title: Assembly-driven community genomics of a hypersaline microbial ecosystem.
abstract: Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The "assembly-driven" community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity.
authors: Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.
authors: Sheila
authors: S
authors: Podell
authors: Juan A
authors: JA
authors: Ugalde
authors: Priya
authors: P
authors: Narasingarao
authors: Jillian F
authors: JF
authors: Banfield
authors: Karla B
authors: KB
authors: Heidelberg
authors: Eric E
authors: EE
authors: Allen
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics; D001419:Bacteria / Q000145:classification; D017753:Ecosystem; D020745:Genome, Archaeal; D060106:Lakes; D008386:Marine Biology; D056186:Metagenomics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D054712:Salinity; D014739:Victoria; D014871:Water Microbiology
chemical_list: D012336:RNA, Ribosomal, 16S
references: Sci Rep. 2011;1:135
references: 22355652
references: ISME J. 2012 Jan;6(1):81-93
references: 21716304
references: Appl Environ Microbiol. 2012 Sep;78(17):6309-20
references: 22773627
references: ISME J. 2007 Jul;1(3):235-45
references: 18043634
references: BMC Bioinformatics. 2009 Oct 27;10:356
references: 19860910
references: Proc Natl Acad Sci U S A. 2006 Jul 25;103(30):11240-5
references: 16840556
references: Environ Microbiol. 2012 Feb;14(2):426-40
references: 22003883
references: Nat Biotechnol. 2006 Oct;24(10):1263-9
references: 16998472
references: BMC Bioinformatics. 2010 Oct 30;11:538
references: 21034504
references: Extremophiles. 2008 Sep;12(5):651-6
references: 18553053
references: Int J Syst Bacteriol. 1995 Oct;45(4):747-54
references: 7547294
references: Microbiol Rev. 1994 Mar;58(1):94-144
references: 8177173
references: Nat Methods. 2011 May;8(5):367
references: 21527926
references: Appl Environ Microbiol. 2009 Dec;75(23):7537-41
references: 19801464
references: Microb Ecol. 2007 Nov;54(4):598-617
references: 17450395
references: ISME J. 2010 Jul;4(7):882-95
references: 20164864
references: Nature. 2004 Mar 4;428(6978):37-43
references: 14961025
references: ISME J. 2011 Dec;5(12):1946-56
references: 21697963
references: Environ Microbiol. 2004 Dec;6(12):1287-91
references: 15560825
references: PLoS One. 2012;7(3):e33802
references: 22479446
references: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references: 16820507
references: Genome Biol. 2007;8(3):R34
references: 17349036
references: PLoS Biol. 2007 Mar;5(3):e82
references: 17355177
references: Science. 2010 May 21;328(5981):994-9
references: 20489017
references: Genome Biol. 2008 Oct 13;9(10):R151
references: 18851752
references: BMC Genomics. 2006 Jul 04;7:171
references: 16820057
references: Environ Microbiol. 2011 Aug;13(8):1956-72
references: 20738373
references: J Biol. 2009;8(6):59
references: 19594957
references: FEMS Microbiol Ecol. 2011 May;76(2):360-72
references: 21255052
references: Nat Rev Microbiol. 2005 Jun;3(6):489-98
references: 15931167
references: Genome Biol. 2007;8(2):R16
references: 17274820
references: FEMS Microbiol Lett. 2012 May;330(1):1-9
references: 22339687
references: Nature. 2011 Nov 06;480(7377):368-71
references: 22056985
references: Lancet. 2005 Jan 15-21;365(9455):253-5
references: 15652608
references: ISME J. 2010 Aug;4(8):962-74
references: 20336157
references: PLoS One. 2011;6(6):e20968
references: 21701686
references: Biotechnol Bioeng. 1998 Dec 5;60(5):636-41
references: 10099472
references: Extremophiles. 2010 Mar;14(2):161-9
references: 20091074
references: Saline Syst. 2008 Apr 15;4:2
references: 18412960
references: Environ Microbiol. 2010 Nov;12(11):2965-76
references: 20561021
references: Nat Rev Microbiol. 2009 Nov;7(11):828-36
references: 19834481
references: PLoS One. 2010 Mar 10;5(3):e9490
references: 20224823
references: Science. 2006 Mar 3;311(5765):1283-7
references: 16513982
references: Int J Syst Evol Microbiol. 2010 May;60(Pt 5):1196-1199
references: 19667389
references: Bioinformatics. 2006 Nov 1;22(21):2688-90
references: 16928733
references: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references: 11917018
references: Genome Res. 2013 Jan;23(1):111-20
references: 22936250
references: Science. 2012 Feb 3;335(6068):587-90
references: 22301318
references: Bioinformatics. 2009 Sep 1;25(17):2271-8
references: 19561336
references: BMC Genomics. 2006 Jul 04;7:169
references: 16820047
references: Science. 2000 Mar 24;287(5461):2196-204
references: 10731133
references: Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2567-72
references: 15701695