Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments
Abstract
Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named "Methylotetracoccus oryzae" C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C_(16:1)ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.
Additional Information
© 2019 Ghashghavi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Received November 20, 2018. Accepted May 9, 2019. Data availability: The high-quality draft genome of strain C50C1 is available at NCBI under BioProject accession number PRJNA361434. We thank Natalia E. Suzina for electron microscopy analyses and Huub Op den Camp for help with methanol dehydrogenase classification. Soil sampling was possible thanks to Zhihong. This project was funded by the European Research Council (ERC advanced grant Ecomom 339880), the Netherlands Organisation for Scientific Research (NWO grants 863.14.019 and 016.Vidi.189.050), and BE-Basic (grant fp07.002.01). The initial enrichment and isolation were done as part of the Biogeochemistry of Paddy Soil Evolution framework, supported by the Deutsche Forschungsgemeinschaft (DFG) and the European Science Foundation EUROCORES program EuroEEFG. S.E.B. and S.N.D. acknowledge budgetary support (research topic 0104-2018-0034).Attached Files
Published - mSphere-2019-Ghashghavi-e00631-18.full.pdf
Supplemental Material - inline-supplementary-material-1.pdf
Supplemental Material - inline-supplementary-material-2.pdf
Supplemental Material - inline-supplementary-material-3.docx
Supplemental Material - inline-supplementary-material-4.docx
Supplemental Material - inline-supplementary-material-5.docx
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Additional details
- PMCID
- PMC6553558
- Eprint ID
- 96187
- Resolver ID
- CaltechAUTHORS:20190606-091001647
- 339880
- European Research Council (ERC)
- 863.14.019
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)
- 016.Vidi.189.050
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)
- fp07.002.01
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)
- Deutsche Forschungsgemeinschaft (DFG)
- European Science Foundation
- 0104-2018-0034
- Russian Academy of Sciences
- Created
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2019-06-06Created from EPrint's datestamp field
- Updated
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2021-11-16Created from EPrint's last_modified field