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Survival dynamics of starving bacteria are determined by ion homeostasis that maintains plasmolysis

Abstract

The ability to survive starvation is an integral part of bacterial fitness and determines composition, turnover and biodiversity in microbial ecosystems. Starving bacteria enter a state known as plasmolysis in which their cytoplasm contracts from the cell wall. Plasmolysis is often thought to be a pathological, passive condition, arising automatically from the lack of ATP. Here we show that contrary to this notion, maintaining plasmolysis is an active, ATP-consuming state that is essential for starvation survival. We show that ion homeostasis to maintain plasmolysis consumes the largest part of the energy budget of starving cells and directly determines death rates in starvation. Our mathematical model accurately predicts death rates for various starvation conditions and perturbations. This enabled the development of an optimized starvation medium that would be ideally suited for preserving and transplanting natural microbial communities by maintaining viability but preventing outgrowth of a subset of the species.

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Fig. 1: Survival dynamics of E. coli in carbon starvation.
Fig. 2: Simulation of maintenance of ion homeostasis.
Fig. 3: Cost of ion homeostasis determines the death rate.
Fig. 4: Rescued starvation survival in a low-salt, osmo-balanced medium.

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All data analysed are available in the supporting information. Raw microscopy data and strains can be shared upon request. Source data are provided with this paper.

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Acknowledgements

We thank S. Jun for sharing strain VIP205, M. Kirschner for helping us with the QPM and R. Ward for many helpful suggestions. This project was supported by NIGMS Maximizing Investigators’ Research Award (Grant No. 5R35GM137895) and a Harvard Medical School Junior Faculty Armenise grant to M.B. S.J.S. was supported by the European Molecular Biology Organization through a long-term fellowship (ALTF 782-2017) and the Human Frontier Science Program through a long-term fellowship (LT000597/2018). M.P. was supported by the Harvard College Research Program. E.A. was supported by the Harvard College Research Program and the Program for Research in Science and Engineering at Harvard. X.L. and S.O. were supported by NIH award AG073341. Microscopy was performed at the Nikon Imaging Center at Harvard Medical School. Electron microscopy was performed at the Center for Nanoscale Systems at Harvard University.

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S.J.S. and M.B. conceived this study, designed the experiments and developed the theory. S.J.S. and M.P. performed the experiments with help from A.M. in electron microscopy and QPM imaging experiments. S.J.S., E.A. and M.B. performed the modelling. S.O. contributed to the QPM instrumentation. S.O. and X.L. designed the QPM image processing pipeline. Y.F.C. constructed the strains. C.A. contributed to the data analysis and ideas on membrane integrity. S.J.S. and M.B. wrote the paper with input from M.P., A.M., E.A., C.A., X.L. and S.O.

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Correspondence to Severin Schink or Markus Basan.

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Nature Physics thanks Marco Cosentino Lagomarsino and Hyun Youk for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Starvation of other substrates and of other bacterial species.

(A) Six gram-positive and gram-negative bacteria starved in N+C- medium, with previous growth on N + C+ with 0.1% glucose. (B) Starvation of the same bacteria as panel B, but in ‘osmo-balanced’ medium, identical to Fig. 4. (C) Comparison of death rates in N+C- (black) and low-salt, osmo-balanced medium (green). In all bacteria death rate in low-salt, osmo-balanced medium is slower than in N+C-, with the effect size being different for individual bacterial species.

Source data

Extended Data Fig. 2 Characterization of cellular dynamics during starvation.

(A) Length of the cytoplasm of 25 individual bacteria measured by thresholding in phase contrast (grey, cut off 1 h before lysis) and the average of 14,498 bacteria (red). (B) Histogram of the contraction of the cytoplasm in individual bacteria at 24 h. Note that in the vast majority of bacteria (99.7%), the cytoplasm shrunk. (C) Surface electron micrographs (SEM) of E. coli during growth show homogenous ridges of the cell envelope. In starvation the ridges on the surface are deeper, and a ‘sock-like’ structure is visible where the cytoplasm has contracted. In a dead cell, the surface is smooth, indicating that the surface structure is actively maintained. (D) Stretching of the cell envelope measured by thresholding in phase contrast. Cell envelope stretching is defined as the maximum length of the cell envelope divided by the average length of the cell envelope prior to expansion. (E) Increase of propidium iodide (PI) staining intensity upon lysis. For about 87% of bacteria a clear increase of staining was observed. A smaller subpopulation of 13% showed no discernable increase of biomass, possibly because DNA, the agent being stained by PI, was expelled upon lysis. (F) Loss of biomass distribution, measured as the ratio of the average biomass up to 6 h prior to lysis and the average biomass 9 h after lysis). # of bacteria: 34.

