title: Global biogeography of Prochlorococcus genome diversity in the surface ocean.
abstract: Prochlorococcus, the smallest known photosynthetic bacterium, is abundant in the ocean's surface layer despite large variation in environmental conditions. There are several genetically divergent lineages within Prochlorococcus and superimposed on this phylogenetic diversity is extensive gene gain and loss. The environmental role in shaping the global ocean distribution of genome diversity in Prochlorococcus is largely unknown, particularly in a framework that considers the vertical and lateral mechanisms of evolution. Here we show that Prochlorococcus field populations from a global circumnavigation harbor extensive genome diversity across the surface ocean, but this diversity is not randomly distributed. We observed a significant correspondence between phylogenetic and gene content diversity, including regional differences in both phylogenetic composition and gene content that were related to environmental factors. Several gene families were strongly associated with specific regions and environmental factors, including the identification of a set of genes related to lower nutrient and temperature regions. Metagenomic assemblies of natural Prochlorococcus genomes reinforced this association by providing linkage of genes across genomic backbones. Overall, our results show that the phylogeography in Prochlorococcus taxonomy is echoed in its genome content. Thus environmental variation shapes the functional capabilities and associated ecosystem role of the globally abundant Prochlorococcus.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
authors.forename: Alyssa G
authors.initials: AG
authors.lastname: Kent
authors.affiliation: Microbial and Environmental Genomics Group, J. Craig Venter Institute, San Diego, CA, USA.
authors.forename: Chris L
authors.initials: CL
authors.lastname: Dupont
authors.affiliation: Informatics Group, J. Craig Venter Institute, San Diego, CA, USA.
authors.forename: Shibu
authors.initials: S
authors.lastname: Yooseph
authors.affiliation: Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.|Department of Earth System Science, University of California, Irvine, CA, USA.
authors.forename: Adam C
authors.identifier: 0000-0003-2829-4314
authors.initials: AC
authors.lastname: Martiny
mesh_terms: D017753:Ecosystem; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D056186:Metagenomics; D009792:Oceans and Seas; D010802:Phylogeny; D048929:Prochlorococcus / Q000145:classification / Q000235:genetics*; D012623:Seawater / Q000382:microbiology
references.citation: BMC Genomics. 2015 Jul 04;16:496
references.pmid: 26141154
references.citation: Microbiol Mol Biol Rev. 2009 Jun;73(2):249-99
references.pmid: 19487728
references.citation: ISME J. 2008 Oct;2(10):1052-65
references.pmid: 18580971
references.citation: Bioinformatics. 2008 Dec 15;24(24):2818-24
references.pmid: 18952627
references.citation: Nature. 1998 Jun 4;393(6684):464-7
references.pmid: 9624000
references.citation: Science. 2014 Apr 25;344(6182):416-20
references.pmid: 24763590
references.citation: PLoS Genet. 2007 Dec;3(12):e231
references.pmid: 18159947
references.citation: Nucleic Acids Res. 2012 Jan;40(Database issue):D632-40
references.pmid: 22102570
references.citation: Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9
references.pmid: 24297252
references.citation: Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9824-9
references.pmid: 23703908
references.citation: Trends Microbiol. 2007 Sep;15(9):398-407
references.pmid: 17693088
references.citation: Mar Genomics. 2014 Jun;15:17-28
references.pmid: 24662471
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12552-7
references.pmid: 16895994
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14288-93
references.pmid: 21825123
references.citation: Proc Natl Acad Sci U S A. 2008 Jul 22;105(29):10039-44
references.pmid: 18632554
references.citation: Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11463-8
references.pmid: 23801761
references.citation: Environ Microbiol. 2008 Jan;10(1):147-61
references.pmid: 17900271
references.citation: Mol Syst Biol. 2012 Jul 17;8:595
references.pmid: 22806143
references.citation: Microbiol Mol Biol Rev. 1999 Mar;63(1):106-27
references.pmid: 10066832
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W7-13
references.pmid: 20435676
references.citation: ISME J. 2015 May;9(5):1195-207
references.pmid: 25350156
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 30;106(26):10787-92
references.pmid: 19549842
references.citation: ISME J. 2015 May;9(5):1076-92
references.pmid: 25333462
references.citation: PLoS Biol. 2007 Mar;5(3):e77
references.pmid: 17355176
references.citation: Ecology. 2009 Dec;90(12):3566-74
references.pmid: 20120823
references.citation: BMC Genomics. 2008 Feb 08;9:75
references.pmid: 18261238
references.citation: Bioinformatics. 2014 May 1;30(9):1312-3
references.pmid: 24451623
references.citation: Proc Natl Acad Sci U S A. 2010 Sep 14;107(37):16184-9
references.pmid: 20733077
references.citation: Nucleic Acids Res. 2006;34(19):5623-30
references.pmid: 17028096
references.citation: Science. 2006 Mar 24;311(5768):1737-40
references.pmid: 16556835
references.citation: FEMS Microbiol Rev. 2011 Sep;35(5):957-76
references.pmid: 21711367
references.citation: PLoS Comput Biol. 2011 Oct;7(10):e1002195
references.pmid: 22039361
references.citation: Environ Microbiol. 2009 Apr;11(4):823-32
references.pmid: 19021692
references.citation: Science. 2000 Aug 4;289(5480):759-62
references.pmid: 10926534
references.citation: Sci Data. 2014 Sep 30;1:140034
references.pmid: 25977791
references.citation: Science. 2006 May 12;312(5775):918-21
references.pmid: 16690867
references.citation: Ecol Evol. 2013 Jun;3(6):1780-97
references.pmid: 23789085
references.citation: Appl Environ Microbiol. 1999 Jun;65(6):2585-91
references.pmid: 10347047
references.citation: Mol Syst Biol. 2011 Mar 15;7:473
references.pmid: 21407210
references.citation: ISME J. 2014 Jun;8(6):1221-36
references.pmid: 24401861
references.citation: Environ Microbiol. 2009 Jun;11(6):1340-7
references.pmid: 19187282
references.citation: BMC Bioinformatics. 2009 Dec 15;10:421
references.pmid: 20003500
references.citation: ISME J. 2013 Apr;7(4):830-8
references.pmid: 23235290
references.citation: BMC Bioinformatics. 2010 Oct 30;11:538
references.pmid: 21034504
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: Science. 2006 Mar 24;311(5768):1768-70
references.pmid: 16556843
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: PLoS Genet. 2009 Oct;5(10):e1000674
references.pmid: 19798447
references.citation: PLoS One. 2014 Feb 27;9(2):e89549
references.pmid: 24586863