Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill
Identifieur interne : 000550 ( Ncbi/Merge ); précédent : 000549; suivant : 000551Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill
Auteurs : Olivia U. Mason [États-Unis] ; James Han [États-Unis] ; Tanja Woyke [États-Unis] ; Janet K. Jansson [États-Unis]Source :
- Frontiers in Microbiology [ 1664-302X ] ; 2014.
Abstract
During the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria.
Url:
DOI: 10.3389/fmicb.2014.00332
PubMed: 25071745
PubMed Central: 4085564
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species that was dominant during the Deepwater Horizon oil spill</title>
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<author><name sortKey="Han, James" sort="Han, James" uniqKey="Han J" first="James" last="Han">James Han</name>
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<author><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name>
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<author><name sortKey="Jansson, Janet K" sort="Jansson, Janet K" uniqKey="Jansson J" first="Janet K." last="Jansson">Janet K. Jansson</name>
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<country>Berkeley, CA, USA</country>
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<affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Department of Plant and Microbial Biology, University of California</institution>
<country>Berkeley, CA, USA</country>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Single-cell genomics reveals features of a <italic>Colwellia</italic>
species that was dominant during the Deepwater Horizon oil spill</title>
<author><name sortKey="Mason, Olivia U" sort="Mason, Olivia U" uniqKey="Mason O" first="Olivia U." last="Mason">Olivia U. Mason</name>
<affiliation wicri:level="1"><nlm:aff id="aff1"><institution>Department of Earth, Ocean and Atmospheric Science, Florida State University</institution>
<country>Tallahassee, FL, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Han, James" sort="Han, James" uniqKey="Han J" first="James" last="Han">James Han</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Energy Joint Genome Institute</institution>
<country>Walnut Creek, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea></wicri:regionArea>
<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<author><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name>
<affiliation wicri:level="1"><nlm:aff id="aff2"><institution>Department of Energy Joint Genome Institute</institution>
<country>Walnut Creek, CA, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<author><name sortKey="Jansson, Janet K" sort="Jansson, Janet K" uniqKey="Jansson J" first="Janet K." last="Jansson">Janet K. Jansson</name>
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<country>Berkeley, CA, USA</country>
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<country xml:lang="fr">États-Unis</country>
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<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<affiliation wicri:level="1"><nlm:aff id="aff4"><institution>Department of Plant and Microbial Biology, University of California</institution>
<country>Berkeley, CA, USA</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
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<wicri:regionArea># see nlm:aff region in country</wicri:regionArea>
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<series><title level="j">Frontiers in Microbiology</title>
<idno type="eISSN">1664-302X</idno>
<imprint><date when="2014">2014</date>
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<front><div type="abstract" xml:lang="en"><p>During the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. <italic>Colwellia</italic>
eventually supplanted <italic>Oceanospirillales</italic>
, which dominated the plume early in the spill. These successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. <italic>Colwellia</italic>
abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by <italic>Colwellia</italic>
in hydrocarbon disposition is unknown. Here we used single-cell genomics to gain insights into the genome properties of a <italic>Colwellia</italic>
