Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The ISME Journal (2014) 8, 1464–1475 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 OPEN www.nature.com/ismej ORIGINAL ARTICLE Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill Olivia U Mason1,2, Nicole M Scott3,4, Antonio Gonzalez5, Adam Robbins-Pianka6, Jacob Bælum2,7, Jeffrey Kimbrel2,8, Nicholas J Bouskill2, Emmanuel Prestat2, Sharon Borglin2, Dominique C Joyner2,9, Julian L Fortney2,9, Diogo Jurelevicius2,10, William T Stringfellow2,11, Lisa Alvarez-Cohen2,12, Terry C Hazen2,9,13, Rob Knight14,15, Jack A Gilbert3,4 and Janet K Jansson2,8,16 1 Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA; Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; 3Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA; 4Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA; 5Biofrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA; 6Department of Computer Science, University of Colorado at Boulder, Boulder, CO, USA; 7 The Technical University of Denmark, Center for Biological Sequence Analysis, Kongens Lyngby, Denmark; 8 Deconstruction Division, Joint Bioenergy Institute (JBEI), Emeryville, CA, USA; 9Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA; 10Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; 11Ecological Engineering Research Program, School of Engineering & Computer Science, University of the Pacific, Stockton, CA, USA; 12Civil and Environmental Engineering Department, University of California, Berkeley, CA, USA; 13Biological Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA; 14Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA; 15Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA and 16Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA 2 The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of B4.1 million barrels of oil to the Gulf of Mexico; 422% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using 14Clabeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of 14C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)’s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem. The ISME Journal (2014) 8, 1464–1475; doi:10.1038/ismej.2013.254; published online 23 January 2014 Subject Category: Integrated genomics and post-genomics approaches in microbial ecology Keywords: DWH oil spill; hydrocarbons; iTag/Metagenomics; microbial community structure; sediments Correspondence: OU Mason, Department of Earth, Ocean and Atmospheric Science, Florida State University, Room 307 OSB, 117 North Woodward Avenue, Tallahassee, FL 32306-4320, USA. E-mail: or JK Jansson, Earth Sciences Division, Lawrence Berkeley National Laboratory, MS 70A-3317, One Cyclotron Road, Berkeley, CA 94720, USA. E-mail: Received 18 October 2013; revised 18 December 2013; accepted 20 December 2013; published online 23 January 2014 Sediment microbial community response to DWH spill OU Mason et al Introduction During the Deepwater Horizon (DWH) oil spill, from April to July 2010, B4.1 million barrels of oil were released by the Macondo Well (Zukunft, 2010). A variety of mitigation strategies and natural processes resulted in depletion of B78% of the oil (Ramseur, 2010; Kimes et al., 2013). The fate of the remaining 22% is unknown. A deep-sea hydrocarbon plume (at B1100 m depth) was observed during the DWH spill and was the focus of considerable attention, especially regarding the potential for microbial degradation of hydrocarbon contaminants. Shortly after the spill, uncultured Oceanospirillales dominated the deep-sea plume (Hazen et al., 2010; Mason et al., 2012; Redmond and Valentine, 2012). A combination of metagenomics, metatranscriptomics and single-cell genome sequencing revealed that representatives of this dominant clade were active and capable of degrading cycloalkanes (Mason et al., 2012). Over time, Oceanospirillales was supplanted by Colwellia and Cycloclasticus (Valentine et al., 2010). Redmond and Valentine (2012) used stable isotope probing in microcosm experiments and reported that Colwellia was likely active in ethane, propane and benzene oxidation in the deep-sea plume. Later, after the spill ceased, methylotrophs, some of which are known methane oxidizers, dominated the region of the plume (Kessler et al., 2011). This succession of microbial community members was replicated in laboratory microcosm studies during which large flocs, also known as ‘marine snow’, comprised largely of Colwellia, extracellular polymeric substances and oil, accumulated in the water (Bælum et al., 2012a). Similarly, during the spill in the Gulf of Mexico, an unusually large marine snow event occurred in surface waters (Passow et al., 2012). One hypothesis to explain this event is that hydrocarbon-degrading bacteria produced oil-emulsifying extracellular polymeric substances, resulting in large sticky aggregates/snow (Passow et al., 2012). Within one month, however, the marine snow was no longer observed in the Gulf of Mexico (Passow et al., 2012), suggesting that it might have been degraded. Alternatively, the flocs and remaining contaminants may have settled to the sea f (...truncated)