Effects of hierarchical resource utilization on the biodiversity of microbial communities


Microbial communities are fascinatingly complex and diverse systems. Studies have shown that they can host hundreds of different species and that there can be several types of interaction between them: beyond direct competition for the same energy sources, for example, microbes can also exchange useful metabolic by-products or produce toxins. A recently emerged promising line of research consists in studying how the metabolism of the species hosted in a community influences its biodiversity. In particular, it is known that bacteria have hierarchical preferences for their energy source that seem to be “hardwired”: when a microbe like E. coli is grown in media containing several sugars, for example, it will always consume first only the one that ensures the fastest growth (i.e. glucose) and then switch to the one that ensure fastest growth among the remaining ones, and so on until all sugars are depleted. Even if these kind of phenomena are known to occur in nature, there have been very few attempts to study how they influence community structure and no one for community dynamics. The aim of this thesis is to use a resource-explicit consumer-resource model to investigate how community dynamics and the biodiversity of microbial ecosystems are influenced by having species with different hierarchical resource preferences. The project requires to study dynamical systems, from an analytical and especially a computational point of view.


  • For the consumer-resource model:
    • Chesson, P. (1990). MacArthur’s consumer-resource model. Theoretical Population Biology, 37(1), 26–38. DOI: 10.1016 /0040-5809(90)90025-Q
    • Posfai, A., Taillefumier, T., & Wingreen, N. S. (2017). Metabolic Trade-Offs Promote Diversity in a Model Ecosystem. Physical Review Letters, 118(2), 28103. DOI: 10.1103/PhysRevLett.118.028103
  • For an example of how hierarchical resource preferences can be used to study community structure:
    • Goyal, A., Dubinkina, V., & Maslov, S. (2018). Multiple stable states in microbial communities explained by the stable marriage problem. ISME Journal. DOI: 10.1038/s41396-018-0222-x
Collaborative LIPh
Collaborative Laboratory of Interdisciplinary Physics