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An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment


San Roman, Magdalena; Wagner, Andreas (2018). An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment. PLoS Computational Biology, 14(7):e1006340.

Abstract

Microorganisms modify their environment by excreting by-products of metabolism, which can create new ecological niches that can help microbial populations diversify. A striking example comes from experimental evolution of genetically identical Escherichia coli populations that are grown in a homogeneous environment with the single carbon source glucose. In such experiments, stable communities of genetically diverse cross-feeding E. coli cells readily emerge. Some cells that consume the primary carbon source glucose excrete a secondary carbon source, such as acetate, that sustains other community members. Few such cross-feeding polymorphisms are known experimentally, because they are difficult to screen for. We studied the potential of bacterial metabolism to create new ecological niches based on cross-feeding. To do so, we used genome scale models of the metabolism of E. coli and metabolisms of similar complexity, to identify unique pairs of primary and secondary carbon sources in these metabolisms. We then combined dynamic flux balance analysis with analytical calculations to identify which pair of carbon sources can sustain a polymorphic cross-feeding community. We identified almost 10,000 such pairs of carbon sources, each of them corresponding to a unique ecological niche. Bacterial metabolism shows an immense potential for the construction of new ecological niches through cross feeding.

Abstract

Microorganisms modify their environment by excreting by-products of metabolism, which can create new ecological niches that can help microbial populations diversify. A striking example comes from experimental evolution of genetically identical Escherichia coli populations that are grown in a homogeneous environment with the single carbon source glucose. In such experiments, stable communities of genetically diverse cross-feeding E. coli cells readily emerge. Some cells that consume the primary carbon source glucose excrete a secondary carbon source, such as acetate, that sustains other community members. Few such cross-feeding polymorphisms are known experimentally, because they are difficult to screen for. We studied the potential of bacterial metabolism to create new ecological niches based on cross-feeding. To do so, we used genome scale models of the metabolism of E. coli and metabolisms of similar complexity, to identify unique pairs of primary and secondary carbon sources in these metabolisms. We then combined dynamic flux balance analysis with analytical calculations to identify which pair of carbon sources can sustain a polymorphic cross-feeding community. We identified almost 10,000 such pairs of carbon sources, each of them corresponding to a unique ecological niche. Bacterial metabolism shows an immense potential for the construction of new ecological niches through cross feeding.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
Dewey Decimal Classification:570 Life sciences; biology
590 Animals (Zoology)
Uncontrolled Keywords:Ecology, Modelling and Simulation, Computational Theory and Mathematics, Genetics, Ecology, Evolution, Behavior and Systematics, Molecular Biology, Cellular and Molecular Neuroscience
Language:English
Date:24 July 2018
Deposited On:05 Mar 2019 14:38
Last Modified:25 Sep 2019 00:22
Publisher:Public Library of Science (PLoS)
ISSN:1553-734X
OA Status:Gold
Free access at:Publisher DOI. An embargo period may apply.
Publisher DOI:https://doi.org/10.1371/journal.pcbi.1006340
Project Information:
  • : FunderH2020
  • : Grant ID739874
  • : Project TitleNoiseRobustEvo - Noise and robustness in the evolution of novel protein phenotypes
  • : FunderSNSF
  • : Grant ID31003A_172887
  • : Project TitleRobustness and weakened selection in the adaptive evolution of fluorescent proteins

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