Evolutionary rescue: The solution for microbial communities to survive environmental stress is self-sufficiency

Microorganisms –defined as very small living beings, invisible to the naked eye, comprising bacteria, fungi, viruses or others– naturally compete and cooperate in nature for survival. However, does ‘environmental stress’ to which they are subjected due to global changes, such as global warming, sea level rise or air pollution, affect them and to what extent?

Ignacio J. Melero-Jiménez, a researcher at the Department of Botany and Plant Physiology of the University of Malaga, has collaborated with an international scientific team that has shown, based on an experimental system that reproduces a mutualistic microbial community, that the most common evolutionary solution for two co-dependent organisms to survive extreme environmental change could be to become self-sufficient. 

This phenomenon is known as ‘evolutionary rescue’: a rapid genetic adaptation that allows organisms to avoid extinction in critical situations. In this case, mutualism is broken as an evolutionary solution to avoid extinction. The results of this study have been recently published in the scientific journal Nature Communications.

The research, conducted for more than two years, is the result of a postdoctoral stay of the UMA scientist, supported by the Margarita Salas Fellowship. The experimental works were initially carried out at the Hebrew University of Jerusalem (Israel) under the coordination of the researcher Jonathan Friedman and, subsequently, the genetic analysis and data processing took place at the Center for Plant Biotechnology and Genomics of the UPM-INIA/CSIC in Madrid, under the leadership of the specialist Alejandro Couce.

Genetic engineering

Together with five authors from these two scientific institutions, Melero-Jiménez has explored how microbial communities evolve when facing extreme stress conditions. For this purpose, they used a synthetic model based on two genetically engineered strains of the intestinal bacteria Escherichia coli, designed to depend strictly on each other: each strain produces an essential amino acid that the other needs to survive.

Specifically, the experimental phase of the study consisted in culturing these microbial communities under controlled laboratory conditions and subjecting them to situations of severe environmental stress, with the aim of observing how they responded evolutionarily over time. 

Experimental evolution, genome sequencing and phenotypic analyses

“We exposed these communities to different conditions of lethal stress and monitored their growth over multiple generations. For comparison, we used an ancestral strain that did not depend on any partner to survive. Interestingly, we observed that when mutualistic communities underwent stress the quickest evolutionary solution was to break down the mutualism,” says the UMA scientist.

The expert explains that they used an experimental evolution approach to analyze how the microbial community responded to stress. Interestingly, during the experiment they observed that, instead of strengthening mutualism, this breaks down under extreme conditions. In order to understand the mechanisms behind this breakdown, genetic and phenotypic techniques were used. The results were surprising: dependence on each other made these bacteria more vulnerable to stress. Instead, those who managed to fend for themselves were more likely to survive.

This finding suggests that while mutualism may be beneficial in a stable environment, it can become a disadvantage when conditions become adverse. Thus, it raises a big question: If cooperation is so common in nature, why does it seem so fragile when conditions change? “This research gives us new clues to understand how far cooperation between microbes can go when the environment becomes hostile”, concludes Melero-Jiménez.

...

Melero-Jiménez, I. J., Sorokin, Y., Merlin, A., Li, J., Couce, A., & Friedman, J. (2025). Mutualism breakdown underpins evolutionary rescue in an obligate cross-feeding bacterial consortium. Nature Communications. DOI:  10.1038/s41467-025-58742-1.