enriched during the DWH deep-sea plume. A single amplified genome (SAG) of a <italic>Colwellia</italic>
cell isolated from a DWH plume, closely related (avg. 98% 16S rRNA gene similarity) to other plume <italic>Colwellia</italic>
, was sequenced and annotated. The SAG was similar to the sequenced isolate <italic>Colwellia psychrerythraea</italic>
34H (84% avg. nucleotide identity). Both had genes for denitrification, chemotaxis, and motility, adaptations to cold environments and a suite of nutrient acquisition genes. The <italic>Colwellia</italic>
SAG may be capable of gaseous and aromatic hydrocarbon degradation, which contrasts with a DWH plume <italic>Oceanospirillales</italic>
SAG which encoded non-gaseous <italic>n</italic>
-alkane and cycloalkane degradation pathways. The disparate hydrocarbon degradation pathways are consistent with hydrocarbons that were abundant at different times in the deep-sea plume; first, non-gaseous <italic>n</italic>
-alkanes and cycloalkanes that could be degraded by <italic>Oceanospirillales</italic>
, followed by gaseous, and simple aromatic hydrocarbons that may have been degraded by <italic>Colwellia</italic>
. These insights into the genomic properties of a <italic>Colwellia</italic>
species, which were supported by existing metagenomic sequence data from the plume and DWH contaminated sediments, help further our understanding of the successional changes in the dominant microbial players in the plume over the course of the DWH spill.</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Arp, D J" uniqKey="Arp D">D. J. Arp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Baelum, J" uniqKey="Baelum J">J. Baelum</name>
</author>
<author><name sortKey="Borglin, S" uniqKey="Borglin S">S. Borglin</name>
</author>
<author><name sortKey="Chakraborty, R" uniqKey="Chakraborty R">R. Chakraborty</name>
</author>
<author><name sortKey="Fortney, J L" uniqKey="Fortney J">J. L. Fortney</name>
</author>
<author><name sortKey="Lamendella, R" uniqKey="Lamendella R">R. Lamendella</name>
</author>
<author><name sortKey="Mason, O U" uniqKey="Mason O">O. U. Mason</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bankevich, A" uniqKey="Bankevich A">A. Bankevich</name>
</author>
<author><name sortKey="Nurk, S" uniqKey="Nurk S">S. Nurk</name>
</author>
<author><name sortKey="Antipov, D" uniqKey="Antipov D">D. Antipov</name>
</author>
<author><name sortKey="Gurevich, A A" uniqKey="Gurevich A">A. A. Gurevich</name>
</author>
<author><name sortKey="Dvorkin, M" uniqKey="Dvorkin M">M. Dvorkin</name>
</author>
<author><name sortKey="Kulikov, A S" uniqKey="Kulikov A">A. S. Kulikov</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bowman, J P" uniqKey="Bowman J">J. P. Bowman</name>
</author>
<author><name sortKey="Gosinkt, J J" uniqKey="Gosinkt J">J. J. Gosinkt</name>
</author>
<author><name sortKey="Mccammon, S A" uniqKey="Mccammon S">S. A. McCammon</name>
</author>
<author><name sortKey="Skerratt, H" uniqKey="Skerratt H">H. Skerratt</name>
</author>
<author><name sortKey="Lewis, T E" uniqKey="Lewis T">T. E. Lewis</name>
</author>
<author><name sortKey="Nichols, D S" uniqKey="Nichols D">D. S. Nichols</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Cooley, R B" uniqKey="Cooley R">R. B. Cooley</name>
</author>
<author><name sortKey="Dubbels, B L" uniqKey="Dubbels B">B. L. Dubbels</name>
</author>
<author><name sortKey="Sayavedra Soto, L A" uniqKey="Sayavedra Soto L">L. A. Sayavedra-Soto</name>
</author>
<author><name sortKey="Bottomley, P J" uniqKey="Bottomley P">P. J. Bottomley</name>
</author>
<author><name sortKey="Arp, D J" uniqKey="Arp D">D. J. Arp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dubbels, B L" uniqKey="Dubbels B">B. L. Dubbels</name>
</author>
<author><name sortKey="Sayavedra Soto, L A" uniqKey="Sayavedra Soto L">L. A. Sayavedra-Soto</name>
</author>
<author><name sortKey="Bottomley, P J" uniqKey="Bottomley P">P. J. Bottomley</name>
</author>
<author><name sortKey="Arp, D J" uniqKey="Arp D">D. J. Arp</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dubinsky, E A" uniqKey="Dubinsky E">E. A. Dubinsky</name>
</author>
<author><name sortKey="Conrad, M E" uniqKey="Conrad M">M. E. Conrad</name>
</author>
<author><name sortKey="Chakraborty, R" uniqKey="Chakraborty R">R. Chakraborty</name>
