The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae

Abstract

Microbial communities are comprised of many species that coexist on small spatial scales. This is difficult to explain because many interspecies interactions are competitive, and ecological theory predicts that one species will drive the extinction of another species that competes for the same resource. Conversely, evolutionary theory proposes that natural selection can lead to coexistence by driving competing species to use non-overlapping resources. However, evolutionary escape from extinction may be slow compared to the rate of competitive exclusion. Here, we use experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae to study the evolution of coexistence in species that compete for resources. We find that while E. coli usually outcompetes S. cerevisiae in co-culture, a few populations evolved stable coexistence after ~1000 generations of coevolution. We sequenced S. cerevisiae and E. coli populations, identified multi-hit genes, and engineered alleles from these genes into several genetic backgrounds, finding that some mutations modified interactions between E. coli and S. cerevisiae. Together, our data demonstrate that coexistence can evolve, de novo, from intense competition between two species with no history of coevolution.

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Fig. 1: Experimental co-evolution of E. coli and S. cerevisiae.
Fig. 2: The evolution of stable E. coliS. cerevisiae co-cultures.
Fig. 3: The genetic causes of co-culture and monoculture specific evolution.
Fig. 4: Amino acid substitutions from BUL1 (D334G), YFR018C (L7F), and TIF35 (V272L) were engineered into the ancestral genetic background of S. cerevisiae (“Methods”).
Fig. 5: The genetic causes of E. coli adaptation.
Fig. 6: Mutations in fhuA cause co-culture specific adaptation.

Data availability statement

Raw sequencing reads have been deposited in the NCBI Biosample database with Bioproject ID: PRJNA668197

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Acknowledgements

MJM was supported by ARC Discovery Grant (DP180102161) and an ARC Future Fellowship (FT170100441).

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MJM conceived the study, JNB, ALS, JMV, TDA and MJM designed and carried out experiments, JNB, ALS, LCW and MJM analysed the data. JNB and MJM wrote the paper. All authors have read and approved the final manuscript.

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Correspondence to Michael J. McDonald.

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Barber, J.N., Sezmis, A.L., Woods, L.C. et al. The evolution of coexistence from competition in experimental co-cultures of Escherichia coli and Saccharomyces cerevisiae. ISME J (2020). https://doi.org/10.1038/s41396-020-00810-z

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