Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains

PLoS Comput Biol. 2022 Oct 3;18(10):e1010565. doi: 10.1371/journal.pcbi.1010565. eCollection 2022 Oct.

Abstract

Although closely related, bacterial strains from the same species show significant diversity in their growth and death dynamics. Yet, our understanding of the relationship between the kinetic parameters that dictate these dynamics is still lacking. Here, we measured the growth and death dynamics of 11 strains of Escherichia coli originating from different hosts and show that the growth patterns are clustered into three major classes with typical growth rates, maximal fold change, and death rates. To infer the underlying phenotypic parameters that govern the dynamics, we developed a phenomenological mathematical model that accounts not only for growth rate and its dependence on resource availability, but also for death rates and density-dependent growth inhibition. We show that density-dependent growth is essential for capturing the variability in growth dynamics between the strains. Indeed, the main parameter determining the dynamics is the typical density at which they slow down their growth, rather than the maximal growth rate or death rate. Moreover, we show that the phenotypic landscape resides within a two-dimensional plane spanned by resource utilization efficiency, death rate, and density-dependent growth inhibition. In this phenotypic plane, we identify three clusters that correspond to the growth pattern classes. Overall, our results reveal the tradeoffs between growth parameters that constrain bacterial adaptation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological*
  • Escherichia coli*

Grants and funding

This work is supported by the Rappaport Family Institute for Research in the Medical Sciences (YS), the Russell Berrie Nanotechnology Institute (YS), UOM-Israel collaboration (YS), The Wolfson Foundation (YS), ISF grant 1860/21 (RH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.