</author>
<author><name sortKey="Bill, M" uniqKey="Bill M">M. Bill</name>
</author>
<author><name sortKey="Borglin, S E" uniqKey="Borglin S">S. E. Borglin</name>
</author>
<author><name sortKey="Hollibaugh, J T" uniqKey="Hollibaugh J">J. T. Hollibaugh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Grimm, A C" uniqKey="Grimm A">A. C. Grimm</name>
</author>
<author><name sortKey="Harwood, C S" uniqKey="Harwood C">C. S. Harwood</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Gutierrez, T" uniqKey="Gutierrez T">T. Gutierrez</name>
</author>
<author><name sortKey="Singleton, D R" uniqKey="Singleton D">D. R. Singleton</name>
</author>
<author><name sortKey="Berry, D" uniqKey="Berry D">D. Berry</name>
</author>
<author><name sortKey="Yang, T" uniqKey="Yang T">T. Yang</name>
</author>
<author><name sortKey="Aitken, M D" uniqKey="Aitken M">M. D. Aitken</name>
</author>
<author><name sortKey="Teske, A" uniqKey="Teske A">A. Teske</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hazen, T C" uniqKey="Hazen T">T. C. Hazen</name>
</author>
<author><name sortKey="Dubinsky, E A" uniqKey="Dubinsky E">E. A. Dubinsky</name>
</author>
<author><name sortKey="Desantis, T Z" uniqKey="Desantis T">T. Z. DeSantis</name>
</author>
<author><name sortKey="Andersen, G L" uniqKey="Andersen G">G. L. Andersen</name>
</author>
<author><name sortKey="Piceno, Y M" uniqKey="Piceno Y">Y. M. Piceno</name>
</author>
<author><name sortKey="Singh, N" uniqKey="Singh N">N. Singh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, D H" uniqKey="Huson D">D. H. Huson</name>
</author>
<author><name sortKey="Xie, C" uniqKey="Xie C">C. Xie</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huston, A L" uniqKey="Huston A">A. L. Huston</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Joung, D" uniqKey="Joung D">D. Joung</name>
</author>
<author><name sortKey="Shiller, A M" uniqKey="Shiller A">A. M. Shiller</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Joye, S B" uniqKey="Joye S">S. B. Joye</name>
</author>
<author><name sortKey="Macdonald, I R" uniqKey="Macdonald I">I. R. MacDonald</name>
</author>
<author><name sortKey="Leifer, I" uniqKey="Leifer I">I. Leifer</name>
</author>
<author><name sortKey="Asper, V" uniqKey="Asper V">V. Asper</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kube, M" uniqKey="Kube M">M. Kube</name>
</author>
<author><name sortKey="Chernikova, T N" uniqKey="Chernikova T">T. N. Chernikova</name>
</author>
<author><name sortKey="Al Ramahi, Y" uniqKey="Al Ramahi Y">Y. Al-Ramahi</name>
</author>
<author><name sortKey="Beloqui, A" uniqKey="Beloqui A">A. Beloqui</name>
</author>
<author><name sortKey="Lopez Cortez, N" uniqKey="Lopez Cortez N">N. Lopez-Cortez</name>
</author>
<author><name sortKey="Guazzaroni, M E" uniqKey="Guazzaroni M">M.-E. Guazzaroni</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kurth, E G" uniqKey="Kurth E">E. G. Kurth</name>
</author>
<author><name sortKey="Doughty, D M" uniqKey="Doughty D">D. M. Doughty</name>
</author>
<author><name sortKey="Bottomley, P J" uniqKey="Bottomley P">P. J. Bottomley</name>
</author>
<author><name sortKey="Arp, D J" uniqKey="Arp D">D. J. Arp</name>
</author>
<author><name sortKey="Sayavedra Soto, L A" uniqKey="Sayavedra Soto L">L. A. Sayavedra-Soto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B. Langmead</name>
</author>
<author><name sortKey="Salzberg, S L" uniqKey="Salzberg S">S. L. Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lundrigan, M D" uniqKey="Lundrigan M">M. D. Lundrigan</name>
</author>
<author><name sortKey="Kadner, R J" uniqKey="Kadner R">R. J. Kadner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mason, O U" uniqKey="Mason O">O. U. Mason</name>
</author>
<author><name sortKey="Hazen, T C" uniqKey="Hazen T">T. C. Hazen</name>
</author>
<author><name sortKey="Borglin, S" uniqKey="Borglin S">S. Borglin</name>
</author>
<author><name sortKey="Chain, P S G" uniqKey="Chain P">P. S. G. Chain</name>
</author>
<author><name sortKey="Dubinsky, E A" uniqKey="Dubinsky E">E. A. Dubinsky</name>
</author>
<author><name sortKey="Fortney, J L" uniqKey="Fortney J">J. L. Fortney</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mason, O U" uniqKey="Mason O">O. U. Mason</name>
