Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill

Probst, Alexander J.; Hu, Ping; Sun, Christine L.; Dubinsky, Eric A.; Sieber, Christian M.  K.; Banfield, Jillian F.; Andersen, Gary L.

doi:10.1073/pnas.1712466114

Title: Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill

Abstract

A laboratory simulation revealed the succession patterns of oil degradation and microbial community changes during the Deepwater Horizon oil spill, one of the largest environmental catastrophes in human history. Hu et al. successfully recovered genomes of several oil-degrading bacteria, including one of “Candidatus Bermanella macondoprimitus,” with high identity to the dominant Oceanospirillales 16S rRNA gene sequences recovered from the deep-ocean hydrocarbon plumes. Delmont and Eren (3) reanalyzed metagenomic data generated from these plumes to argue that this Bermanella was not present.

Authors:

Probst, Alexander J. ^[1]; Hu, Ping ^[2]; Sun, Christine L. ^[3];

^[2]; Sieber, Christian M. K. ^[4]; Banfield, Jillian F. ^[5];

^[2]

Univ. of Duisburg-Essen (Germany); Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Stanford Univ., CA (United States)
Univ. of California, Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of California, Berkeley, CA (United States)

Publication Date:: Tue Oct 10 00:00:00 EDT 2017

Research Org.:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC)

OSTI Identifier:: 1482524

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Proceedings of the National Academy of Sciences of the United States of America

Additional Journal Information:: Journal Volume: 114; Journal Issue: 43; Journal ID: ISSN 0027-8424

Publisher:: National Academy of Sciences, Washington, DC (United States)

Country of Publication:: United States

Language:: English

Subject:: 54 ENVIRONMENTAL SCIENCES

Citation Formats


                    Probst, Alexander J., Hu, Ping, Sun, Christine L., Dubinsky, Eric A., Sieber, Christian M.  K., Banfield, Jillian F., and Andersen, Gary L. Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill.  United States: N. p., 2017. 
Web.  doi:10.1073/pnas.1712466114.

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                    Probst, Alexander J., Hu, Ping, Sun, Christine L., Dubinsky, Eric A., Sieber, Christian M.  K., Banfield, Jillian F., & Andersen, Gary L. Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill.  United States.  https://doi.org/10.1073/pnas.1712466114

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                    Probst, Alexander J., Hu, Ping, Sun, Christine L., Dubinsky, Eric A., Sieber, Christian M.  K., Banfield, Jillian F., and Andersen, Gary L. Tue .  
"Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill".  United States.  https://doi.org/10.1073/pnas.1712466114.  https://www.osti.gov/servlets/purl/1482524.

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@article{osti_1482524,

  title        = {Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill},

  author       = {Probst, Alexander J. and Hu, Ping and Sun, Christine L. and Dubinsky, Eric A. and Sieber, Christian M.  K. and Banfield, Jillian F. and Andersen, Gary L.},

  abstractNote = {A laboratory simulation revealed the succession patterns of oil degradation and microbial community changes during the Deepwater Horizon oil spill, one of the largest environmental catastrophes in human history. Hu et al. successfully recovered genomes of several oil-degrading bacteria, including one of “Candidatus Bermanella macondoprimitus,” with high identity to the dominant Oceanospirillales 16S rRNA gene sequences recovered from the deep-ocean hydrocarbon plumes. Delmont and Eren (3) reanalyzed metagenomic data generated from these plumes to argue that this Bermanella was not present.},

  doi          = {10.1073/pnas.1712466114},

  journal      = {Proceedings of the National Academy of Sciences of the United States of America},

  number       = 43,

  volume       = 114,

  place        = {United States},

  year         = {Tue Oct 10 00:00:00 EDT 2017},

  month        = {Tue Oct 10 00:00:00 EDT 2017}

}

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Works referenced in this record:

Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders
journal, June 2017

Hu, Ping; Dubinsky, Eric A.; Probst, Alexander J.
Proceedings of the National Academy of Sciences, Vol. 114, Issue 28
DOI: 10.1073/pnas.1703424114

Pulsed blooms and persistent oil-degrading bacterial populations in the water column during and after the Deepwater Horizon blowout
journal, July 2016

Yang, Tingting; Nigro, Lisa M.; Gutierrez, Tony
Deep Sea Research Part II: Topical Studies in Oceanography, Vol. 129
DOI: 10.1016/j.dsr2.2014.01.014

Anvi’o: an advanced analysis and visualization platform for ‘omics data
journal, January 2015

Eren, A. Murat; Esen, Özcan C.; Quince, Christopher
PeerJ, Vol. 3
DOI: 10.7717/peerj.1319

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill
journal, June 2012

Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon
The ISME Journal, Vol. 6, Issue 9
DOI: 10.1038/ismej.2012.59

Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill
journal, October 2011

Redmond, M. C.; Valentine, D. L.
Proceedings of the National Academy of Sciences, Vol. 109, Issue 50
DOI: 10.1073/pnas.1108756108

Genomic resolution of a cold subsurface aquifer community provides metabolic insights for novel microbes adapted to high CO ₂ concentrations : Genomic resolution of a high-CO
journal, July 2016

Probst, Alexander J.; Castelle, Cindy J.; Singh, Andrea
Environmental Microbiology, Vol. 19, Issue 2
DOI: 10.1111/1462-2920.13362

Simulations predict microbial responses in the environment? This environment disagrees retrospectively
journal, October 2017

Delmont, Tom O.; Eren, A. Murat
Proceedings of the National Academy of Sciences, Vol. 114, Issue 43
DOI: 10.1073/pnas.1712186114

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
journal, February 2012

Mende, Daniel R.; Waller, Alison S.; Sunagawa, Shinichi
PLoS ONE, Vol. 7, Issue 2
DOI: 10.1371/journal.pone.0031386

Identification of ancient remains through genomic sequencing
journal, August 2008

Blow, M. J.; Zhang, T.; Woyke, T.
Genome Research, Vol. 18, Issue 8
DOI: 10.1101/gr.076091.108

Deep-Sea Oil Plume Enriches Indigenous Oil-Degrading Bacteria
journal, August 2010

Hazen, Terry C.; Dubinsky, Eric A.; DeSantis, Todd Z.
Science, Vol. 330, Issue 6001
DOI: 10.1126/science.1195979

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Similar Records

Title: Reply to Delmont and Eren: Strain variants and population structure during the Deepwater Horizon oil spill

Abstract

Citation Formats

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Pulsed blooms and persistent oil-degrading bacterial populations in the water column during and after the Deepwater Horizon blowout journal, July 2016

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