Home LiteratureArticle Details
PMID: 22806143 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Global biogeography of SAR11 marine bacteria.

Molecular systems biology ·Vol. 8 ·2012-07-17 ·Pages 595

Brown MV, Lauro FM, DeMaere MZ, Muir L, Wilkins D, Thomas T, Riddle MJ, Fuhrman JA, Andrews-Pfannkoch C, Hoffman JM, McQuaid JB, Allen A, Rintoul SR, Cavicchioli R

Abstract

The ubiquitous SAR11 bacterial clade is the most abundant type of organism in the world's oceans, but the reasons for its success are not fully elucidated. We analysed 128 surface marine metagenomes, including 37 new Antarctic metagenomes. The large size of the data set enabled internal transcribed spacer (ITS) regions to be obtained from the Southern polar region, enabling the first global characterization of the distribution of SAR11, from waters spanning temperatures -2 to 30°C. Our data show a stable co-occurrence of phylotypes within both 'tropical' (>20°C) and 'polar' (<10°C) biomes, highlighting ecological niche differentiation between major SAR11 subgroups. All phylotypes display transitions in abundance that are strongly correlated with temperature and latitude. By assembling SAR11 genomes from Antarctic metagenome data, we identified specific genes, biases in gene functions and signatures of positive selection in the genomes of the polar SAR11-genomic signatures of adaptive radiation. Our data demonstrate the importance of adaptive radiation in the organism's ability to proliferate throughout the world's oceans, and describe genomic traits characteristic of different phylotypes in specific marine biomes.

