterium species that dominates a cave microbial ecosystem
Van spanning, Rob J. M.; Guan, Qingtian; Melkonian, Chrats; Gallant, James; Polerecky, Lubos; Flot, Jean-françois; Brandt, Bernd W.; Braster, Martin; Iturbe espinoza, Paul; Aerts, Joost W.; Meima-Franke, Marion M.; Piersma, Sander R.; Bunduc, Catalin M.; Ummels, Roy; Pain, Arnab; Fleming, Emily J.; Van der wel, Nicole N.; Gherman, Vasile D.; Sarbu, Serban M.; Bodelier, Paul L. E.; Bitter, Wilbert
(2022) Nature Microbiology, volume 7, issue 12, pp. 2089 - 2100
(Article)
Abstract
So far, only members of the bacterial phyla Proteobacteria and Verrucomicrobia are known to grow methanotrophically under aerobic conditions. Here we report that this metabolic trait is also observed within the Actinobacteria. We enriched and cultivated a methanotrophic Mycobacterium from an extremely acidic biofilm growing on a cave wall at
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a gaseous chemocline interface between volcanic gases and the Earth's atmosphere. This Mycobacterium, for which we propose the name Candidatus Mycobacterium methanotrophicum, is closely related to well-known obligate pathogens such as M. tuberculosis and M. leprae. Genomic and proteomic analyses revealed that Candidatus M. methanotrophicum expresses a full suite of enzymes required for aerobic growth on methane, including a soluble methane monooxygenase that catalyses the hydroxylation of methane to methanol and enzymes involved in formaldehyde fixation via the ribulose monophosphate pathway. Growth experiments combined with stable isotope probing using 13C-labelled methane confirmed that Candidatus M. methanotrophicum can grow on methane as a sole carbon and energy source. A broader survey based on 16S metabarcoding suggests that species closely related to Candidatus M. methanotrophicum may be abundant in low-pH, high-methane environments.
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Keywords: Alcohol-dehydrogenase, Bacteria, Eastern carpathians, Gas, Methane, Monooxygenase gene-cluster, Multiple sequence alignment, Oxidation, Pathways, Tool, Taverne
ISSN: 1740-1526
Publisher: Nature Publishing Group
Note: Funding Information: The authors thank C. Murrell for valuable discussions, C. P. Antony for assistance in metagenomics, A. Grootemaat for TEM imaging, M. Kienhuis for technical support with nanoSIMS analysis, I. Grigoriev for support during fluorescence microsopy, and Z. Para and B. Hegyeli, the Romanian custodians, for facilitating the experiments in Sulfur Cave. Also, we thank Utrecht Sequencing Facility (useq.nl) for providing sequencing service and data. The nanoSIMS facility at Utrecht University was financed through a large infrastructure grant by the Netherlands Organisation for Scientific Research (NWO, grant no. 175.010.2009.011). C.M. was supported by the Dutch Research Council, as part of the MiCRop Consortium (NWO/OCW grant no. 024.004.014). A.P. and Q.G. are supported by a faculty baseline grant (BAS/1/1020-01-01) from KAUST to A.P. The authors also thank members of the Bioscience Core Laboratory in KAUST for providing assistance with the generation of raw genome sequence datasets. PIE research was funded by FONDECYT-CONCYTEC (216-2015-FONDECYT). This is publication number 7467 of the Netherlands Institute of Ecology (NIOO-KNAW). Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature Limited. Funding Information: The authors thank C. Murrell for valuable discussions, C. P. Antony for assistance in metagenomics, A. Grootemaat for TEM imaging, M. Kienhuis for technical support with nanoSIMS analysis, I. Grigoriev for support during fluorescence microsopy, and Z. Para and B. Hegyeli, the Romanian custodians, for facilitating the experiments in Sulfur Cave. Also, we thank Utrecht Sequencing Facility (useq.nl) for providing sequencing service and data. The nanoSIMS facility at Utrecht University was financed through a large infrastructure grant by the Netherlands Organisation for Scientific Research (NWO, grant no. 175.010.2009.011). C.M. was supported by the Dutch Research Council, as part of the MiCRop Consortium (NWO/OCW grant no. 024.004.014). A.P. and Q.G. are supported by a faculty baseline grant (BAS/1/1020-01-01) from KAUST to A.P. The authors also thank members of the Bioscience Core Laboratory in KAUST for providing assistance with the generation of raw genome sequence datasets. PIE research was funded by FONDECYT-CONCYTEC (216-2015-FONDECYT). This is publication number 7467 of the Netherlands Institute of Ecology (NIOO-KNAW). Funding Information: The authors thank C. Murrell for valuable discussions, C. P. Antony for assistance in metagenomics, A. Grootemaat for TEM imaging, M. Kienhuis for technical support with nanoSIMS analysis, I. Grigoriev for support during fluorescence microsopy, and Z. Para and B. Hegyeli, the Romanian custodians, for facilitating the experiments in Sulfur Cave. Also, we thank Utrecht Sequencing Facility (useq.nl) for providing sequencing service and data. The nanoSIMS facility at Utrecht University was financed through a large infrastructure grant by the Netherlands Organisation for Scientific Research (NWO, grant no. 175.010.2009.011). C.M. was supported by the Dutch Research Council, as part of the MiCRop Consortium (NWO/OCW grant no. 024.004.014). A.P. and Q.G. are supported by a faculty baseline grant (BAS/1/1020-01-01) from KAUST to A.P. The authors also thank members of the Bioscience Core Laboratory in KAUST for providing assistance with the generation of raw genome sequence datasets. PIE research was funded by FONDECYT-CONCYTEC (216-2015-FONDECYT). This is publication number 7467 of the Netherlands Institute of Ecology (NIOO-KNAW). Publisher Copyright: © 2022, The Author(s), under exclusive licence to Springer Nature Limited.
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