Compound-Specific Isotope Analysis for Studying the Biological Degradation of Hydrocarbons

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


Compound-specific isotope fractionation analysis (CSIA) has become a promising approach for studying biological degradation of hydrocarbons in the environment. The approach makes use of isotope fractionation processes taking place during enzymatic cleavage of carbon and hydrogen bonds formed by isotopologues due to rate limitations upon the first irreversible step of the reaction mechanism. The magnitude of isotope fractionation is usually expressed by the isotope enrichment factor ε for carbon (εC) and/or hydrogen (εH) using the Rayleigh equation, correlating isotope fractionation with concentration changes of the residual fraction of the substrate. For evaluating the magnitude of biodegradation at environmental sites, εC and/or εH determined from model cultures expressing known biochemical degradation pathways are used. By correlating the magnitude of carbon and hydrogen isotope fractionation (dual or multi-element compound-specific stable isotope analysis (ME-CSIA), resulting in lambda (Λ) values: Λ = Δ(δ2H)/Δ(δ13C) ≈ εHC), distinct (bio)chemical reactions of degradation pathways can be further identified. In this review, we summarize εC, εH, and Λ values of currently known initial enzymatic reaction steps of aerobic and anaerobic hydrocarbon degradation pathways (dioxygenation, monooxygenation, hydroxylation with water, carboxylation, fumarate addition, and reactions by coenzyme M reductase) and discuss the opportunities for using them to identify degradation pathways and to quantify hydrocarbon degradation in environmental studies.



We acknowledge the support by the Helmholtz Centre for Environmental Research – UFZ, the Max Planck Institute for Marine Microbiology, and the Deutsche Forschungsgemeinschaft (DFG) within the framework of the Priority Programme 1319 “Biological transformations of hydrocarbons without oxygen: from the molecular to the global scale,” grants MU 2950/1-1 to F. Musat and RI 903/4-1 & 2 to H.H. Richnow and C. Vogt.


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© Springer Nature Switzerland AG 2020

Authors and Affiliations

  1. 1.Department of Isotope BiogeochemistryHelmholtz Centre for Environmental Research – UFZLeipzigGermany

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