MINI-REVIEW Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications Sebastián Fuentes & Valentina Méndez & Patricia Aguila & Michael Seeger Received: 30 January 2014 /Revised: 10 March 2014 /Accepted: 11 March 2014 # Springer-Verlag Berlin Heidelberg 2014 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, hydrocar- bon solubility, nutrient balance) and managing hydrocarbon- degrading microorganisms, in order to overcome the rate- limiting factors that slow down hydrocarbon biodegradation. Keywords Petroleum . Hydrocarbon . Bioremediation . Biodegradation . Microbial community . Catabolic genes Introduction Petroleum is a natural resource confined in large deposits in the Earth crust. Accidental petroleum spills alter the impacted environment and trigger the development and implementation of remediation strategies for cleaning up the polluted sites. Oil spills became an international concern in 1967, when ~120,000 tons of crude oil was released by the Torrey Canyon supertanker into the English Channel. This first large-scale oil spill forced UNO’ s International Maritime Organization to create in 1973 the International Convention for the Prevention of Pollution from Ships MARPOL with the aim of designing emergency protocols and strategies toward oil spills. Since then, there have been a number of significant marine oil spills, even only the emblematic spills usually alert the public opinion. Oil spills are difficult to avoid during the petroleum processing and delivery. Petroleum is mainly composed by three hydrocarbon frac- tions. Paraffin is usually the most abundant fraction and contains linear and branched aliphatic hydrocarbons. Naphthenes are alicyclic hydrocarbons composed by one or more saturated rings with or without lateral aliphatic branches. The aromatic fraction is composed by hydrocarbons contain- ing at least one aromatic ring. Hydrocarbons can possess from few up to >60 carbons. A higher molecule size correlates with a higher boiling point. Petroleum-derived products are obtain- ed by fractional distillation, by which different fractions are enriched according to its boiling range (Speight 2001). For the cleanup of hydrocarbon-polluted sites, diverse physicochemical and bioremediation treatments have been applied. Bioremediation techniques are cost-effective, envi- ronmental sustainable, and can achieve complete pollutant S. Fuentes : V. Méndez : P. Aguila : M. Seeger (*) Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología & Center of Nanotechnology and Systems Biology, Universidad Técnica Federico Santa María, Valparaíso, Chile e-mail: michael.seeger@usm.cl Appl Microbiol Biotechnol DOI 10.1007/s00253-014-5684-9