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

Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)


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.


Fumarate-adding enzymes Benzylsuccinate synthase FLX+ pyrosequencing Degrader communities Functional marker genes 



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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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Helmholtz Zentrum München – German Research Center for Environmental Health, Institute of Groundwater EcologyNeuherbergGermany
  2. 2.Department of Civil and Environmental EngineeringUniversity of WashingtonSeattleUSA
  3. 3.Research Unit Comparative Microbiome AnalysisHelmholtz Zentrum München – German Research Center for Environmental HealthNeuherbergGermany
  4. 4.Department of EnergyJoint Genome InstituteWalnut CreekUSA
  5. 5.Department of Environmental and Natural Resources ManagementUniversity of PatrasAgrinioGreece

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