Responses of synthetic microbial communities perturbed in multiplexed continuous bioreactors as an ecologically relevant proxy for microbial robustness prediction in natural and engineered ecosystems

Augelletti, Floriana [UCL] Agathos, Spiros N. [UCL] Stenuit, Benoit [Yachay Tech University, Ecuador]

Biological robustness is a key attribute of biosystems that guarantees the maintenance of structural organization and/or function performance in the face of disturbances and uncertainty. Particularly, microbial ecosystems exhibit specific robustness attributes arising from the assembly and interaction networks of diverse, heterogeneous communities challenged by fluctuating environmental conditions. Stability, resistance and ecological resilience of natural, host-associated and engineered microbial communities rely on specific trade-offs between modularity, taxonomic and functional diversity and redundancy. Because of the complexity of naturally-occurring microbial systems, synthetic ecology, i.e., the rational design and theory-driven manipulation of artificial microbial ecosystems, is highly relevant to decipher key biodiversity-stability relationships thanks to the analysis of replicate systems of lower complexity and higher controllability and reproducibility in the presence of specific perturbations. Here, we present the design and construction of multiplexed continuous bioreactors used as a microbial cultivation and perturbation platform for the assessment and prediction of microbial community robustness. Continuous culture systems can provide several advantages over batch systems, such as (i) perturbation experiments using microbial communities maintained under controlled and environmentally-relevant conditions (e.g., oligotrophic environments) and (ii) relevance to meta-omics approaches that require data obtained under rigorously defined and regulated conditions. The multiplexing of chemostats enables the simultaneous realization of biological replicates with appropriate controls to compare disturbance responses of planktonic cultures using sustained selective pressure (press disturbance), pulse perturbation, or both.