Experimental Evolution Expands the Breadth of Adaptation to an Environmental Gradient Correlated With Genome Reduction.

Masaomi Kurokawa,Bei-Wen Ying,Issei Nishimura

doi:10.3389/fmicb.2022.826894

Abstract

Whether and how adaptive evolution adjusts the breadth of adaptation in coordination with the genome are essential issues for connecting evolution with ecology. To address these questions, experimental evolution in five Escherichia coli strains carrying either the wild-type genome or a reduced genome was performed in a defined minimal medium (C0). The ancestral and evolved populations were subsequently subjected to fitness and chemical niche analyses across an environmental gradient with 29 combinations of eight chemical components of the minimal medium. The results showed that adaptation was achieved not only specific to the evolutionary condition (C0), but also generally, to the environmental gradient; that is, the breadth of adaptation to the eight chemical niches was expanded. The magnitudes of the adaptive improvement and the breadth increase were both correlated with genome reduction and were highly significant in two out of eight niches (i.e., glucose and sulfate). The direct adaptation-induced correlated adaptation to the environmental gradient was determined by only a few genome mutations. An additive increase in fitness associated with the stepwise fixation of mutations was consistently observed in the reduced genomes. In summary, this preliminary survey demonstrated that evolution finely tuned the breadth of adaptation correlated with genome reduction.

Highlights

Microorganisms living in nature show highly diverse habitats as a consequence of local adaptation (Kawecki and Ebert, 2004) and are constrained by evolutionary costs (Bono et al, 2020)
The ecological niche is believed to be associated with genomic information (Alneberg et al, 2020), which is considered to be a result of adaptive evolution (Batut et al, 2014)
Direct adaptation mediated by experimental evolution (Figure 2) was found to trigger correlated adaptation to the environmental gradient, consistently in five E. coli strains carrying the reduced genomes of size variation (Figures 3–5)

Summary

Introduction

Microorganisms living in nature show highly diverse habitats (i.e., ecological niches) as a consequence of local adaptation (Kawecki and Ebert, 2004) and are constrained by evolutionary costs (Bono et al, 2020). Numerous studies have reported adaptation to a certain niche related to genetic causes, such as linkages between genome streamlining and niche partitioning (Graham and Tully, 2021), gene loss and niche shifts (Chu et al, 2021), genome reduction and habitat transition (Salcher et al, 2019), metabolic costs (Ankrah et al, 2018), genome architecture and habitat (Getz et al, 2018) or niche-directed evolution (Andrei et al, 2019). These findings provide strong evidence linking adaptive evolution to ecological niches in terms of the spatial and environmental differentiation of species. As environmental changes are more often gradual under temporal and spatial restrictions, whether the breadth of adaptation to environmental gradients is shaped by evolution is an intriguing question.

Methods

Results

Conclusion