The responses of microbial communities to hydrocarbon exposures are complex and variable, driven to a large extent by the nature of hydrocarbon infusion, local environmental conditions, and factors that regulate microbial physiology (e.g., substrate and nutrient availability). Although present at low abundance in the ocean, hydrocarbon-degrading seed populations are widely distributed, and they respond rapidly to hydrocarbon inputs at natural and anthropogenic sources. Microbiomes from environments impacted by hydrocarbon discharge may appear similar at a higher taxonomic rank (e.g., genus level) but diverge at increasing phylogenetic resolution (e.g., sub-OTU [operational taxonomic unit] levels). Such subtle changes are detectable by computational methods such as oligotyping or by genome reconstruction from metagenomic sequence data. The ability to reconstruct these genomes, and to characterize their transcriptional activities in different environmental contexts through metatranscriptomic mapping, is revolutionizing our ability to understand the diverse and adaptable microbial communities in marine ecosystems. Our knowledge of the environmental factors that regulate microbial hydrocarbon degradation and the efficiency with which marine hydrocarbon-degrading microbial communities bioremediate hydrocarbon contamination is incomplete. Moreover, detailed baseline descriptions of naturally occurring hydrocarbon-degrading microbial communities and a more robust understanding of the factors that regulate their activity are needed.

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