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Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications

Abstract

Bioremediation is an environmental sustainable and cost-effective technology for the cleanup of hydrocarbon-polluted soils and coasts. In spite of that longer times are usually required compared with physicochemical strategies, complete degradation of the pollutant can be achieved, and no further confinement of polluted matrix is needed. Microbial aerobic degradation is achieved by the incorporation of molecular oxygen into the inert hydrocarbon molecule and funneling intermediates into central catabolic pathways. Several families of alkane monooxygenases and ring hydroxylating dioxygenases are distributed mainly among Proteobacteria, Actinobacteria, Firmicutes and Fungi strains. Catabolic routes, regulatory networks, and tolerance/resistance mechanisms have been characterized in model hydrocarbon-degrading bacteria to understand and optimize their metabolic capabilities, providing the basis to enhance microbial fitness in order to improve hydrocarbon removal. However, microbial communities taken as a whole play a key role in hydrocarbon pollution events. Microbial community dynamics during biodegradation is crucial for understanding how they respond and adapt to pollution and remediation. Several strategies have been applied worldwide for the recovery of sites contaminated with persistent organic pollutants, such as polycyclic aromatic hydrocarbons and petroleum derivatives. Common strategies include controlling environmental variables (e.g., oxygen availability, hydrocarbon solubility, nutrient balance) and managing hydrocarbon-degrading microorganisms, in order to overcome the rate-limiting factors that slow down hydrocarbon biodegradation.

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Acknowledgments

The authors gratefully acknowledge Conicyt PhD (SF, VM), Mecesup FMS0710 PhD (PA, SF), and Fulbright (SF) fellowships. MS acknowledges financial support of FONDECYT (1110992 and 1070507) (http://www.fondecyt.cl), Conicyt-BMBF, Center for Nanotechnology and Systems Biology (http://www.usm.cl), and USM (131342, 131109, 130948) (http://www.usm.cl) grants. The funders had no role in study design, data collection and analyses, decision to publish, or preparation of the manuscript.

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Correspondence to Michael Seeger.

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Fuentes, S., Méndez, V., Aguila, P. et al. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications. Appl Microbiol Biotechnol 98, 4781–4794 (2014). https://doi.org/10.1007/s00253-014-5684-9

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Keywords

  • Petroleum
  • Hydrocarbon
  • Bioremediation
  • Biodegradation
  • Microbial community
  • Catabolic genes