Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria (original) (raw)

Nature volume 446, pages 537–541 (2007) Cite this article

Abstract

Microbes comprise the majority of extant organisms, yet much remains to be learned about the nature and driving forces of microbial diversification. Our understanding of how microorganisms adapt and evolve can be advanced by genome-wide documentation of the patterns of genetic exchange, particularly if analyses target coexisting members of natural communities. Here we use community genomic data sets to identify, with strain specificity, expressed proteins from the dominant member of a genomically uncharacterized, natural, acidophilic biofilm. Proteomics results reveal a genome shaped by recombination involving chromosomal regions of tens to hundreds of kilobases long that are derived from two closely related bacterial populations. Inter-population genetic exchange was confirmed by multilocus sequence typing of isolates and of uncultivated natural consortia. The findings suggest that exchange of large blocks of gene variants is crucial for the adaptation to specific ecological niches within the very acidic, metal-rich environment. Mass-spectrometry-based discrimination of expressed protein products that differ by as little as a single amino acid enables us to distinguish the behaviour of closely related coexisting organisms. This is important, given that microorganisms grouped together as a single species may have quite distinct roles in natural systems1,2,3 and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strain-resolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis4,5,6 of microorganisms in the natural environment.

This is a preview of subscription content, access via your institution

Access options

Subscribe to this journal

Receive 52 print issues and online access

$199.00 per year

only $3.83 per issue

Buy this article

USD 39.95

Prices may be subject to local taxes which are calculated during checkout

Additional access options:

Similar content being viewed by others

References

  1. Acinas, S. G. et al. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430, 551–554 (2004)
    Article ADS CAS Google Scholar
  2. Johnson, Z. I. et al. Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311, 1737–1740 (2006)
    Article ADS CAS Google Scholar
  3. DeLong, E. F. Microbial community genomics in the ocean. Nature Rev. Microbiol. 3, 459–469 (2005)
    Article CAS Google Scholar
  4. Tyson, G. W. et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428, 37–43 (2004)
    Article ADS CAS Google Scholar
  5. Venter, J. C. et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304, 66–74 (2004)
    Article ADS CAS Google Scholar
  6. DeLong, E. F. et al. Community genomics among stratified microbial assemblages in the ocean's interior. Science 311, 496–503 (2006)
    Article ADS CAS Google Scholar
  7. Ram, R. J. et al. Community proteomics of a natural microbial biofilm. Science 308, 1915–1920 (2005)
    Article ADS CAS Google Scholar
  8. Bond, P. L., Smriga, S. P. & Banfield, J. F. Phylogeny of microorganisms populating a thick, subaerial, predominantly lithotrophic biofilm at an extreme acid mine drainage site. Appl. Environ. Microbiol. 66, 3842–3849 (2000)
    Article CAS Google Scholar
  9. Coram, N. J. & Rawlings, D. E. Molecular relationship between two groups of the genus Leptospirillum and the finding that Leptospirillum ferriphilum sp. nov. dominates South African commercial biooxidation tanks that operate at 40 °C. Appl. Environ. Microbiol. 68, 838–845 (2002)
    Article CAS Google Scholar
  10. Tyson, G. W. et al. Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community. Appl. Environ. Microbiol. 71, 6319–6324 (2005)
    Article CAS Google Scholar
  11. Johnson, D. B. & Hallberg, K. B. The microbiology of acidic mine waters. Res. Microbiol. 154, 466–473 (2003)
    Article CAS Google Scholar
  12. Cohan, F. M. What are bacterial species? Annu. Rev. Microbiol. 56, 457–487 (2002)
    Article CAS Google Scholar
  13. Maiden, M. C. et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl Acad. Sci. USA 95, 3140–3145 (1998)
    Article ADS CAS Google Scholar
  14. Mau, B., Glasner, J. D., Darling, A. E. & Perna, N. T. Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli. Genome Biol. 7, R44 (2006)
    Article Google Scholar
  15. Whitaker, R. J., Grogan, D. W. & Taylor, J. W. Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol. Biol. Evol. 22, 2354–2361 (2005)
    Article CAS Google Scholar
  16. Papke, R. T., Koenig, J. E., Rodriguez-Valera, F. & Doolittle, W. F. Frequent recombination in a saltern population of Halorubrum. Science 306, 1928–1929 (2004)
    ADS CAS PubMed Google Scholar
  17. Nesbo, C. L., Dlutek, M. & Doolittle, W. F. Recombination in Thermotoga: implications for species concepts and biogeography. Genetics 172, 759–769 (2006)
    Article CAS Google Scholar
  18. Falush, D. et al. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc. Natl Acad. Sci. USA 98, 15056–15061 (2001)
    Article ADS CAS Google Scholar
  19. Rocha, E., Cornet, E. & Michel, B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet. 1, 247–259 (2005)
    Article CAS Google Scholar
  20. Majewski, J. & Cohan, F. M. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153, 1525–1533 (1999)
    CAS PubMed PubMed Central Google Scholar
  21. Majewski, J. & Cohan, F. M. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152, 1459–1474 (1999)
    CAS PubMed PubMed Central Google Scholar
  22. Syvanen, A. C. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Rev. Genet. 2, 930–942 (2001)
    Article CAS Google Scholar
  23. Manabe, T. Capillary electrophoresis of proteins for proteomic studies. Electrophoresis 20, 3116–3121 (1999)
    Article CAS Google Scholar
  24. Dalluge, J. J. Mass spectrometry: an emerging alternative to traditional methods for measurement of diagnostic proteins, peptides and amino acids. Curr. Protein Pept. Sci. 3, 181–190 (2002)
    Article CAS Google Scholar
  25. Johnson, D. B. Selective solid media for isolating and enumerating acidophilic bacteria. J. Microbiol. Methods 23, 205–218 (1995)
    Article Google Scholar

