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Title: Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation

Abstract

Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics-inferred genome typing (PIGT) was used to determine the genomic make-up of Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a four-year period. We observed six distinct genotypes that are recombinants comprised of segments from two parental genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were overrepresented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly underrepresented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system.

Authors:
 [1];  [2];  [2];  [2];  [3];  [1]
  1. University of California, Berkeley
  2. ORNL
  3. McGill University, Montreal, Quebec
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
958921
DOE Contract Number:  
DE-AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 11; Journal Issue: 2; Journal ID: ISSN 1462-2912
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; 99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; ABUNDANCE; ACID MINE DRAINAGE; BACTERIA; DISTRIBUTION; ECOSYSTEMS; GENES; IRON; RECOMBINATION; SHAPE; TRANSPORT

Citation Formats

Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Abraham, Paul E, Lefsrud, Mark G, Hettich, Robert, and Banfield, Jillian F. Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation. United States: N. p., 2009. Web. doi:10.1111/j.1462-2920.2008.01769.x.
Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Abraham, Paul E, Lefsrud, Mark G, Hettich, Robert, & Banfield, Jillian F. Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation. United States. https://doi.org/10.1111/j.1462-2920.2008.01769.x
Denef, Vincent, Verberkmoes, Nathan C, Shah, Manesh B, Abraham, Paul E, Lefsrud, Mark G, Hettich, Robert, and Banfield, Jillian F. 2009. "Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation". United States. https://doi.org/10.1111/j.1462-2920.2008.01769.x.
@article{osti_958921,
title = {Proteomics-inferred genome typing (PIGT) demonstrates inter-populationrecombination as a strategy for environmental adaptation},
author = {Denef, Vincent and Verberkmoes, Nathan C and Shah, Manesh B and Abraham, Paul E and Lefsrud, Mark G and Hettich, Robert and Banfield, Jillian F.},
abstractNote = {Analyses of ecological and evolutionary processes that shape microbial consortia are facilitated by comprehensive studies of ecosystems with low species richness. In the current study we evaluated the role of recombination in altering the fitness of chemoautotrophic bacteria in their natural environment. Proteomics-inferred genome typing (PIGT) was used to determine the genomic make-up of Leptospirillum group II populations in 27 biofilms sampled from six locations in the Richmond Mine acid mine drainage system (Iron Mountain, CA) over a four-year period. We observed six distinct genotypes that are recombinants comprised of segments from two parental genotypes. Community genomic analyses revealed additional low abundance recombinant variants. The dominance of some genotypes despite a larger available genome pool, and patterns of spatiotemporal distribution within the ecosystem, indicate selection for distinct recombinants. Genes involved in motility, signal transduction and transport were overrepresented in the tens to hundreds of kilobase recombinant blocks, whereas core metabolic functions were significantly underrepresented. Our findings demonstrate the power of PIGT and reveal that recombination is a mechanism for fine-scale adaptation in this system.},
doi = {10.1111/j.1462-2920.2008.01769.x},
url = {https://www.osti.gov/biblio/958921}, journal = {Environmental Microbiology},
issn = {1462-2912},
number = 2,
volume = 11,
place = {United States},
year = {Thu Jan 01 00:00:00 EST 2009},
month = {Thu Jan 01 00:00:00 EST 2009}
}