Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.
The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% 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 (14)C-labeled 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 (14)C-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.
1] Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA [2] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Olivia U
OU
Mason
1] Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA [2] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
Nicole M
0000000301930528
NM
Scott
Biofrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA.
Antonio
A
Gonzalez
Department of Computer Science, University of Colorado at Boulder, Boulder, CO, USA.
Adam
A
Robbins-Pianka
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] The Technical University of Denmark, Center for Biological Sequence Analysis, Kongens Lyngby, Denmark.
Jacob
J
Bælum
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Deconstruction Division, Joint Bioenergy Institute (JBEI), Emeryville, CA, USA.
Jeffrey
J
Kimbrel
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Nicholas J
NJ
Bouskill
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Emmanuel
E
Prestat
Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Sharon
S
Borglin
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA.
Dominique C
DC
Joyner
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA.
Julian L
JL
Fortney
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Laboratório de Genética Microbiana, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
Diogo
D
Jurelevicius
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Ecological Engineering Research Program, School of Engineering & Computer Science, University of the Pacific, Stockton, CA, USA.
William T
WT
Stringfellow
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of California, Berkeley, CA, USA.
Lisa
L
Alvarez-Cohen
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA [3] Biological Sciences Division, Oak Ridge National Lab, Oak Ridge, TN, USA.
Terry C
TC
Hazen
1] Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, CO, USA [2] Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA.
Rob
R
Knight
1] Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA [2] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
Jack A
JA
Gilbert
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Deconstruction Division, Joint Bioenergy Institute (JBEI), Emeryville, CA, USA [3] Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.
Janet K
JK
Jansson
D034241:Alteromonadaceae / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002250:Carbon Radioisotopes; D017753:Ecosystem; D020563:Gammaproteobacteria / Q000235:genetics* / Q000378:metabolism; D015870:Gene Expression; D060851:Gulf of America; D056186:Metagenomics; D006899:Mixed Function Oxygenases / Q000235:genetics / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D059392:Petroleum Pollution; D011084:Polycyclic Aromatic Hydrocarbons / Q000378:metabolism; D012329:RNA, Bacterial / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012623:Seawater / Q000382:microbiology
D001426:Bacterial Proteins; D002250:Carbon Radioisotopes; D011084:Polycyclic Aromatic Hydrocarbons; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D006899:Mixed Function Oxygenases; D009584:Nitrogen