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Effect of oxygen on the anaerobic methanotroph ‘Candidatus Methylomirabilis oxyfera’: kinetic and transcriptional analysis

Authors

  • Francisca A. Luesken,

    1. Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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    • These authors contributed equally to this study.

  • Ming L. Wu,

    1. Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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    • These authors contributed equally to this study.

  • Huub J. M. Op den Camp,

    1. Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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  • Jan T. Keltjens,

    1. Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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  • Henk Stunnenberg,

    1. Department of Molecular Biology, Faculty of Sciences, Nijmegen, Centre of Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, NL-6525 GA, Nijmegen, The Netherlands
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  • Kees-Jan Francoijs,

    1. Department of Molecular Biology, Faculty of Sciences, Nijmegen, Centre of Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, NL-6525 GA, Nijmegen, The Netherlands
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  • Marc Strous,

    1. MPI for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
    2. Centre for Biotechnology, University of Bielefeld, Germany
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  • Mike S. M. Jetten

    Corresponding author
    1. Department of Microbiology, Radboud University Nijmegen, Institute for Water and Wetland Research, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
      E-mail m.jetten@science.ru.nl; Tel. (+31) 24 3562969; Fax (+31) 24 3652830.
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E-mail m.jetten@science.ru.nl; Tel. (+31) 24 3562969; Fax (+31) 24 3652830.

Summary

Candidatus Methylomirabilis oxyfera’ is a denitrifying methanotroph that performs nitrite-dependent anaerobic methane oxidation through a newly discovered intra-aerobic pathway. In this study, we investigated the response of a M. oxyfera enrichment culture to oxygen. Addition of either 2% or 8% oxygen resulted in an instant decrease of methane and nitrite conversion rates. Oxygen exposure also led to a deviation in the nitrite to methane oxidation stoichiometry. Oxygen-uptake and inhibition studies with cell-free extracts displayed a change from cytochrome c to quinol as electron donor after exposure to oxygen. The change in global gene expression was monitored by deep sequencing of cDNA using Illumina technology. After 24 h of oxygen exposure, transcription levels of 1109 (out of 2303) genes changed significantly when compared with the anoxic period. Most of the genes encoding enzymes of the methane oxidation pathway were constitutively expressed. Genes from the denitrification pathway, with exception of one of the putative nitric oxide reductases, norZ2, were severely downregulated. The majority of known genes involved in the vital cellular functions, such as nucleic acid and protein biosynthesis and cell division processes, were downregulated. The alkyl hydroperoxide reductase, ahpC, and genes involved in the synthesis/repair of the iron–sulfur clusters were among the few upregulated genes. Further, transcription of the pmoCAB genes of aerobic methanotrophs present in the non-M. oxyfera community were triggered by the presence of oxygen. Our results show that oxygen-exposed cells of M. oxyfera were under oxidative stress and that in spite of its oxygenic capacity, exposure to microoxic conditions has an overall detrimental effect.

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