Source data

Extended Data Fig. 3 Impact of DiBac4(3) staining on lysis dynamics in a side-by-side comparison.

A no-flow chamber with two channels was used, and both channels were filled with the cells from the same culture. (A & B) Fluorescence signal of PI of individual cells over time (pixels along a column) for cultures stained either with PI and DiBac4(3) (4447 cells) or only with PI (5254 cells). Cells are sorted according to their time-point of lysis, defined as the first time-point when PI fluorescence signal crossed a threshold. Because cells stained with both DiBac and PI showed a lower PI fluorescence signal, the threshold used for DiBac4(3) + PI was chosen lower than for PI only. (C) Viability, defined as the fraction of cells that have not yet crossed the threshold defined in PI signal, decreases similarly for both cases. While the overall survival curve is similar between both experiments, there is a slight increase in death in early starvation (0 to 0.5 days) for cultures stained with DiBac4(3). (D) The delay between swelling and lysis was calculated as the time difference between the maximum increase in length prior to the cell crossing the PI threshold. The delay for DiBac4(3) and PI-stained cells is \(\tau =\left(2.4\pm 1.2\right){\rm{h}}\) and for PI only we obtained \(\tau =\left(2.5\pm 1.2\right){\rm{h}}\), obtained by measuring mean and standard deviation in the regime from 0 to 10 h.

Source data

Extended Data Fig. 4 Recovery after nutrient addition.

E. coli, previously grown on minimal medium supplemented with glucose, were starved by washing and transferred to a chip with attached medium reservoirs. After 14.4 h (red dashed lines in panels A-D) fresh minimal medium with 0.2% glucose was flushed through the chip by exchanging the fluid in the reservoirs. Length, DiBac4(3) and PI fluorescence was recorded throughout starvation and recovery. DiBac4(3) is an indicator of membrane potential, while PI indicates lysis. Only cells that could be tracked for at least 2.5 h after glucose addition are included in the analysis (5256 total). (A, C) Length, normalized to the first 3 hours of starvation of individual cells that were either polarized or depolarized. DiBac4(3) thresholded at 150 A.U. Percentages indicate the fraction of cells of the respective classification that were able to recover within the time course of the experiment. (B, D) DiBac4(3) signal of the cells shown in panels A &C. Note that some bacteria in panel B depolarize after nutrient addition (orange arrows), while in panel D a cell can be seen that repolarizes (purple arrows). (E & F) Dibac4(3) at 14 h plotted against the maximum PI staining prior to 14 h for individual cells that either recovered or did not recover. Cells are only shown if they could be tracked for at least 2.5 h post glucose addition. Red lines indicated thresholds of ‘depolarization’ and ‘lysis’. Numbers indicate the number of cells in each quadrant. The depolarized, but not PI-stained cells in panel E had in common that they depolarized only shortly prior to nutrient supplementation (more than 1 h, less than 2 h), which indicates that depolarization is reversible unless it lasts too long. No PI-stained cell recovered.

Source data

Extended Data Fig. 5 Simulation with explicit nutrient recycling.

We used the same parameters as in the simulation shown in the main text but implemented nutrient recycling explicitly. Cell death would release nutrients into the medium, from where they are taken up by viable cells in a Michaelis-Menten type manner. (A) Viability in the simulation decreases exponentially. (B) Nutrients resources \({\boldsymbol{\nu }}\) of an individual cell (blue), with time average (red). Nutrient resources are constant during the simulation. (C) and (D) same as left panels, but with external nutrient supply. Simulation with alternative parameters: (E) Viability, (F) nutrient resources. In this implementation we reduced the Hill coefficient of membrane stretching to 5 and the Km of membrane stretching to 0.4. Death rate is unchanged due to the self-adjusting manner of the system (compare to panels A-D).

