Elucidation of in situ polycyclic aromatic hydrocarbon degradation by functional metaproteomics (protein-SIP)

Authors

  • Florian-Alexander Herbst,

    1. Department of Proteomics, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. Faculty of Biology, University of Freiburg, Freiburg, Germany
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  • Arne Bahr,

    1. Department of Isotope Biogeochemistry, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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  • Marcia Duarte,

    1. Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research-HZI, Braunschweig, Germany
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  • Dietmar H. Pieper,

    1. Microbial Interactions and Processes Research Group, Helmholtz Center for Infection Research-HZI, Braunschweig, Germany
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  • Hans-Hermann Richnow,

    1. Department of Isotope Biogeochemistry, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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  • Martin von Bergen,

    1. Department of Proteomics, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
    2. Department of Metabolomics, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
    3. Department of Biotechnology, Chemistry and Environmental Engineering, University of Aalborg, Aalborg, Denmark
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  • Jana Seifert,

    Corresponding author
    1. Institute of Animal Nutrition, University of Hohenheim, Stuttgart, Germany
    • Department of Proteomics, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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  • Petra Bombach

    Corresponding author
    1. Isodetect GmbH – Leipzig Branch, Leipzig, Germany
    • Department of Isotope Biogeochemistry, UFZ – Helmholtz Centre for Environmental Research, Leipzig, Germany
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Correspondence: Dr. Jana Seifert, Department of Proteomics, UFZ – Helmholtz Centre for Environmental Research, PermoserStrasse 15, D-04318 Leipzig, Germany

E-mail: jana.seifert@ufz.de

Additional corresponding author: Dr. Petra Bombach, E-mail: petra.bombach@ufz.de

Abstract

Current knowledge of the physiology and phylogeny of polycyclic aromatic hydrocarbon (PAH) degrading bacteria often relies on laboratory enrichments and isolations. In the present study, in situ microcosms consisting of activated carbon pellets (BACTRAP®s) were loaded with either 13C-naphthalene or 13C-fluorene and were subsequently exposed in the contaminant source and plume fringe region of a PAH-contaminated aquifer. Metaproteomic analysis and protein-stable isotope probing revealed Burkholderiales, Actinomycetales, and Rhizobiales as the most active microorganisms in the groundwater communities. Proteins identified of the naphthalene degradation pathway showed a relative 13C isotope abundance of approximately 50 atom% demonstrating that the identified naphthalene-degrading bacteria gained at least 80% of their carbon by PAH degradation. Although the microbial community grown on the fluorene-BACTRAPs showed a structure similar to the naphthalene-BACTRAPs, the identification of fluorene degraders and degradation pathways failed in situ. In complementary laboratory microcosms, a clear enrichment in proteins related to Rhodococcus and possible fluorene degradation enzymes was observed. This result demonstrates the impact of laboratory conditions on microbial community structure and activity of certain species and underlines the need on in situ exploration of microbial community functions. In situ microcosms in combination with protein-stable isotope probing may be a significant tool for in situ identification of metabolic key players as well as degradation pathways.

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