The enduring utility of continuous culturing in experimental evolution

Abstract

Studying evolution in the laboratory provides a means of understanding the processes, dynamics and outcomes of adaptive evolution in precisely controlled and readily replicated conditions. The advantages of experimental evolution are maximized when selection is well defined, which enables linking genotype, phenotype and fitness. One means of maintaining a defined selection is continuous culturing: chemostats enable the study of adaptive evolution in nutrient-limited environments in which growth is sub-maximal, whereas cells in turbidostats evolve in nutrient abundance that allows maximal growth. Although the experimental effort required for continuous culturing is considerable relative to the experimental simplicity of serial batch culture, the opposite is true of the environments they produce: continuous culturing results in simplified and constant conditions whereas serial batch cultures are complex and dynamic. The comparative simplicity of the selective environment that is unique to continuous culturing provides an ideal experimental system for addressing key questions in adaptive evolution.

Elucidating the molecular architecture of adaptation via evolve and resequence experiments

“…Consequently, parallelism is rarely observed at the level of individual mutations 79,105 , but instead at the gene level and often at higher levels of functional integration such as the operon or sets of functionally related genes (e.g., genes involved in cell shape) 79,103,104 . The genomic precision of targeting seems to depend on the selective regime employed including the media used for selection 89 as well as the mode of culture (chemostats versus batch culture) 106 . For example, antibiotic treatments select almost exclusively for mutations in the active site of very specific target genes 107 , whereas for less-specific environmental stressors in highly replicated E&R experiments many genes and alternative mutations among genes are recovered 64,79 .…”

Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation

“…In a chemostat, cells are maintained at a physiological steady state. A constant growth rate is achieved by the continuous influx of medium in which a single nutrient is limiting [48][49][50]. In a turbidostat on the other hand, there is continuous feedback between inflow of (nutrient abundant) medium and cell density [51].…”

“…Importantly, experimental evolution studies that select for adaptation to specific stresses, such as heat stress, nutrient limitation and drug treatments have revealed mutations in experimentally evolved lineages that closely resemble those found in natural populations, including specific SNPs, indels, chromosomal copy number variations and changes in ploidy [49,52,58,59]. The adaptive potential of specific genomic changes can be investigated by introducing the identified mutations into the ancestral background (Figure 3), as well as by studying (epistatic) interactions between the different mutations.…”

Experimental Microbial Evolution of Extremophiles

“…Under these conditions, microbes are advantageous as evolutionary models due to their large population size, short generation time, relatively small genome and generally high supply of mutations (Gresham and Dunham 2014). Extremophiles may exhibit elongated generation times and but maintain normal mutation rates (Grogan et al 2001), necessitating longer culture durations to achieve equivalent degrees of mutation formation.…”

“…The main difference is that nutrients are not limited, and that fresh medium introduction is proportional to maximum culture turbidity, resulting in maximum growth rates of microorganisms in mid-exponential phase (Gresham and Dunham 2014). Both the chemostat and turbidostat maintain a steady-state environment, but represent minimal or optimal resource conditions, respectively.…”