</author>
<author><name sortKey="Scott, N M" uniqKey="Scott N">N. M. Scott</name>
</author>
<author><name sortKey="Gonzalez, A" uniqKey="Gonzalez A">A. Gonzalez</name>
</author>
<author><name sortKey="Robbins Pianka, A" uniqKey="Robbins Pianka A">A. Robbins-Pianka</name>
</author>
<author><name sortKey="B Lum, J" uniqKey="B Lum J">J. Bælum</name>
</author>
<author><name sortKey="Kimbrel, J" uniqKey="Kimbrel J">J. Kimbrel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Methe, B A" uniqKey="Methe B">B. A. Methé</name>
</author>
<author><name sortKey="Nelson, K E" uniqKey="Nelson K">K. E. Nelson</name>
</author>
<author><name sortKey="Deming, J W" uniqKey="Deming J">J. W. Deming</name>
</author>
<author><name sortKey="Momen, B" uniqKey="Momen B">B. Momen</name>
</author>
<author><name sortKey="Melamud, E" uniqKey="Melamud E">E. Melamud</name>
</author>
<author><name sortKey="Zhang, X" uniqKey="Zhang X">X. Zhang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Parales, R E" uniqKey="Parales R">R. E. Parales</name>
</author>
<author><name sortKey="Ditty, J L" uniqKey="Ditty J">J. L. Ditty</name>
</author>
<author><name sortKey="Harwood, C S" uniqKey="Harwood C">C. S. Harwood</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Reardon, K F" uniqKey="Reardon K">K. F. Reardon</name>
</author>
<author><name sortKey="Mosteller, D C" uniqKey="Mosteller D">D. C. Mosteller</name>
</author>
<author><name sortKey="Bull Rogers, J D" uniqKey="Bull Rogers J">J. D. Bull Rogers</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Redmond, M C" uniqKey="Redmond M">M. C. Redmond</name>
</author>
<author><name sortKey="Valentine, D L" uniqKey="Valentine D">D. L. Valentine</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Richter, M" uniqKey="Richter M">M. Richter</name>
</author>
<author><name sortKey="Rossell M Ra, R" uniqKey="Rossell M Ra R">R. Rosselló-Móra</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rinke, C" uniqKey="Rinke C">C. Rinke</name>
</author>
<author><name sortKey="Schwientek, P" uniqKey="Schwientek P">P. Schwientek</name>
</author>
<author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A. Sczyrba</name>
</author>
<author><name sortKey="Ivanova, N N" uniqKey="Ivanova N">N. N. Ivanova</name>
</author>
<author><name sortKey="Anderson, I J" uniqKey="Anderson I">I. J. Anderson</name>
</author>
<author><name sortKey="Cheng, J F" uniqKey="Cheng J">J.-F. Cheng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rivers, A R" uniqKey="Rivers A">A. R. Rivers</name>
</author>
<author><name sortKey="Sharma, S" uniqKey="Sharma S">S. Sharma</name>
</author>
<author><name sortKey="Tringe, S G" uniqKey="Tringe S">S. G. Tringe</name>
</author>
<author><name sortKey="Martin, J" uniqKey="Martin J">J. Martin</name>
</author>
<author><name sortKey="Joye, S B" uniqKey="Joye S">S. B. Joye</name>
</author>
<author><name sortKey="Moran, M A" uniqKey="Moran M">M. A. Moran</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Roberts, I S" uniqKey="Roberts I">I. S. Roberts</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rodrigue, S" uniqKey="Rodrigue S">S. Rodrigue</name>
</author>
<author><name sortKey="Malmstrom, R R" uniqKey="Malmstrom R">R. R. Malmstrom</name>
</author>
<author><name sortKey="Berlin, A M" uniqKey="Berlin A">A. M. Berlin</name>
</author>
<author><name sortKey="Birren, B W" uniqKey="Birren B">B. W. Birren</name>
</author>
<author><name sortKey="Henn, M R" uniqKey="Henn M">M. R. Henn</name>
</author>
<author><name sortKey="Chisholm, S W" uniqKey="Chisholm S">S. W. Chisholm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Russell, N J" uniqKey="Russell N">N. J. Russell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sun, S" uniqKey="Sun S">S. Sun</name>
</author>
<author><name sortKey="Chen, J" uniqKey="Chen J">J. Chen</name>
</author>
<author><name sortKey="Li, W" uniqKey="Li W">W. Li</name>
</author>
<author><name sortKey="Altintas, I" uniqKey="Altintas I">I. Altintas</name>
</author>
<author><name sortKey="Lin, A" uniqKey="Lin A">A. Lin</name>
</author>
