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Next-Generation Sequencing of Functional Marker Genes for Anaerobic Degraders of Petroleum Hydrocarbons in Contaminated Environments

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Anaerobic Utilization of Hydrocarbons, Oils, and Lipids

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

Abstract

The anaerobic degradation of petroleum hydrocarbons is an important ecosystem service provided by microbes in systems impacted by pollution. Research in recent years has resulted in substantial advances in our understanding of the diversity and ecology of natural populations of anaerobic hydrocarbon degraders, both in marine and terrestrial sedimentary and subsurface habitats. Part of this research has been fueled by the development and optimization of specific functional marker genes for anaerobic hydrocarbon degraders, i.e., qualitative and quantitative molecular assays, allowing for the detection of key catabolic genes or transcripts involved in degradation. These include the so-called “fumarate-adding enzymes” benzylsuccinate synthase (bssA) and alkylsuccinate synthase (assA/masD) involved in the primary activation of alkanes and alkylated aromatic hydrocarbons under anaerobic conditions. Here, we summarize the most important advances in the field and highlight the appeal of recent next-generation sequencing-based approaches toward catabolic marker genes for in-depth degrader community dissection. This contributes to a more routine and thorough inspection of intrinsic degrader populations responsible for key catabolic services in systems contaminated with petroleum hydrocarbons.

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Acknowledgments

The authors wish to thank the Deutsche Forschungsgemeinschaft (DFG) for the support of parts of the research summarized and presented here within the Priority Programme “Biological transformation of hydrocarbons in the absence of oxygen” (SPP 1319, grants LU 118/4-1 and 4-2). We also acknowledge support of the Helmholtz Society within the “Helmholtz Wasserzentrum München.”

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Authors and Affiliations

  1. Helmholtz Zentrum München – German Research Center for Environmental Health, Institute of Groundwater Ecology, Neuherberg, Germany

    Frederick von Netzer, Anna R. Szalay & Tillmann Lueders

  2. Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA

    Frederick von Netzer

  3. Research Unit Comparative Microbiome Analysis, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany

    Michael S. Granitsiotis

  4. Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA

    Michael S. Granitsiotis

  5. Department of Environmental and Natural Resources Management, University of Patras, Agrinio, Greece

    Michael S. Granitsiotis

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  1. Frederick von Netzer
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  2. Michael S. Granitsiotis
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  3. Anna R. Szalay
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  4. Tillmann Lueders
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Correspondence to Tillmann Lueders .

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  1. Microbiology, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany

    Matthias Boll

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von Netzer, F., Granitsiotis, M.S., Szalay, A.R., Lueders, T. (2020). Next-Generation Sequencing of Functional Marker Genes for Anaerobic Degraders of Petroleum Hydrocarbons in Contaminated Environments. In: Boll, M. (eds) Anaerobic Utilization of Hydrocarbons, Oils, and Lipids. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-50391-2_15

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