Download references

Acknowledgements

We thank T. W. Arman, President, Iron Mountain Mines and R. Sugarek, EPA, for site access, and R. Carver for on-site assistance. We thank D. B. Johnson, University of Wales, Bangor, for assistance with culturing; and F. Larimer and M. Land of the ORNL Genome Analysis and System Modeling Group for computational resources for proteomic analysis. DNA sequencing was carried out at the DOE Joint Genome Institute. Funding was provided by the DOE Genomics:GTL Program (Office of Science), the NSF Biocomplexity Program and the NASA Astrobiology Institute.

Author Contributions I.L. isolated the Leptospirillum group II strains; I.L., V.J.D., G.D. and R.J.R. performed MLST; J.C.D. and P.R. made clone libraries and produced the sequencing reads; G.W.T., E.E.A. and J.F.B. assembled and binned the sequencing reads and produced the automatic annotation; D.G., G.D., V.J.D., G.W.T. and J.F.B manually curated the Leptospirillum group II genome assemblies and annotation; N.C.V. optimized and performed proteomic experiments; M.B.S. created the proteomic analytical pipeline; V.J.D., N.C.V and J.F.B. analysed the data; J.F.B. designed the research; and I.L., V.J.D., N.C.V., M.P.T., R.L.H. and J.F.B. wrote the paper.

The UBA community Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AAWO00000000. The version described in this paper, containing the assembled and annotated Leptospirillum group II UBA genome, is the first version, AAWO01000000. Sequencing reads were deposited in the NCBI trace archive. All proteomics datasets were submitted to PRIDE (http://www.ebi.ac.uk/pride/; experiment accession numbers 1854–1867). All proteomic datasets, databases and supplementary files can also be found at http://compbio.ornl.gov/biofilm_amd_recombination

Author information

Authors and Affiliations

  1. University of California, Berkeley, California 94720, USA,
    Ian Lo, Vincent J. Denef, Daniela Goltsman, Genevieve DiBartolo, Gene W. Tyson, Eric E. Allen, Rachna J. Ram & Jillian F. Banfield
  2. Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA,
    Nathan C. VerBerkmoes, Manesh B. Shah & Robert L. Hettich
  3. Joint Genome Institute, Walnut Creek, California 94598, USA,
    J. Chris Detter & Paul Richardson
  4. Lawrence Livermore National Laboratory, Livermore, California 94550, USA,
    Michael P. Thelen

Authors

  1. Ian Lo
  2. Vincent J. Denef
  3. Nathan C. VerBerkmoes
  4. Manesh B. Shah
  5. Daniela Goltsman
  6. Genevieve DiBartolo
  7. Gene W. Tyson
  8. Eric E. Allen
  9. Rachna J. Ram
  10. J. Chris Detter
  11. Paul Richardson
  12. Michael P. Thelen
  13. Robert L. Hettich
  14. Jillian F. Banfield

Corresponding author

Correspondence toJillian F. Banfield.

Ethics declarations

Competing interests

. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

Supplementary information

Supplementary Information (download PDF )

This file contains Supplementary Figures S1-S3 Supplementary Methods, Supplementary Tables S1-S7, Supplementary Data and additional references. The file includes the draft annotation of the aligned UBA type and 5-way CG type Leptospirillum group II genomes and supplementary analyses of the false positive rate of the proteomics data (PDF 4568 kb)

Rights and permissions

About this article

Cite this article

Lo, I., Denef, V., VerBerkmoes, N. et al. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria.Nature 446, 537–541 (2007). https://doi.org/10.1038/nature05624

Download citation