Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill

Abstract

The Deepwater Horizon blowout in the Gulf of Mexico in 2010, one of the largest marine oil spills(1), changed bacterial communities in the water column and sediment as they responded to complex hydrocarbon mixtures(2-4). Shifts in community composition have been correlated to the microbial degradation and use of hydrocarbons(2,5,6), but the full genetic potential and taxon-specific metabolisms of bacterial hydrocarbon degraders remain unresolved. Here, we have reconstructed draft genomes of marine bacteria enriched from sea surface and deep plume waters of the spill that assimilate alkane and polycyclic aromatic hydrocarbons during stable-isotope probing experiments, and we identify genes of hydrocarbon degradation pathways. Alkane degradation genes were ubiquitous in the assembled genomes. Marinobacter was enriched with n-hexadecane, and uncultured Alpha- and Gammaproteobacteria populations were enriched in the polycyclic-aromatic-hydrocarbon-degrading communities and contained a broad gene set for degrading phenanthrene and naphthalene. The repertoire of polycyclic aromatic hydrocarbon use varied among different bacterial taxa and the combined capabilities of the microbial community exceeded those of its individual components, indicating that the degradation of complex hydrocarbon mixtures requires the non-redundant capabilities of a complex oil-degrading community.

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders

“…Genome assembly of Cycloloclsticus sp. Phe_8 by Dombrowski et al (37) was not included in our tree, because it was highly incomplete. Length of bar represents relative abundance of resolved genomes for each time point.…”

Microbial responses to anthropogenic dissolved organic carbon in the Arctic and Antarctic coastal seawaters

“…The study of interactions between microorganisms and OPs has primarily focused on microbial consumption of hydrocarbons in oil spills (Head et al, 2006;Mason et al, 2012). These bacterial groups have the capacity to use alkanes and PAHs as a carbon and energy source Dombrowski et al, 2016). These bacterial groups have the capacity to use alkanes and PAHs as a carbon and energy source Dombrowski et al, 2016).…”

Biogeochemical cycling and phyto- and bacterioplankton communities in a large and shallow tropical lagoon (Términos Lagoon, Mexico) under 2009–2010 El Niño Modoki drought conditions

“…17 (Grimaud et al, 2012) may have the capability to degrade PAHs and survive in rivers, lagoons, and seawater. Further studies using PAH-stable isotopes coupled with pyrosequencing (Dombrowski et al, 2016;Sauret et al, 2016) are necessary to identify the dynamics of these functional communities in the Términos Lagoon. Using similar approaches, previous reports have shown that the pollutant content and PAHs, in particular, were responsible for the bacterial community structure dynamic in the sediment of the Bizerte Lagoon, Tunisia (Ben Said et al, 2010).…”