Vying Over Spilt Oil Tu Anh Pham N

NEWS & ANALYSIS

GENOME WATCH Vying over spilt oil Tu Anh Pham N. and Blessing O. Anonye

This month’s Genome Watch explores the diverse microbial community involved in the bioremediation of oil spills. NPG The Deepwater Horizon (DWH) oil rig explo- degradation accompanied the early rise enzymes at deep-sea tempera- sion in the Gulf of Mexico in April 2010 led of Oceanospirillales. By contrast, genes tures might actually be suf- to the accidental release of at least 4 million encoding proteins that have a role in ficient to outcompete other barrels of crude oil. The resulting deep-sea the breakdown of benzene, toluene microbial community members, making hydrocarbon plume was one of the largest and polycyclic hydrocarbons were O. antarctica a highly successful oil degrader. spills in recorded history and it caused drastic downregulated. As Oceanospirillales are In another recent report, Chauhan et al.4 changes in the microbial communities, some particularly recalcitrant to laboratory culti- sequenced the genomes of five bacteria that of which contributed to the bioremediation of vation, the authors used single-cell sequenc- were isolated from the tissues and mantle fluid the spill. Within this noxious habitat, a group ing to determine draft genomes from two of oysters residing in contaminated DWH of indigenous microorganisms that mostly representative isolates. These genomes were reefs. The draft genomes of the isolated bac- belonged to the class Gammaproteobacteria highly enriched for factors that are involved teria harboured several factors involved in thrived. Culture-independent analyses of in alkane degradation, chemotaxis and motil- aliphatic and aromatic hydrocarbon degrada- these bacteria identified many lineages ity, which suggests that Oceanospirillales can tion, which indicates that even bacteria that such as the Oceanospirillales, including quickly aggregate and scavenge hydrocarbon colonize the surrounding reef ecosystems may Oleispira spp., which can metabolize hydro- nutrients. possess the capacity to metabolize crude oil. carbons at extremely low temperatures. Other The two Oceanospirillales species that Each year, millions of gallons of oil are enriched genera included the alkane degrader were analysed are closely related to Oleispira released into natural environments worldwide. Alcanivorax spp., as well as Cycloclasticus spp. antarctica, which is the only cultured spe- By applying genomic approaches to under- and Pseudoalteromonas spp., which can break cies among this bacterial family. Kube et al.3 stand the enzymatic processes and community down aromatic hydrocarbons1. recently sequenced the complete 4.4 Mb dynamics of oil-degrading bacteria, valuable The characteristics of the DWH micro- genome of O. antarctica and uncovered mul- insights that inform ongoing bioremediation bial response varied substantially over time. tiple genes encoding proteins that are linked efforts can be gained. Samples taken over the course of the oil to alkane oxidation, motility and siderophore Tu Anh Pham N. and Blessing O. Anonye are at the spill indicated that a succession of hydro- production. Consistent with the ability of Sanger Institute, Wellcome Trust Genome Campus, carbon degraders were responsible for O. antarctica to adapt to an extreme-cold Hinxton, Cambridge CB10 1SA, UK. the rapid DWH bioremediation1. Whereas habitat, the genome also harbours two genetic e‑mail: [email protected] doi:10.1038/nrmicro3224 Oceanospirillales were predominant 1 month systems that are responsible for the synthe- Published online 10 February 2014 after the explosion, plume samples that were sis of osmoprotectants. In addition, 12.2% of 1. Dubinsky, E. A. et al. Succession of hydrocarbon- taken in June were enriched in Colwellia spp. the O. antarctica genome consists of mobile degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the gulf of Mexico. Environ. Sci. and Cycloclasticus spp., and methylotrophs genomic islands, which is a much higher Technol. 47, 10860–10867 (2013). were most abundant in later samples. This value than that reported in other oil degrad- 2. Mason, O. U. et al. Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to succession of hydrocarbon-degrading bac- ers. The authors therefore proposed that Deepwater Horizon oil spill. ISME J. 6, 1715–1727 teria corresponded to a relative decline in O. antarctica may participate in horizontal (2012). 3. Kube, M. et al. Genome sequence and functional saturated hydrocarbons and an increase in the gene transfer more often by functioning as genomic analysis of the oil-degrading bacterium more persistent aromatic hydrocarbons over a donor of mobile vectors in other bacte- Oleispira antarctica. Nature Commun. 4, 2156 (2013). 1 4. Chauhan, A., Green, S., Pathak, A., Thomas, J. & time . ria. Interestingly, only a small fraction of the Venkatramanan, R. Whole-genome sequences of five Using metagenomic and metatranscrip- intracellular enzymes that were cloned from oyster-associated bacteria show potential for crude oil 2 hydrocarbon degradation. Genome Announc. tomic analyses, Mason et al. further showed O. antarctica had a true psychrophilic profile, 1, e00802‑13 (2013). o that an enrichment of genes encoding as most showed maximal activity at 20–35 C. Competing interests statement proteins involved in aliphatic hydrocarbon Nevertheless, the suboptimal activity of these The authors declare no competing interests.

156 | MARCH 2014 | VOLUME 12 www.nature.com/reviews/micro