Extended Data Fig. 6 Titration of cell length with ptac-ftsZ, induced with IPTG during growth.

Dark shades of cyan indicate high expression of ftsZ, while bright shades indicate low expression of ftsZ. (A) Cumulative distribution of cell length for different induction levels (cyan) and wild-type (red). Note that at low induction levels the spread of the distribution increases. (B) Example images of the lowest and highest induction of FtsZ.

Source data

Extended Data Fig. 7 Propidium iodide and DiBac4(3) staining.

(A) Viability of E. coli after 24 h of starvation in the presence of either DiBac4(3) or Propidium Iodide at the indicated concentrations show no significant decrease in viability compared to an untreated control culture. Error bars show standard deviation of three biological replicates. (B) Propidium iodide staining dynamics of individual viable bacteria stained for 24 h in batch, washed and resuspended in fresh, carbon-free and stain-free medium. (C) Distribution of staining rates (slope of exponential fits to PI fluorescence signal) in carbon-free and stain-free medium. Mean unstaining rate is slow compared to the timescale of the experiment, meaning that staining can be considered irreversible. (D) Example of a PI staining time-trace. Lysis leads to a rapid increase of PI staining. Prior to lysis, we observe a slow increase of permeability. Because PI staining is irreversible, the slope of the absolute fluorescence signal is a measure for the total permeability of a bacterium. (E) Comparison of the permeability (measured between 0 and 10 h after entry to starvation) for a culture permeabilized with 1 mM EDTA compared to control.

Source data

Extended Data Fig. 8 Effect of MOPS on death rate.

MOPS, balanced with KOH to pH7 was to culture media, such as the base concentration of N-C- medium remained constant. Data points and error bars show mean and standard deviation of three biological repeats. Compare this figure to Fig. 3C, where 0.5 M NaCl or KCl led to a 10-fold increase of death rate.

Source data

Extended Data Fig. 9 Effect of medium composition on death rate.

All cultures were grown in regular N + C+ medium supplemented with 10 mM glycerol and starved by switching medium. Reference: regular N + C- medium (red) n = 3. Change in medium concentration means that the starvation medium was prepared with increased or decreased concentrations of all N + C- salts (white), n = 1. In all conditions, the concentration of the phosphate buffer was sufficient to balance the pH during starvation, checked with pH strips.

Source data

Extended Data Fig. 10 Dependence of the maintenance rate on the medium.

(A) Example of a lag time measurement used for quantification of maintenance rate. After 1 day in starvation the culture in minimal medium with glucose as the previous carbon source we readded a small concentration of glucose (40 µM) and measured viability (grey) relative to a control without glucose addition (black). Using the average change in viability \({{\bf{K}}}^{{\boldsymbol{-}}{\bf{1}}}{\sum }_{{\bf{k}}}{{\bf{N}}}_{{\bf{k}}}^{{\boldsymbol{+}}}/{{\bf{N}}}_{{\bf{k}}}^{{\boldsymbol{-}}}\) where k are individual data points and \({\bf{K}}\) is the total number of data points per lag time (here: 3) and the death rate \({\boldsymbol{\gamma }}\), determined using the entire death curve shown in Fig. 4. Note that to achieve the change in viability (here: 47%) by growth, the culture would require addition of at least 500 µM. Concentrations of glucose added in the experiment are below levels for which growth is observed. Details on the maintenance rate protocol can be found in Ref. 5. (B, C) Lag times of three independent experiments, where each culture was split, and varying glucose concentrations were added (symbols correspond to identical experiments). Maintenance rate \({\boldsymbol{\beta }}\) is extracted as the inverse of the slope. Maintenance rate in N + C- minimal medium is around 10-fold higher than in ‘Osmo-balanced’ minimal medium.

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Schink, S., Polk, M., Athaide, E. et al. Survival dynamics of starving bacteria are determined by ion homeostasis that maintains plasmolysis. Nat. Phys. (2024). https://doi.org/10.1038/s41567-024-02511-2

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