High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy

Abstract

Background: Microbes live in dynamic environments where nutrient concentrations fluctuate. Quantifying fitness in terms of birth rate and death rate in a wide range of environments is critical for understanding microbial evolution and ecology.

Methods: Here, using high-throughput time-lapse microscopy, we have quantified how Saccharomyces cerevisiae mutants incapable of synthesizing an essential metabolite (auxotrophs) grow or die in various concentrations of the required metabolite. We establish that cells normally expressing fluorescent proteins lose fluorescence upon death and that the total fluorescence in an imaging frame is proportional to the number of live cells even when cells form multiple layers. We validate our microscopy approach of measuring birth and death rates using flow cytometry, cell counting, and chemostat culturing.

Results: For lysine-requiring cells, very low concentrations of lysine are not detectably consumed and do not support cell birth, but delay the onset of death phase and reduce the death rate compared to no lysine. In contrast, in low hypoxanthine, hypoxanthine-requiring cells can produce new cells, yet also die faster than in the absence of hypoxanthine. For both strains, birth rates under various metabolite concentrations are better described by the sigmoidal-shaped Moser model than the well-known Monod model, while death rates can vary with metabolite concentration and time.

Conclusions: Our work reveals how time-lapse microscopy can be used to discover non-intuitive microbial birth and death dynamics and to quantify growth rates in many environments.

Graphical abstract

Keywords

Saccharomyces cerevisiae / fluorescence microscopy / microbial growth / birth rate / death rate

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SUPPLEMENTARY MATERIALS

The supplementary materials can be found online with this article at https://doi.org/10.1007/s40484-018-0160-7.

ACKNOWLEDGEMENTS

We thank Jose Pineda for performing the experiment in Supplementary Figure S3 and Li Xie for consultation regarding models.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Samuel F. M. Hart, David Skelding, Adam J. Waite, Justin C. Burton and Wenying Shou He declare that they have no conflict of interests.

All procedures performed in studies involving animals were in accordance with the ethical standards of the institution or practice at which the studies were conducted, and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.

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