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Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

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.

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Figure 1: Protein coverage ratios across scaffold 7931.
Figure 2: Protein coverage ratios and unique peptide counts across scaffold 8241.
Figure 3: Inferred recombinant ABend Leptospirillum group II genome structure.
Figure 4: Peptide-resolved analysis of a recombination point.
Figure 5: Evidence for the recombinant nature of a Rubisco-like protein.

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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

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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

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Correspondence to Jillian F. Banfield.

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Supplementary information

Supplementary Information

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)

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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

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