The functional basis of adaptive evolution in chemostats

Abstract

Two central problems in biology are determining the molecular basis of adaptive evolution and understanding how cells regulate their growth. The chemostat is a device for culturing cells that provides great utility in tackling both of these problems: it enables precise control of the selective pressure under which organisms evolve and it facilitates experimental control of cell growth rate. The aim of this review is to synthesize results from studies of the functional basis of adaptive evolution in long-term chemostat selections using Escherichia coli and Saccharomyces cerevisiae. We describe the principle of the chemostat, provide a summary of studies of experimental evolution in chemostats and use these studies to assess our current understanding of selection in the chemostat. Functional studies of adaptive evolution in chemostats provide a unique means of interrogating the genetic networks that control cell growth, which complements functional genomic approaches and quantitative trait loci (QTL) mapping in natural populations. An integrated approach to the study of adaptive evolution that accounts for both molecular function and evolutionary processes is critical to advancing our understanding of evolution. By renewing efforts to integrate these two research programs experimental evolution in chemostats is ideally suited to extending this functional synthesis to the study of genetic networks.

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

“…The fact that E . coli adapted to the gut environment by up-regulating (directly or indirectly) nutrient transport functions bears an interesting resemblance to the observations of microbes adapting to limiting nutrient conditions in chemostats [42]. For instance, E .…”

Advanced continuous cultivation methods for systems microbiology

“…2). However, such stepwise chemostats are very time-consuming due to the need to stabilize the culture after each step change, making them also prone to the emergence of unwanted mutations (Ferenci, 2007;Gresham & Hong, 2015;Harder et al, 1977;Helling et al, 1987;Novick & Szilard, 1950). Both of these issues can be circumvented by using changestat cultivation methods (e.g.…”

“…Additionally, a very long changestat experiment due to slow acceleration risks the of emergence of unwanted mutations in the cell culture, similar to what is seen in chemostats (Ferenci, 2007;Gresham & Hong, 2015;Harder et al, 1977;Helling et al, 1987;Novick & Szilard, 1950). Importantly, it has been shown using whole-genome DNA sequencing that no mutations arose during a regular-length changestat study of cell physiology in glucose-limited E. coli A-stat cultures if appropriate acceleration is used .…”

Carbon Availability Modifies Temperature Responses of Heterotrophic Microbial Respiration, Carbon Uptake Affinity, and Stable Carbon Isotope Discrimination

“…When C availability decreases, microorganisms can adjust their ability to take up C as a compensatory measure (Death et al, 1993; Williams et al, 1994; Ferenci, 1999; Gresham and Hong, 2015). The ability to take up C, or C uptake affinity, is often defined as the ratio of the maximum uptake rate ( V max ) to the half-saturation concentration of C ( k m ) of the Michaelis-Menten function (Healey, 1980; Aksnes and Egge, 1991; Button, 1993; Reay et al, 1999).…”