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Hydrocarbon-Degrading Microbes as Sources of New Biocatalysts

  • Cristina Coscolín
  • Rafael Bargiela
  • Mónica Martínez-Martínez
  • Sandra Alonso
  • Alexander Bollinger
  • Stephan Thies
  • Tatyana N. Chernikova
  • Tran Hai
  • Olga V. Golyshina
  • Karl-Erich Jaeger
  • Michail M. Yakimov
  • Peter N. Golyshin
  • Manuel FerrerEmail author
Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

Petroleum hydrocarbons, including those discharged to the marine environment, are metabolized through different catabolic pathways by a number of microorganisms. Each hydrocarbon-degrading microorganism produces interesting enzymes for degrading alkanes and/or aromatic compounds that allow them to be used as sources of carbon and energy, and thus, these microbes occupy hydrocarbon-rich ecological niches. Their diversity and hydrocarbon-degrading metabolic abilities have been extensively examined in multiple environmental and phylogenetic contexts. Genes encoding enzymes involved in degradation, such as alkane hydroxylases and other monooxygenases, P450 cytochromes, rubredoxin reductases, and ferredoxin reductases, have been examined by genome analysis, and a number of them have been successfully cloned, expressed, purified, and their activities confirmed. However, in these microorganisms, the accumulated information regarding other types of enzymes, particularly those most used at industrial level, is limited. Here, we compile information about the accumulated enzymatic knowledge of obligate marine hydrocarbonoclastic bacteria (OMHCB), key players in bioremediation of hydrocarbons in contaminated marine ecosystems. We focused on bacteria of the genera Cycloclasticus, Alcanivorax, Oleispira, Thalassolituus, and Oleiphilus. Enzymatic data of these representative OMHCB members are restricted to enzymes of the class hydroxylases, cytochrome P450, dioxygenases, synthases, dehalogenases, ligases, and mostly for hydrolases with a typical α/β hydrolase fold. Despite the limited information reported, the available data suggest that these organisms may be important sources of industrial biocatalysts, the analysis of which may deserve deeper investigation. Comparative information is provided regarding the occurrence of key biotechnologically relevant ester-hydrolases in the genomes of OMHCB and suggesting which of the OMHCB may potentially have higher promise as a source of biocatalysts. We also discuss how the properties of these enzymes could be biologicallly important for these bacteria, as some of them can convert a broad range of compounds.

Notes

Acknowledgments

This project 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). This research was also supported by the grants PCIN-2014-107 (within ERA NET IB2 grant no. ERA-IB-14-030 - MetaCat), PCIN-2017-078 (within the ERA-MarineBiotech grant ProBone), BIO2014-54494-R, and BIO2017-85522-R from the Spanish Ministry of Economy, Industry and Competitiveness (actually, Ministry of Science, Innovation and Universities). P.N.G. gratefully acknowledges funding from the UK Biotechnology and Biological Sciences Research Council (grant no. BB/M029085/1). R.B. and P.N.G. acknowledge the support of the Supercomputing Wales project, which is part-funded by the European Regional Development Fund (ERDF) via Welsh Government. P.N.G. acknowledges the support of the Centre of Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through Welsh Government. The authors gratefully acknowledge financial support provided by the European Regional Development Fund (ERDF). C. Coscolín thanks the Spanish Ministry of Economy, Industry and Competitiveness for a PhD fellowship (Grant BES-2015-073829).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Cristina Coscolín
    • 1
  • Rafael Bargiela
    • 2
  • Mónica Martínez-Martínez
    • 1
  • Sandra Alonso
    • 1
  • Alexander Bollinger
    • 3
  • Stephan Thies
    • 3
  • Tatyana N. Chernikova
    • 2
  • Tran Hai
    • 2
  • Olga V. Golyshina
    • 2
    • 6
  • Karl-Erich Jaeger
    • 8
    • 9
  • Michail M. Yakimov
    • 4
    • 5
  • Peter N. Golyshin
    • 2
    • 6
  • Manuel Ferrer
    • 7
    Email author
  1. 1.Institute of CatalysisConsejo Superior de Investigaciones Científicas (CSIC)MadridSpain
  2. 2.School of Natural SciencesBangor UniversityBangorUK
  3. 3.Institute of Molecular Enzyme TechnologyHeinrich Heine University Düsseldorf and Forschungszentrum Jülich GmbHJülichGermany
  4. 4.Institute for Biological Resources and Marine BiotechnologyIRBIM-CNR, MessinaItaly
  5. 5.Institute of Living Systems, Immanuel Kant Federal Baltic UniversityKaliningradRussia
  6. 6.Centre for Environmental BiotechnologyBangor UniversityBangorUK
  7. 7.Department of Applied BiocatalysisCSIC – Institute of CatalysisMadridSpain
  8. 8.Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfJülichGermany
  9. 9.Institute of Bio- and Geosciences IBG-1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany

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