Modelling microbial evolution: from ecological interactions to developmental programs

Enrico-Sandro Colizzi
INRIA - Lyon

Multicellular dynamics, long considered a hallmark of complex life, are now recognised as widespread among prokaryotes and microbial eukaryotes. Collective behaviours such as biofilm formation, fruiting body development, and filamentous growth appear to be a fundamental part of microbial life.

How, then, does multicellularity evolve? And what consequences does it have for an organism’s potential to adapt, diversify, and evolve novel traits? 

To address these questions, I will present two computational models of microbial multicellularity, one focused on bacterial biofilms and the other on eukaryotic multicellular life cycles. The first model, drawing on experiments in the multicellular bacterium Streptomyces coelicolor, shows how in-silico bacteria evolve a distinctive genome architecture that uses targeted DNA deletions to generate specialised cell types during colony development. The second model, exploring eukaryotic (amoeboid) cell interactions, demonstrates that multicellularity can be selected through emergent group-level dynamics. I then present the resulting reproductive strategies, which arise from the interplay between collective behavior and spatial heterogeneity in resources. A key feature of these models is that the resulting multicellular behaviours are not pre-defined but emerge autonomously through the evolution of genome, gene regulatory network and cell interactions. 

This work suggests that multicellular dynamics are central to understanding how bacterial behaviour and evolution unfold. Moreover, because these simulations require little input data, they are a practical framework for predicting microbial dynamics inemerging experimental systems.