MeSH Terms
Alphaproteobacteria/genetics Antarctic Regions Climate Genome, Bacterial/genetics,radiation effects Marine Biology Metagenome/genetics,radiation effects Models, Biological Phylogeny Phylogeography Seawater/microbiology Sequence Alignment Temperature
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
Brown Mark V
School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia.
Lauro Federico M
DeMaere Matthew Z
Muir Les
Wilkins David
Thomas Torsten
Riddle Martin J
Fuhrman Jed A
Andrews-Pfannkoch Cynthia
Hoffman Jeffrey M
McQuaid Jeffrey B
Allen Andrew
Rintoul Stephen R
Cavicchioli Ricardo
References (43)
43 references, click to expand
  1. Genome streamlining in a cosmopolitan oceanic bacterium.
    Science. 2005 Aug 19;309(5738):1242-5 PMID: 16109880
  2. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade.
    Sci Rep. 2011;1:13 PMID: 22355532
  3. Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource.
    Nucleic Acids Res. 2011 Jan;39(Database issue):D546-51 PMID: 21045053
  4. Complete genome sequence of strain IMCC9063, belonging to SAR11 subgroup 3, isolated from the Arctic Ocean.
    J Bacteriol. 2011 Jul;193(13):3379-80 PMID: 21515764
  5. Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica.
    ISME J. 2010 Aug;4(8):1002-19 PMID: 20237513
  6. The hydrophobic moment detects periodicity in protein hydrophobicity.
    Proc Natl Acad Sci U S A. 1984 Jan;81(1):140-4 PMID: 6582470
  7. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities.
    Int J Syst Evol Microbiol. 2007 Jan;57(Pt 1):81-91 PMID: 17220447
  8. An integrative study of a meromictic lake ecosystem in Antarctica.
    ISME J. 2011 May;5(5):879-95 PMID: 21124488
  9. Cultivation of the ubiquitous SAR11 marine bacterioplankton clade.
    Nature. 2002 Aug 8;418(6898):630-3 PMID: 12167859
  10. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
    Nucleic Acids Res. 1994 Nov 11;22(22):4673-80 PMID: 7984417
  11. Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea.
    ISME J. 2009 Mar;3(3):283-95 PMID: 19052630
  12. Environmental genome shotgun sequencing of the Sargasso Sea.
    Science. 2004 Apr 2;304(5667):66-74 PMID: 15001713
  13. Diversity and depth-specific distribution of SAR11 cluster rRNA genes from marine planktonic bacteria.
    Appl Environ Microbiol. 1997 Jan;63(1):63-70 PMID: 8979340
  14. The genome sequence of the psychrophilic archaeon, Methanococcoides burtonii: the role of genome evolution in cold adaptation.
    ISME J. 2009 Sep;3(9):1012-35 PMID: 19404327
  15. Structural insights into FtsZ protofilament formation.
    Nat Struct Mol Biol. 2004 Dec;11(12):1243-50 PMID: 15558053
  16. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific.
    PLoS Biol. 2007 Mar;5(3):e77 PMID: 17355176
  17. ARB: a software environment for sequence data.
    Nucleic Acids Res. 2004 Feb 25;32(4):1363-71 PMID: 14985472
  18. Molecular basis of porin selectivity: membrane experiments with OmpC-PhoE and OmpF-PhoE hybrid proteins of Escherichia coli K-12.
    Biochim Biophys Acta. 1989 May 19;981(1):8-14 PMID: 2470409
  19. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.
    Appl Environ Microbiol. 2006 Jul;72(7):5069-72 PMID: 16820507
  20. Large-scale transposon mutagenesis of Photobacterium profundum SS9 reveals new genetic loci important for growth at low temperature and high pressure.
    J Bacteriol. 2008 Mar;190(5):1699-709 PMID: 18156275
  21. PAML 4: phylogenetic analysis by maximum likelihood.
    Mol Biol Evol. 2007 Aug;24(8):1586-91 PMID: 17483113
  22. Effect of cold shock on lipid A biosynthesis in Escherichia coli. Induction At 12 degrees C of an acyltransferase specific for palmitoleoyl-acyl carrier protein.
    J Biol Chem. 1999 Apr 2;274(14):9677-85 PMID: 10092655
  23. Hawkeye: an interactive visual analytics tool for genome assemblies.
    Genome Biol. 2007;8(3):R34 PMID: 17349036
  24. SAR11 clade dominates ocean surface bacterioplankton communities.
    Nature. 2002 Dec 19-26;420(6917):806-10 PMID: 12490947
  25. The SAR11 group of alpha-proteobacteria is not related to the origin of mitochondria.
    PLoS One. 2012;7(1):e30520 PMID: 22291975
  26. Genome assembly forensics: finding the elusive mis-assembly.
    Genome Biol. 2008;9(3):R55 PMID: 18341692
  27. Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series.
    Environ Microbiol. 2005 Sep;7(9):1466-79 PMID: 16104869
  28. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade.
    Mol Biol Evol. 2012 Feb;29(2):599-615 PMID: 21900598
  29. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I.
    Mol Ecol. 2000 Jul;9(7):935-48 PMID: 10886656
  30. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.
    Mol Biol Evol. 1986 Sep;3(5):418-26 PMID: 3444411
  31. A computer program for predicting protein antigenic determinants.
    Mol Immunol. 1983 Apr;20(4):483-9 PMID: 6191210
  32. Ortholog detection using the reciprocal smallest distance algorithm.
    Methods Mol Biol. 2007;396:95-110 PMID: 18025688
  33. Simple high-throughput annotation pipeline (SHAP).
    Bioinformatics. 2011 Sep 1;27(17):2431-2 PMID: 21775307
  34. ACT: the Artemis Comparison Tool.
    Bioinformatics. 2005 Aug 15;21(16):3422-3 PMID: 15976072
  35. Global proteomic analysis of the insoluble, soluble, and supernatant fractions of the psychrophilic archaeon Methanococcoides burtonii. Part I: the effect of growth temperature.
    J Proteome Res. 2010 Feb 5;9(2):640-52 PMID: 20039705
  36. Dynamics of the SAR11 bacterioplankton lineage in relation to environmental conditions in the oligotrophic North Pacific subtropical gyre.
    Environ Microbiol. 2009 Sep;11(9):2291-300 PMID: 19490029
  37. Defining seasonal marine microbial community dynamics.
    ISME J. 2012 Feb;6(2):298-308 PMID: 21850055
  38. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site.
    ISME J. 2007 Aug;1(4):361-71 PMID: 18043647
  39. Natural variation in SAR11 marine bacterioplankton genomes inferred from metagenomic data.
    Biol Direct. 2007 Nov 07;2:27 PMID: 17988398
  40. Emergent biogeography of microbial communities in a model ocean.
    Science. 2007 Mar 30;315(5820):1843-6 PMID: 17395828
  41. The presence of the glycolysis operon in SAR11 genomes is positively correlated with ocean productivity.
    Environ Microbiol. 2010 Feb;12(2):490-500 PMID: 19889000
  42. Bacterial growth in the cold: evidence for an enhanced substrate requirement.
    Appl Environ Microbiol. 1992 Jan;58(1):359-64 PMID: 16348634
  43. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients.
    Science. 2006 Mar 24;311(5768):1737-40 PMID: 16556835
Article Info
Journal
Molecular systems biology
Abbr.
Mol Syst Biol
ISSN
1744-4292
DOI
10.1038/msb.2012.28
Published
2012-07-17
Epub
2012-00-17
Pages
595
Language
English
Region
England
NLM ID
101235389
PMCID
PMC3421443
Subset
IM
Corrections
CommentIn
PMID: 23169001
External Links
PubMed source DOI: 10.1038/msb.2012.28 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2