CaltechAUTHORS
  A Caltech Library Service

Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments

Ghashghavi, Mohammad and Belova, Svetlana E. and Bodelier, Paul L. E. and Dedysh, Svetlana N. and Kox, Martine A. R. and Speth, Daan R. and Frenzel, Peter and Jetten, Mike S. M. and Lücker, Sebastian and Lüke, Claudia (2019) Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere, 4 (3). Art. No. e00631-18. ISSN 2379-5042. PMCID PMC6553558. https://resolver.caltech.edu/CaltechAUTHORS:20190606-091001647

[img] PDF - Published Version
Creative Commons Attribution.

990Kb
[img] PDF (Fig. S1) - Supplemental Material
Creative Commons Attribution.

335Kb
[img] PDF (Fig. S2) - Supplemental Material
Creative Commons Attribution.

38Kb
[img] MS Word (Table S1) - Supplemental Material
Creative Commons Attribution.

15Kb
[img] MS Word (Table S2) - Supplemental Material
Creative Commons Attribution.

15Kb
[img] MS Word (Table S3) - Supplemental Material
Creative Commons Attribution.

16Kb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20190606-091001647

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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1128/msphere.00631-18DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553558/PubMed CentralArticle
ORCID:
AuthorORCID
Kox, Martine A. R.0000-0001-5795-1411
Speth, Daan R.0000-0002-2361-5935
Jetten, Mike S. M.0000-0002-4691-7039
Lücker, Sebastian0000-0003-2935-4454
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).
Funders:
Funding AgencyGrant Number
European Research Council (ERC)339880
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)863.14.019
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)016.Vidi.189.050
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)fp07.002.01
Deutsche Forschungsgemeinschaft (DFG)UNSPECIFIED
European Science FoundationUNSPECIFIED
Russian Academy of Sciences0104-2018-0034
Issue or Number:3
PubMed Central ID:PMC6553558
Record Number:CaltechAUTHORS:20190606-091001647
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190606-091001647
Official Citation:Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. Mohammad Ghashghavi, Svetlana E. Belova, Paul L. E. Bodelier, Svetlana N. Dedysh, Martine A. R.Kox, Daan R. Speth, Peter Frenzel, Mike S. M. Jetten, Sebastian Lücker, Claudia Lüke. mSphere Jun 2019, 4 (3) e00631-18; DOI: 10.1128/mSphere.00631-18
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:96187
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:06 Jun 2019 22:25
Last Modified:03 Oct 2019 21:20

Repository Staff Only: item control page