<author><name sortKey="Peltier, S" uniqKey="Peltier S">S. Peltier</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Takahashi, J" uniqKey="Takahashi J">J. Takahashi</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Valentine, D L" uniqKey="Valentine D">D. L. Valentine</name>
</author>
<author><name sortKey="Kessler, J D" uniqKey="Kessler J">J. D. Kessler</name>
</author>
<author><name sortKey="Redmond, M C" uniqKey="Redmond M">M. C. Redmond</name>
</author>
<author><name sortKey="Mendes, S D" uniqKey="Mendes S">S. D. Mendes</name>
</author>
<author><name sortKey="Heintz, M B" uniqKey="Heintz M">M. B. Heintz</name>
</author>
<author><name sortKey="Farwell, C" uniqKey="Farwell C">C. Farwell</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Woyke, T" uniqKey="Woyke T">T. Woyke</name>
</author>
<author><name sortKey="Sczyrba, A" uniqKey="Sczyrba A">A. Sczyrba</name>
</author>
<author><name sortKey="Lee, J" uniqKey="Lee J">J. Lee</name>
</author>
<author><name sortKey="Rinke, C" uniqKey="Rinke C">C. Rinke</name>
</author>
<author><name sortKey="Tighe, D" uniqKey="Tighe D">D. Tighe</name>
</author>
<author><name sortKey="Clingenpeel, S" uniqKey="Clingenpeel S">S. Clingenpeel</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wuebbles, D J" uniqKey="Wuebbles D">D. J. Wuebbles</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
</TEI>
<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Front Microbiol</journal-id>
<journal-id journal-id-type="iso-abbrev">Front Microbiol</journal-id>
<journal-id journal-id-type="publisher-id">Front. Microbiol.</journal-id>
<journal-title-group><journal-title>Frontiers in Microbiology</journal-title>
</journal-title-group>
<issn pub-type="epub">1664-302X</issn>
<publisher><publisher-name>Frontiers Media S.A.</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25071745</article-id>
<article-id pub-id-type="pmc">4085564</article-id>
<article-id pub-id-type="doi">10.3389/fmicb.2014.00332</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Microbiology</subject>
<subj-group><subject>Original Research Article</subject>
</subj-group>
</subj-group>
</article-categories>
<title-group><article-title>Single-cell genomics reveals features of a <italic>Colwellia</italic>
species that was dominant during the Deepwater Horizon oil spill</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Mason</surname>
<given-names>Olivia U.</given-names>
</name>
<xref ref-type="aff" rid="aff1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="fn001"><sup>*</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/76628"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Han</surname>
<given-names>James</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/128979"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Woyke</surname>
<given-names>Tanja</given-names>
</name>
<xref ref-type="aff" rid="aff2"><sup>2</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/23125"></uri>
</contrib>
<contrib contrib-type="author"><name><surname>Jansson</surname>
<given-names>Janet K.</given-names>
</name>
<xref ref-type="aff" rid="aff3"><sup>3</sup>
</xref>
<xref ref-type="aff" rid="aff4"><sup>4</sup>
</xref>
<xref ref-type="author-notes" rid="fn002"><sup>*</sup>
</xref>
<uri xlink:type="simple" xlink:href="http://community.frontiersin.org/people/u/128958"></uri>
</contrib>
</contrib-group>
<aff id="aff1"><sup>1</sup>
<institution>Department of Earth, Ocean and Atmospheric Science, Florida State University</institution>
<country>Tallahassee, FL, USA</country>
</aff>
<aff id="aff2"><sup>2</sup>
<institution>Department of Energy Joint Genome Institute</institution>
<country>Walnut Creek, CA, USA</country>
</aff>
<aff id="aff3"><sup>3</sup>
<institution>Lawrence Berkeley National Laboratory, Earth Sciences Division, Ecology Department</institution>
<country>Berkeley, CA, USA</country>
</aff>
<aff id="aff4"><sup>4</sup>
<institution>Department of Plant and Microbial Biology, University of California</institution>
<country>Berkeley, CA, USA</country>
</aff>
<author-notes><fn fn-type="edited-by"><p>Edited by: Ian M. Head, Newcastle University, UK</p>
</fn>
<fn fn-type="edited-by"><p>Reviewed by: Vanessa Karel Michelou, University of Hawaii, USA; Kasper Urup Kjeldsen, Aarhus University, Denmark</p>
</fn>
