Engineering transitions between alternative stable states in a microbial ecosystem

Temporary perturbations (such as exposure to antibiotics) can threaten the stability of microbial ecosystems such as the human microbiome. However, there is still little knowledge on the mechanisms driving long-term community dynamics after short-term perturbations. Here, we experimentally study transitions between stable states in a two-species laboratory ecosystem, in which bistability results from the fact that the two species are inhibiting each other via incompatible pH modifications of the environment. We found that a broad range of temporary perturbations induced transitions from one stable state but not the other, revealing a striking difference in resilience between the two states. Interestingly, it was the slow growing species that dominated in the more resilient state, in contrast with the theoretical prediction from the Lotka-Volterra model (in which the fast grower is generally favored by short-term perturbations). Guided by a modified model, we found that Allee effects (cooperative growth) acting on the fast grower are able to explain its low resilience to perturbations. Our results illustrate that cooperative growth dynamics may play an important role in determining the resilience of complex communities to environmental perturbations.