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Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments

Nature Microbiology volume 1, Article number: 16055 (2016) Cite this article

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Abstract

Most microorganisms live in environments where nutrients are limited and fluctuate over time. Cells respond to nutrient fluctuations by sensing and adapting their physiological state. Recent studies suggest phenotypic heterogeneity1 in isogenic populations as an alternative strategy in fluctuating environments, where a subpopulation of cells express a function that allows growth under conditions that might arise in the future2–9. It is unknown how environmental factors such as nutrient limitation shape phenotypic heterogeneity in metabolism and whether this allows cells to respond to nutrient fluctuations. Here, we show that substrate limitation increases phenotypic heterogeneity in metabolism, and this heterogeneity allows cells to cope with substrate fluctuations. We subjected the N2-fixing bacterium Klebsiella oxytoca to different levels of substrate limitation and substrate shifts, and obtained time-resolved single-cell measurements of metabolic activities using nanometre-scale secondary ion mass spectrometry (NanoSIMS). We found that the level of NH4+ limitation shapes phenotypic heterogeneity in N2 fixation. In turn, the N2 fixation rate of single cells during NH4+ limitation correlates positively with their growth rate after a shift to NH4+ depletion, experimentally demonstrating the benefit of heterogeneity. The results indicate that phenotypic heterogeneity is a general solution to two important ecological challenges—nutrient limitation and fluctuations—that many microorganisms face.

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Figure 1: Mixed-substrate metabolism of N2 and NH4+ by K. oxytoca populations under NH4+ limitation.
Figure 2: NH4+ limitation affects single-cell heterogeneity in N2 fixation and nif gene expression in chemostat-grown K. oxytoca populations.
Figure 3: Consequences of heterogeneity in N2 fixation for growth during a shift from limited NH4+ supply to NH4+ depletion.
Figure 4: Effect of heterogeneity in N2-fixing populations on initial population growth after a switch simulated with a stochastic growth model.

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Acknowledgements

The authors thank M. Zimmermann and T. Röösli for support during NanoSIMS and mRNA image segmentation, D. Franzke and D. Nini for support during NanoSIMS measurements, G. Klockgether and T. Max for IRMS measurements, and T. Egli, D.J. Kiviet, D.R. Johnson and H.-M. Fischer for discussions. The NanoSIMS instrument in the Laboratory for Biological Geochemistry was funded in part by the European Research Council Advanced Grant 246749 (BIOCARB) to A.M. This research was supported by a Leopoldina postdoctoral fellowship (LPDS 2009-42), a Marie-Curie Intra-European fellowship for career development (FP7-MC-IEF, 271929; Phenofix) and a Synthesis Grant of the ETH Zurich Center for Adaptation to a Changing Environment (ACE) to F.S., the Max Planck Society, ETH Zurich and Eawag.

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Authors and Affiliations

  1. Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Universitätsstrasse 16, 8092 Zurich, Switzerland

    Frank Schreiber & Martin Ackermann

  2. Department of Environmental Microbiology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland

    Frank Schreiber & Martin Ackermann

  3. Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany

    Sten Littmann, Gaute Lavik & Marcel M. M. Kuypers

  4. Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering (ENAC), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

    Stéphane Escrig & Anders Meibom

  5. Center for Advanced Surface Analysis, Institute of Earth Sciences, University of Lausanne, Lausanne, Switzerland

    Anders Meibom

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  1. Frank Schreiber
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Contributions

F.S., M.M.M.K. and M.A. designed the research. FS performed the experiments. S.L., S.E. and F.S. carried out the NanoSIMS measurements. S.L., G.L., S.E., A.M. and M.M.M.K. contributed analytical tools. F.S. and M.A. analysed data. F.S. and M.A. wrote the paper with input from all co-authors.

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Correspondence to Frank Schreiber.

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The authors declare no competing financial interests.

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Supplementary information

Sequence Information, Supplementary Figures 1-5, Table 1, Discussion and References. (PDF 537 kb)

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Schreiber, F., Littmann, S., Lavik, G. et al. Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments. Nat Microbiol 1, 16055 (2016). https://doi.org/10.1038/nmicrobiol.2016.55

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