ERC Project – ECOADAPT

Adaptation Within Ecosystems

(2010-2015)

All natural populations are constantly subject to new mutations, and frequently face new environments, to which they adapt. Knowledge of the genetics of adaptation should provide the centre piece of a unified theory of evolution. Despite its extreme importance, the process of adaptation is far from being understood. How does the shape of distribution of fitness effects of mutations depend on the environment? How do biotic interactions affect the speed and mode of adaptation? are still open questions.

Experimental evolution with bacteria presents us with the opportunity to directly measure key parameters and to test theoretical predictions about the genetic basis of adaptive evolution in increasingly complex ecosystems. As Dobzansky pointed out “The greater the diversity of inhabitants in a territory, the more adaptive opportunities exist in it”.

In this project we combine different methods in a novel experimental evolution system to study adaptation of Escherichia coli in the context of its antagonistic interaction with cells of the innate immune system macrophages. The main goal of this research project is to measure rates and effects of adaptive mutations, as well as patterns of epistasis amongst beneficial mutations in environments with different strengths of abiotic versus biotic interactions.

Publications related with this project:

Moura de Sousa JA, Alpedrinha J, Campos PRA, Gordo I (2016) Competition and fixation of cohorts of adaptive mutations under Fisher geometrical model. PeerJ 4:e2256 https://doi.org/10.7717/peerj.2256

Ramiro RS, Costa H and Gordo I (2016), Macrophage adaptation leads to parallel evolution of genetically diverse Escherichia coli small-colony variants with increased fitness in vivo and antibiotic collateral sensitivity. Evol Appl, 9: 994–1004. doi:10.1111/eva.12397 Press coverage

Durão P, Gülereşi D, Proença J, Gordo I (2016) Enhanced Survival of Rifampin- and Streptomycin-Resistant Escherichia coli Inside Macrophages. Antimicrobial Agents and Chemotherapy. 60(7):4324-4332. doi:10.1128/AAC.00624-16. Press coverage

Azevedo M, Sousa A, Moura de Sousa J, Thompson JA, Proença JT, Gordo I (2016) Trade-Offs of Escherichia coli Adaptation to an Intracellular Lifestyle in Macrophages. PLoS ONE. 11(1):e0146123. doi:10.1371/journal.pone.0146123.

Moura de Sousa JA, Sousa A, Bourgard C, Gordo I (2015) Potential for Adaptation Overrides Cost of Resistance. Future Microbiol. 10:1415-31. doi: 10.2217/fmb.15.61

Durão P, Trindade S, Sousa A & Gordo I (2015) Multiple Resistance at no cost: Rifampicin and Streptomycin a dangerous liaison in the spread of antibiotic resistance. Mol Biol Evol. 32(10):2675-80. doi: 10.1093/molbev/msv143

Gordo I, M Miskinyte (2014) Fitness Measurements of Evolved Esherichia coli. Bio-protocol 4 (17), e1228. DOI: 10.21769/BioProtoc.1228

Gordo I, M Miskinyte (2014) Evolution of Escherichia coli to macrophage cell line. Bio-protocol 4 (17), e1227. DOI: 10.21769/BioProtoc.1227

Miskinyte, M., Sousa, A., Ramiro, R.S., de Sousa, J.A.M., Kotlinowski, J., Caramalho, I, Magalhães, S., Soares, M.P. & Gordo, I. 2013 The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages. PLoS Pathog. 9(12): e1003802. (doi:10.1371/journal.ppat.1003802) Press coverage

Sousa, A., Bourgard, C., Wahl, L.M. & Gordo, I. 2013 Rates of transposition in Escherichia coli. Biol. Lett. 9: 20130838 (doi:10.1098/rsbl.2013.0838)

Perfeito, L., Sousa, A., Bataillon, T. & Gordo, I. 2013 Rates of fitness decline and rebound suggest pervasive epistasis. Evolution. (doi: 10.1111/evo.12234)

de Sousa, J. A. M., P. R. A. Campos, and I. Gordo. 2013. An ABC method for estimating the rate and distribution of effects of beneficial mutations. Genome Biology and Evolution.

Gordo, I. & Campos, P. R. A. 2013 Evolution of clonal populations approaching a fitness peak. Biol. Lett. 9. (doi:10.1098/rsbl.2012.0239)

Miskinyte, M. & Gordo, I. 2013 Increased Survival of Antibiotic-Resistant Escherichia coli inside Macrophages. Antimicrob. Agents Chemother. 57, 189–195. (doi:10.1128/AAC.01632-12)

Trindade, S., Sousa, A. & Gordo, I. 2012 Antibiotic Resistance and Stress in the Light of Fisher’s Model. Evolution 66, 3815–3824. (doi:10.1111/j.1558-5646.2012.01722.x)

Brito, P. H., Rocha, E. P. C., Xavier, K. B. & Gordo, I. 2013 Natural Genome Diversity of AI-2 Quorum Sensing in Escherichia coli: Conserved Signal Production but Labile Signal Reception. Genome Biol. Evol. 5, 16–30. (doi:10.1093/gbe/evs122)

Gordo, I., Perfeito, L. & Sousa, A. 2011 Fitness Effects of Mutations in Bacteria. J. Mol. Microbiol. Biotechnol. 21, 20–35. (doi:10.1159/000332747)