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Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations

View ORCID ProfileJessica A. Lee, Siavash Riazi, Shahla H. Nemati, View ORCID ProfileAndreas E. Vasdekis, View ORCID ProfileBenjamin J. Ridenhour, Christopher H. Remien, View ORCID ProfileChristopher J. Marx
doi: https://doi.org/10.1101/529156
Jessica A. Lee
1Department of Biological Sciences, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
6Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
7Global Viral, San Francisco, CA
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Siavash Riazi
2Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
6Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
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Shahla H. Nemati
3Department of Physics, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
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Andreas E. Vasdekis
3Department of Physics, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
6Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
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Benjamin J. Ridenhour
4Department of Mathematics, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
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Christopher H. Remien
4Department of Mathematics, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
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Christopher J. Marx
1Department of Biological Sciences, University of Idaho, Moscow, ID
5Center for Modeling Complex Interactions, University of Idaho, Moscow, ID
6Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
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Abstract

While microbiologists often make the simplifying assumption that genotype determines phenotype in a given environment, it is becoming increasingly apparent that phenotypic heterogeneity (in which one genotype generates multiple phenotypes simultaneously even in a uniform environment) is common in many microbial populations. The importance of phenotypic heterogeneity has been demonstrated in a number of model systems involving binary phenotypic states (e.g., growth/non-growth); however, less is known about systems involving phenotype distributions that are continuous across an environmental gradient, and how those distributions change when the environment changes. Here, we describe a novel instance of phenotypic diversity in tolerance to a metabolic toxin within wild-type populations of Methylobacterium extorquens, a ubiquitous phyllosphere methylotroph capable of growing on the methanol periodically released from plant leaves. The first intermediate in methanol metabolism is formaldehyde, a potent cellular toxin that is lethal in high concentrations. We have found that at moderate concentrations, formaldehyde tolerance in M. extorquens is heterogeneous, with individual cells’ minimum tolerance levels ranging between 0 mM and 8 mM. This form of heterogeneity is continuous in terms of threshold (in the range of maximum tolerances possible), yet binary in outcome (at a given formaldehyde concentration, cells either grow normally or die, with no intermediate phenotype), and it is not associated with any detectable genetic mutations. Moreover, tolerance distributions within the population are dynamic, changing over time in response to growth conditions. We characterized this phenomenon using bulk liquid culture experiments, colony growth tracking, flow cytometry, time-lapse microscopy, and genome resequencing. Finally, we used mathematical modeling to better understand the processes by which cells change phenotype, and found evidence for both stochastic, bidirectional phenotype diversification and responsive, directed phenotype shifts, depending on the growth substrate and the presence of toxin.

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Posted January 23, 2019.
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Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Jessica A. Lee, Siavash Riazi, Shahla H. Nemati, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
bioRxiv 529156; doi: https://doi.org/10.1101/529156
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Microbial phenotypic heterogeneity in response to a metabolic toxin: continuous, dynamically shifting distribution of formaldehyde tolerance in Methylobacterium extorquens populations
Jessica A. Lee, Siavash Riazi, Shahla H. Nemati, Andreas E. Vasdekis, Benjamin J. Ridenhour, Christopher H. Remien, Christopher J. Marx
bioRxiv 529156; doi: https://doi.org/10.1101/529156

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