The metabolic pathways and environmental controls of hydrocarbon biodegradation in marine ecosystems

Abstract

Hydrocarbon-degrading microorganisms are ubiquitous in the world's oceans (Head et al., [7]; Yakimov et al., [26]), and biodegradation mediated by indigenous microbial communities is the ultimate fate of the majority of oil hydrocarbon that enters the marine environment (Leahy and Colwell, [13]; Prince, [17]; Atlas and Hazen, [1]). In response to the natural complexity of hydrocarbon compounds found in petroleum deposits, diverse marine microorganisms have evolved with an equal complexity of metabolic pathways to take advantage of hydrocarbons as a rich carbon and energy source. To minimize the environmental impact of oil spills and to optimize the environmental benefits of biodegradation, it is essential to uncover the metabolic potential of hydrocarbon-degrading bacteria and to address the factors that limit microbially-catalyzed biodegradation in situ. Microbial community structure and diversity likely defines the metabolic potential of oil-degrading communities (Head et al., [7]). Thus, it is critical to understand the relationships between microbial community structure and the metabolic activity of hydrocarbon-degrading microbial groups. Much progress has been made to determine the response of specific microbial taxa to oil discharge in marine environments impacted by oil spills or natural seeps. However, the majority of studies of hydrocarbon-degrading microorganisms have been conducted in laboratory cultures, and our ability to understand and predict the dynamics of in situ microbial communities responding to environmental stimuli such as the presence of oil hydrocarbons remains in its infancy (Prosser et al., [18]). In situ characterization of hydrocarbon-degrading microbial communities was hampered until recently by practical limitations of molecular biology techniques in phylogenetic resolution and depth of coverage (Gilbert and Dupont, [6]; Jansson et al., [8]). Advances in next generation sequencing technologies and the use of stable isotope tracers have greatly improved our ability to interrogate the phylogenetic and functional diversity of hydrocarbon-degrading microorganisms in the field.