Evidence map›Paper›PMID 24451203›Full record

ArticleThe ISME journal2014

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

Olivia U Mason, Nicole M Scott, Antonio Gonzalez, Adam Robbins-Pianka, Jacob Bælum, Jeffrey Kimbrel, Nicholas J Bouskill, Emmanuel Prestat, Sharon Borglin, Dominique C Joyner and 8 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The ISME journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.

0numbers the graph read from it
0cells of the map it votes in
110citing papers in PubMed
38.4field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

110 citing papers in PubMed, 384 citations in OpenAlex.

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50 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors at 8 institutions in 3 countries.

Olivia U Mason1] Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL, USA [2] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Nicole M Scott1] Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA [2] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.ORCID 0000000301930528
Antonio GonzalezBiofrontiers Institute, University of Colorado at Boulder, Boulder, CO, USA.
Adam Robbins-PiankaDepartment of Computer Science, University of Colorado at Boulder, Boulder, CO, USA.
Jacob Bælum1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] The Technical University of Denmark, Center for Biological Sequence Analysis, Kongens Lyngby, Denmark.
Jeffrey Kimbrel1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Deconstruction Division, Joint Bioenergy Institute (JBEI), Emeryville, CA, USA.
Nicholas J BouskillEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Emmanuel PrestatEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Sharon BorglinEarth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Dominique C Joyner1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA.
Julian L Fortney1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of Tennessee, Knoxville, TN, USA.
Diogo Jurelevicius1] 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.
William T Stringfellow1] 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.
Lisa Alvarez-Cohen1] Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Civil and Environmental Engineering Department, University of California, Berkeley, CA, USA.
Terry C Hazen1] 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.
Rob Knight1] 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.
Jack A Gilbert1] Institute for Genomic and Systems Biology, Argonne National Laboratory, Lemont, IL, USA [2] Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
Janet K Jansson1] 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.
Lawrence Berkeley National Laboratory · USArgonne National Laboratory · USUniversity of Colorado Boulder · USFlorida State University · USHoward Hughes Medical Institute · USOak Ridge National Laboratory · USUniversidade Federal do Rio de Janeiro · BRUniversity of the Pacific · US

Funding

Training CoreP42ES004705 · NIEHS · UNIVERSITY OF CALIFORNIA BERKELEY · PI MORELLO-FROSCH, RACHEL ADELE · 1987 to 2025
$74.6M
A Quality Assurance, Coordination and Analysis Center for HMPU01HG004866 · NHGRI · UNIVERSITY OF MARYLAND BALTIMORE · PI WHITE, OWEN R · 2008 to 2012
$12.5M
Howard Hughes Medical InstituteNHGRI NIH HHS U01 HG004866NIEHS NIH HHS P42 ES004705
6 · The paper itself

Abstract

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.

Indexed as

MetagenomicsPetroleum PollutionAlteromonadaceaeBacterial ProteinsCarbon RadioisotopesEcosystemGammaproteobacteriaGene ExpressionGulf of AmericaMixed Function OxygenasesNitrogenPolycyclic Aromatic HydrocarbonsRNA, BacterialRNA, Ribosomal, 16SSeawaterBacterial ProteinsCarbon RadioisotopesMixed Function OxygenasesNitrogenPolycyclic Aromatic HydrocarbonsRNA, BacterialRNA, Ribosomal, 16S

Identifiers

PMID24451203
PMCPMC4069396
OpenAlexW2142040626

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.