Lindqvist, M. | Search bioRxiv

bioRxiv2026

Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation

Microbial communities frequently encounter recurrent antibiotic disturbance, yet how ecological, evolutionary, and environmental processes jointly shape the response remains unresolved. Here we experimentally disentangle these mechanisms using a 23-species bacterial community exposed to ampicillin pulses with pre-pulse and resistance priming. Pre-pulse priming preconditioned community composition toward resistant taxa, reducing compositional change during the main pulse. Resistance priming was the dominant determinant of community response, buffering compositional change, relaxing selection, and altering gene expression. This buffering arose from both evolution of higher resistance and accelerated ampicillin detoxification by a dominant degrader, which transiently reduced antibiotic effects and favoured non-degrading taxa. Yet buffering did not translate into better recovery: because resistance was coupled to competitive dominance, diversity remained comparable to or below that of ancestral communities, and dominance was reinforced. Together, we show that antibiotic history reshapes microbial disturbance response through coupled eco-evolutionary and environmental feedbacks, generating a trade-off between resistance and recovery.

evolutionary biology↗

bioRxiv2026

Ecological tristability driven by total carbon availability over resource complexity in a synthetic microbial community

Even though complex microbial communities are ubiquitous and provide essential services for natural and human-associated ecosystems, our knowledge about their assembly and dynamics is incomplete. There is an ongoing debate whether the behavior of complex communities can be predicted from the outcome of pairwise competition of species, and whether communities reach alternative stable states depending on the level and complexity of resource provided for growth. To estimate the effect of two resource gradients, total carbon availability and resource complexity, on the compositional dynamics of a complex microbial community, we conducted a 16-day serial passage experiment, transferring a 16-species synthetic community in 96 different resource environments. We observed that although both resource dimensions influenced community composition, total carbon exerted a considerably larger effect. Additionally, we saw the emergence of a tristable pattern along the total carbon gradient, a feature not observed for the resource complexity gradient. Using monoculture assays, we identified lag phase duration as the dominant predictor of competitive success at carbon extremes, with maximum growth rate increasing in importance as lag times converged. Total carbon availability thus structured community state transitions and regulated which growth trait governed competitive sorting. These results suggest the importance of total carbon level over resource complexity and identifying dominant species for the quest to successfully manage, maintain and manipulate complex microbial communities.

ecology↗