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Title: Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria

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, metalrich 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 systems1-3 and their interactions might be key to ecosystemmore » optimization. Because proteomic data simultaneously convey information about genome type and activity, strainresolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis4-6 of microorganisms in the natural environment.« less

Authors:
 [1];  [1];  [2];  [2];  [1];  [3];  [1];  [1];  [1];  [3];  [3];  [1];  [4];  [1]
  1. University of California, Berkeley
  2. ORNL
  3. U.S. Department of Energy, Joint Genome Institute
  4. {Bob} L [ORNL
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
931009
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nature; Journal Volume: 446; Journal Issue: 1
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; AMINO ACIDS; BACTERIA; MICROORGANISMS; STRAINS

Citation Formats

Lo, I, Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert, and Banfield, Jillian F. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. United States: N. p., 2007. Web. doi:10.1038/nature05624.
Lo, I, Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert, & Banfield, Jillian F. Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. United States. doi:10.1038/nature05624.
Lo, I, Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert, and Banfield, Jillian F. Mon . "Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria". United States. doi:10.1038/nature05624.
@article{osti_931009,
title = {Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria},
author = {Lo, I and Denef, Vincent and Verberkmoes, Nathan C and Shah, Manesh B and Goltsman, Daniela and DiBartolo, Genevieve and Tyson, Gene W. and Allen, Eric E. and Ram, Rachna J. and Detter, J. Chris and Richardson, Paul and Thelen, Michael P. and Hettich, Robert and Banfield, Jillian F.},
abstractNote = {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, metalrich 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 systems1-3 and their interactions might be key to ecosystem optimization. Because proteomic data simultaneously convey information about genome type and activity, strainresolved community proteomics is an important complement to cultivation-independent genomic (metagenomic) analysis4-6 of microorganisms in the natural environment.},
doi = {10.1038/nature05624},
journal = {Nature},
number = 1,
volume = 446,
place = {United States},
year = {Mon Jan 01 00:00:00 EST 2007},
month = {Mon Jan 01 00:00:00 EST 2007}
}