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Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Oleiphilaceae and Relatives

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Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

Despite the ubiquity of marine hydrocarbon-degrading bacteria from the family Oleiphilaceae, until now there is only one strain from this family with a validly published name and fully assembled genome, Oleiphilus messinensis strain ME102 (= DSM 13489). The availability of draft genomes of 27 other isolates gave us the opportunity to get an insight into the genome evolution and speciation patterns within this group. Whole-genome alignments and genome-to-genome distance calculation data demonstrated that Oleiphilaceae consists of four distinct genome clusters that correspond to the species level. Furthermore, we suggest that all known Oleiphilaceae genomes cluster into two genera, the first one being Oleiphilus, which includes O. messinensis ME102 and the second represented by bacteria isolated near Hawaii. The Oleiphilaceae pangenome of 1796 core gene clusters roughly corresponds to the two-thirds of an Oleiphilaceae genome. All high-quality genomes had double copies of almA coding for flavin-binding family monooxygenase linked with degradation of long-chain alkanes. Alkane monooxygenases with pairwise identities between 43% and 86.5% were encoded by four genomes, with two of them having double loci. Cytochromes P450 were present in all genomes and were assigned to two distinct clusters, which, together with the low redundancy of alkane monooxygenases, points at different microorganisms as the sources of acquisition of alkane-monooxygenation enzymes by Oleiphilaceae.

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Acknowledgments

The work of ST was supported by the RSF project # 17-74-30025. MF acknowledges grants PCIN-2014-107 (within ERA NET IB2 grant nr. ERA-IB-14-030—MetaCat), PCIN-2017-078 (within the Marine Biotechnology ERA-NET (ERA-MBT) funded under the European Commission’s Seventh Framework Programme, 2013–2017, Grant agreement 604814), BIO2014-54494-R, and BIO2017-85522-R from the Ministerio de Ciencia, Innovación y Universidades, formerly Ministerio de Economía, Industria y Competitividad. MMY, TNC, OVG, MF, KEJ, and PNG received funding from the European Union’s Horizon 2020 research and innovation program Blue Growth: Unlocking the potential of Seas and Oceans under grant agreement no. [634486] (project acronym INMARE). PNG acknowledges ERA NET IB2, grant no. ERA-IB-14-030, and UK Biotechnology and Biological Sciences Research Council (BBSRC), grant no. BB/M029085/1. TCH, OVG, and PNG acknowledge the support of the Centre for Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through the Welsh Government.

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Authors and Affiliations

  1. National Research Centre “Kurchatov Institute”, Moscow, Russia

    Aleksei A. Korzhenkov

  2. Winogradsky Institute of Microbiology, FRC “Biotechnology” RAS, Moscow, Russia

    Stepan V. Toshchakov

  3. School of Natural Sciences, Bangor University, Bangor, UK

    Olga V. Golyshina, Tatyana N. Chernikova & Peter N. Golyshin

  4. Department of Applied Biocatalysis, CSIC – Institute of Catalysis, Madrid, Spain

    Manuel Ferrer

  5. Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Jülich, Germany

    Karl-Erich Jaeger

  6. Institute for Biological Resources and Marine Biotechnology, IRBIM-CNR, Messina, Italy

    Michail M. Yakimov

  7. Centre for Environmental Biotechnology, Bangor University, Bangor, UK

    Olga V. Golyshina & Peter N. Golyshin

  8. Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

    Karl-Erich Jaeger

  9. Institute of Living Systems, Immanuel Kant Federal Baltic University, Kaliningrad, Russia

    Michail M. Yakimov

Authors
  1. Aleksei A. Korzhenkov
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  2. Stepan V. Toshchakov
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  3. Olga V. Golyshina
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  4. Manuel Ferrer
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  5. Tatyana N. Chernikova
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  6. Karl-Erich Jaeger
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  7. Michail M. Yakimov
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  8. Peter N. Golyshin
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Corresponding author

Correspondence to Peter N. Golyshin .

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Editors and Affiliations

  1. School of Life Sciences, University of Essex, Colchester, UK

    Terry J. McGenity

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Korzhenkov, A.A. et al. (2019). Aerobic Hydrocarbon-Degrading Gammaproteobacteria: Oleiphilaceae and Relatives. In: McGenity, T. (eds) Taxonomy, Genomics and Ecophysiology of Hydrocarbon-Degrading Microbes. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-030-14796-9_23

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