Coexisting ecotypes in long-term evolution emerged from interacting trade-offs

• Published in: Nature communications Vol. 14; no. 1; pp. 3805 - 8
• Main Authors: Mukherjee, Avik, Ealy, Jade, Huang, Yanqing, Benites, Nina Catherine, Polk, Mark, Basan, Markus
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 26.06.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 14/35; 631/181/2468; 631/181/2475; 631/326/2565/855; Acetates; Acetic acid; Biological Evolution; Breath tests; Coexistence; Computer Simulation; E coli; Ecological niches; Ecosystem; Ecotype; Ecotypes; Escherichia coli - genetics; Evolution; Experiments; Fermentation; Glucose; Humanities and Social Sciences; Mathematical models; Metabolism; multidisciplinary; Science; Science (multidisciplinary); Tradeoffs
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-39471-9

Evolution of complex communities of coexisting microbes remains poorly understood. The long-term evolution experiment on Escherichia coli (LTEE) revealed the spontaneous emergence of stable coexistence of multiple ecotypes, which persisted for more than 14,000 generations of continuous evolution. Here, using a combination of experiments and computer simulations, we show that the emergence and persistence of this phenomenon can be explained by the combination of two interacting trade-offs, rooted in biochemical constraints: First, faster growth is enabled by higher fermentation and obligate acetate excretion. Second, faster growth results in longer lag times when utilizing acetate after glucose is depleted. This combination creates an ecological niche for a slower-growing ecotype, specialized in switching to acetate. These findings demonstrate that trade-offs can give rise to surprisingly complex communities with evolutionarily stable coexistence of multiple variants in even the simplest environments. Previous, a long-term evolution experiment in E.coli resulted in spontaneous emergence of ecotypes that coexisted for more than 14,000 generations. Here, the authors show that the emergence and persistence of this phenomenon results from two interacting trade-offs, rooted in biochemical constraints.