Comparison of ecological and evolutionary strategies to address bacterial genome reduction

Biological adaptation has traditionally been regarded as a process driven by evolution, as well as an ecological consequence of the niche reconstruction of habitats. The question remains whether direct niche reconstruction and evolution result in comparable adaptiveness. Our study addresses this question by establishing a comparative framework designed to compare the strategies of niche optimization and experimental evolution for an increase in bacterial fitness. To address this issue, we employed two approaches in parallel, using the Escherichia coli strain carrying a reduced genome. As an evolutionary strategy, we conducted experimental evolution in a defined minimal medium to acquire the evolved strains carrying genetic mutations that compensate for the reduced genome. As an ecological strategy, we employed machine learning to predict and optimize the chemical compositions of the minimal medium used for experimental evolution. The results showed that both strategies successfully increased the growth fitness of the genome-reduced Escherichia coli strain. Transcriptome analysis was performed to identify the similarities and differences in the changes in gene expression caused by the two strategies. Specific biological processes and transcriptional regulations were observed in response to niche optimization and experimental evolution. The findings provided us with insights into how niche reconstruction and genome evolution compensated for the genome reduction in bacteria. Our study demonstrated that biological adaptation can be confined to genetic changes during evolution as well as achieved by reconfiguring the niche environment, which is comparable to fitness increase.