Red Sea SAR11 and

Alphaproteobacteria / genetics Genome, Bacterial Indian Ocean Metagenome Phylogeny Prochlorococcus / genetics Seawater / microbiology
Pelagibacter metagenomics metatranscriptomics population genomics single-cell genomics

Journal

Applied and environmental microbiology
ISSN: 1098-5336
Titre abrégé: Appl Environ Microbiol
Pays: United States
ID NLM: 7605801

Informations de publication

Date de publication:
01 07 2019
Historique:
received: 13 02 2019
accepted: 19 04 2019
pubmed: 28 4 2019
medline: 5 6 2020
entrez: 28 4 2019
Statut: epublish

Résumé

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5

Identifiants

DOI: 10.1128/AEM.00369-19 PMID: 31028022 PMC: PMC6581160
pubmed: 31028022
pii: AEM.00369-19
doi: 10.1128/AEM.00369-19
pmc: PMC6581160
pii:
doi:

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Références

BMC Genomics. 2013;14 Suppl 1:S7
pubmed: 23368723
mBio. 2012 Sep 18;3(5):
pubmed: 22991429
PLoS One. 2012;7(5):e37118
pubmed: 22615914
Nature. 2003 Aug 28;424(6952):1042-7
pubmed: 12917642
Appl Environ Microbiol. 2013 Dec;79(24):7696-701
pubmed: 24096415
PeerJ. 2018 Jan 25;6:e4320
pubmed: 29423345
BMC Genomics. 2008 Feb 08;9:75
pubmed: 18261238
PLoS One. 2009 Sep 02;4(9):e6864
pubmed: 19724646
Front Microbiol. 2012 Dec 05;3:410
pubmed: 23227024
Nat Rev Microbiol. 2015 Jan;13(1):13-27
pubmed: 25435307
Ecol Evol. 2013 Jun;3(6):1780-97
pubmed: 23789085
FEMS Microbiol Lett. 2014 Jul;356(1):118-26
pubmed: 24888561
PLoS One. 2012;7(11):e50274
pubmed: 23185592
Sci Data. 2016 Jul 05;3:160050
pubmed: 27377622
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Nat Microbiol. 2016 Jun 13;1(8):16086
pubmed: 27573109
Bioinformatics. 2009 Aug 1;25(15):1968-9
pubmed: 19497936
Sci Data. 2014 Sep 30;1:140034
pubmed: 25977791
Appl Environ Microbiol. 2004 Nov;70(11):6542-50
pubmed: 15528517
Trends Microbiol. 2007 Sep;15(9):398-407
pubmed: 17693088
Bioinformatics. 2012 Dec 15;28(24):3211-7
pubmed: 23071270
Nucleic Acids Res. 1995 Dec 25;23(24):4992-9
pubmed: 8559656
Proc Natl Acad Sci U S A. 2007 May 22;104(21):9052-7
pubmed: 17502618
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
PLoS One. 2012;7(8):e43432
pubmed: 22952681
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Science. 2014 Apr 25;344(6182):416-20
pubmed: 24763590
Proc Natl Acad Sci U S A. 2013 Mar 19;110(12):4651-5
pubmed: 23487761
Nature. 2002 Feb 7;415(6872):630-3
pubmed: 11832943
ISME J. 2015 May;9(5):1195-207
pubmed: 25350156
Proc Natl Acad Sci U S A. 2008 Mar 11;105(10):3805-10
pubmed: 18316740
Mol Ecol. 2012 Jan;21(2):388-405
pubmed: 22133021
ISME J. 2017 Jan;11(1):138-151
pubmed: 27420030
PLoS Genet. 2007 Dec;3(12):e231
pubmed: 18159947
Genome Res. 2003 Sep;13(9):2178-89
pubmed: 12952885
Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18634-9
pubmed: 20937887
FEMS Microbiol Ecol. 2018 Nov 1;94(12):
pubmed: 30188995
FEMS Microbiol Ecol. 2017 Jul 1;93(7):
pubmed: 28645159
J Comput Biol. 2012 May;19(5):455-77
pubmed: 22506599
Appl Environ Microbiol. 2002 Mar;68(3):1180-91
pubmed: 11872466
Mol Biol Evol. 2015 Oct;32(10):2738-48
pubmed: 26116859
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Nat Methods. 2015 Jan;12(1):59-60
pubmed: 25402007
Appl Environ Microbiol. 1997 Jan;63(1):50-6
pubmed: 8979338
Genome Biol. 2004;5(10):117
pubmed: 15461805
Proc Natl Acad Sci U S A. 1985 Oct;82(20):6955-9
pubmed: 2413450
Bioinformatics. 2009 Sep 1;25(17):2271-8
pubmed: 19561336
Mol Biol Evol. 2012 Jun;29(6):1695-701
pubmed: 22319168
Science. 2015 May 22;348(6237):1261359
pubmed: 25999513
Science. 2006 Mar 24;311(5768):1737-40
pubmed: 16556835
Nature. 2017 Nov 2;551(7678):45-50
pubmed: 29045390
Nature. 2000 May 18;405(6784):299-304
pubmed: 10830951
Nucleic Acids Res. 2005 Jan 20;33(2):511-8
pubmed: 15661851

Auteurs

Luke R Thompson (LR)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia lukethompson@gmail.com ulistingl@gmail.com.
Department of Biological Sciences and Northern Gulf Institute, University of Southern Mississippi, Hattiesburg, Mississippi, USA.
Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA.
ORCID: 0000-0002-3911-1280

Mohamed F Haroon (MF)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

Ahmed A Shibl (AA)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
ORCID: 0000-0002-8147-8406

Matt J Cahill (MJ)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

David K Ngugi (DK)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
ORCID: 0000-0002-0442-4279

Gareth J Williams (GJ)

School of Ocean Sciences, Bangor University, Anglesey, United Kingdom.

James T Morton (JT)

Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

Rob Knight (R)

Department of Pediatrics, University of California San Diego, La Jolla, California, USA.
Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.
Center for Microbiome Innovation, University of California, San Diego, California, USA.

Kelly D Goodwin (KD)

Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, stationed at Southwest Fisheries Science Center, La Jolla, California, USA.
ORCID: 0000-0001-9583-8073

Ulrich Stingl (U)

Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia lukethompson@gmail.com ulistingl@gmail.com.
Department of Microbiology & Cell Science, Fort Lauderdale Research and Education Center, UF/Institute of Food and Agricultural Sciences, University of Florida, Davie, Florida, USA.

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Classifications MeSH

questionsmedicales.fr › Bactéries › Proteobacteria › Alphaproteobacteria › Red Sea SAR11 and
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Red Sea SAR11 and
questionsmedicales.fr › Régions géographiques › Océans et mers › Océan Indien › Red Sea SAR11 and
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Métagénome › Red Sea SAR11 and
questionsmedicales.fr › Sciences de l'information › Phylogenèse › Red Sea SAR11 and
questionsmedicales.fr › Bactéries › Bactéries à Gram négatif › Bactéries à Gram négatif photosynthétiques › Cyanobactéries › Prochlorophytes › Prochlorococcus › Red Sea SAR11 and
questionsmedicales.fr › Phénomènes biologiques › Phénomènes écologiques et environnementaux › Eaux salées › Eau de mer › Red Sea SAR11 and