During this project, I focused my research on the evolution of the adaptive niche. The adaptive niche could be defined as the space of parameters in which an organism can survive and reproduce. For instance, any organism can survive in only a limited section of environmental gradients like temperature, or pH (e.g. E. coli can survive from 0 to 42°C, while S. thermophilus can survive from 37 to 60°C).

We were interested in two different aspects of E. coli niche evolution: 1. adaptive processes involved during dramatic environmental changes, 2. adaptation to various antibiotic concentrations. To address these questions, we have developed a method (using flow cytometry) allowing to measure selection coefficients in E. coli with high precision.

The dynamics of niche evolution upon abrupt environmental change - Gallet et al. (2014)

Using this method we could study the evolution of E. coli adaptive niche when adapting to a drastic environmental variation. We started by studying the adaptation of E. coli to a dramatic pH variation. Several independent E. coli populations were grown for 2000 generations at pH 7, and than placed in the same medium but with pH = 5.3, at the limit of E. coli adaptive niche. In response to this important environmental variation, we observed that while the niche optimum shifted toward acidic pHs, the niche also got temporarily wider due to the selection of an increased phenotypic plasticity. Eventually, the niche recovered its initial width at the end of the adaptive process.

Evolution of bacteria specialization along an antibiotic dose gradient - Harmand et al. (2018)

Antibiotic resistance is a major and pressing worldwide issue. Resistance evolution is often considered in simplified ecological contexts: treated versus nontreated environments. In contrast, antibiotic usually present important dose gradients: from ecosystems to hospitals to polluted soils, in treated patients across tissues. However, we do not know whether adaptation to low or high doses involves different phenotypic traits, and whether these traits trade-off with each other. In this study, we investigated the occurrence of such fitness trade-offs along a dose gradient by evolving experimentally resistant lines of Escherichia coli at different antibiotic concentrations for ∼400 generations. Our results reveal fast evolution toward specialization following the first mutational step toward resistance, along with pervasive trade-offs among different evolution doses. We found clear and regular fitness patterns of specialization, which converged rapidly from different initial starting points. These findings are consistent with a simple fitness peak shift model as described by the classical evolutionary ecology theory of adaptation across environmental gradients. We also found that the fitness costs of resistance tend to be compensated through time at low doses whereas they increase through time at higher doses. This cost evolution follows a linear trend with the log-dose of antibiotic along the gradient. These results suggest a general explanation for the variability of the fitness costs of resistance and their evolution. Overall, these findings call for more realistic models of resistance management incorporating dose-specialization.