<corresp id="fn001">*Correspondence: Olivia U. Mason, Department of Earth, Ocean and Atmospheric Science, Florida State University, 117 N Woodward Avenue, Rogers Building Rm. 307, Tallahassee, FL, USA e-mail: <email xlink:type="simple">omason@fsu.edu</email>
;</corresp>
<corresp id="fn002">Janet K. Jansson, 1 Cyclotron Road, Berkeley, CA, USA e-mail: <email xlink:type="simple">jrjansson@lbl.gov</email>
</corresp>
<fn fn-type="other" id="fn003"><p>This article was submitted to Aquatic Microbiology, a section of the journal Frontiers in Microbiology.</p>
</fn>
</author-notes>
<pub-date pub-type="epub"><day>08</day>
<month>7</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="collection"><year>2014</year>
</pub-date>
<volume>5</volume>
<elocation-id>332</elocation-id>
<history><date date-type="received"><day>01</day>
<month>11</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>16</day>
<month>6</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2014 Mason, Han, Woyke and Jansson.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.</license-p>
</license>
</permissions>
<abstract><p>During the Deepwater Horizon (DWH) oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. <italic>Colwellia</italic>
eventually supplanted <italic>Oceanospirillales</italic>
, which dominated the plume early in the spill. These successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. <italic>Colwellia</italic>
abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by <italic>Colwellia</italic>
in hydrocarbon disposition is unknown. Here we used single-cell genomics to gain insights into the genome properties of a <italic>Colwellia</italic>
enriched during the DWH deep-sea plume. A single amplified genome (SAG) of a <italic>Colwellia</italic>
cell isolated from a DWH plume, closely related (avg. 98% 16S rRNA gene similarity) to other plume <italic>Colwellia</italic>
, was sequenced and annotated. The SAG was similar to the sequenced isolate <italic>Colwellia psychrerythraea</italic>
34H (84% avg. nucleotide identity). Both had genes for denitrification, chemotaxis, and motility, adaptations to cold environments and a suite of nutrient acquisition genes. The <italic>Colwellia</italic>
SAG may be capable of gaseous and aromatic hydrocarbon degradation, which contrasts with a DWH plume <italic>Oceanospirillales</italic>
SAG which encoded non-gaseous <italic>n</italic>
-alkane and cycloalkane degradation pathways. The disparate hydrocarbon degradation pathways are consistent with hydrocarbons that were abundant at different times in the deep-sea plume; first, non-gaseous <italic>n</italic>
-alkanes and cycloalkanes that could be degraded by <italic>Oceanospirillales</italic>
, followed by gaseous, and simple aromatic hydrocarbons that may have been degraded by <italic>Colwellia</italic>
. These insights into the genomic properties of a <italic>Colwellia</italic>
species, which were supported by existing metagenomic sequence data from the plume and DWH contaminated sediments, help further our understanding of the successional changes in the dominant microbial players in the plume over the course of the DWH spill.</p>
</abstract>
<kwd-group><kwd>DWH oil spill</kwd>
<kwd><italic>Colwellia</italic>
</kwd>
<kwd>single-cell genomics</kwd>
<kwd>deep-sea plume</kwd>
<kwd>hydrocarbon degradation</kwd>
<kwd>bacteria</kwd>
</kwd-group>
<counts><fig-count count="2"></fig-count>
<table-count count="0"></table-count>
<equation-count count="0"></equation-count>
<ref-count count="35"></ref-count>
<page-count count="8"></page-count>
<word-count count="6743"></word-count>
</counts>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Mason, Olivia U" sort="Mason, Olivia U" uniqKey="Mason O" first="Olivia U." last="Mason">Olivia U. Mason</name>
</noRegion>
<name sortKey="Han, James" sort="Han, James" uniqKey="Han J" first="James" last="Han">James Han</name>
<name sortKey="Jansson, Janet K" sort="Jansson, Janet K" uniqKey="Jansson J" first="Janet K." last="Jansson">Janet K. Jansson</name>
<name sortKey="Jansson, Janet K" sort="Jansson, Janet K" uniqKey="Jansson J" first="Janet K." last="Jansson">Janet K. Jansson</name>
<name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name>
</country>
</tree>
</affiliations>
</record>
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