Biology subjects

Pausio, S.

Publications and source records attributed to Pausio, S..

4 recordsLinked to original sources

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↗

bioRxiv2025

Normative assembly rule reveals fairness in microbial communities

Understanding and predicting how communities assemble is a paramount challenge in ecology. Here we address these questions normatively by comparing the ecological distribution of growth surplus to a game-theoretically fair distribution based on each species Shapley value. By analyzing in total 56 distinct community outcomes, we assess how fairly biomass is distributed in microbial communities displaying both competitive and cooperative interactions in different environmental conditions. We find examples of fair communities that closely follow their Shapley value across all environments as well as counterexamples where the true abundances deviate from the species objective contribution to community biomass. Our results give unique empirical insights into the distributive function of ecological dynamics and lay down the theoretical foundations of what might become a normative community assembly theory.

ecology↗

bioRxiv2025

Evolution induced state shifts in a long-term microbial community experiment

Biological communities are complex, dynamic systems that underpin ecosystem functionality1, yet their long-term dynamics and predictability remain poorly understood2. Understanding how Darwinian evolution shapes these systems through eco-evolutionary feedbacks is a central challenge in ecology and evolution. Experimental studies using simplified microbial assemblages have yielded important insights into the ecological principles governing community states3-5. However, an important knowledge gap is how selection within member species drives changes of community state in multispecies systems. Here, we present a four-year evolution experiment involving a 23-species synthetic bacterial community propagated in two environments: a control medium and the same medium supplemented with the antibiotic streptomycin. Through combined analyses of community composition and genome evolution, we quantified the temporal changes in species abundances and the evolutionary trajectories of individual community members. The extended duration of the experiment enabled the detection of adaptive mutations and community state shifts that occur only over long evolutionary timescales. We show that community dynamics are environment dependent and reproducible across replicates, and that evolution of streptomycin resistance in a previously streptomycin-sensitive species on its own can induce abrupt community state shifts. Our results provide a direct demonstration of eco-evolutionary feedbacks within a multi-species community, revealing how a single adaptive mutation can reorganize complex ecological networks.

ecology↗