About the IAP

The role of ecological theory in microbial ecology has until now been neglected. Most microbiologists and ecologist consider certain ecological theories as proven, however when the scientific literature is examined more in detail, only indirect proof is given. Within this project, we will employ straightforward approaches using in vitro and in silico “synthetic ecosystems” to test new microbial ecological hypotheses. These experiments will be designed to specifically examine research hypotheses. The role of (i) metabolic networking, (ii) community dynamics, (iii) community structure (richness, evenness), (iv) community architecture, (v) cell to cell interactions, (vi) genetic interactions, (vii) invasion etc. on ecosystem performance will be examined in the different Work Packages (WPs).

Work packages

An overview of the WPs is given in Figure 1. In WP1 to WP4, in vitro synthetic ecosystems containing synthetic communities will be used to examine microbial interactions with biotic and abiotic factors in increasingly complex systems. The synthetic ecosystems will be directed towards 3 different ecosystems, i.e., sandfilters used for drinking water purification, soil and marine sediments. The synthetic microbial communities will be assembled using relevant mixtures of isolated species from culture collections. As such, for each ecosystem, a model microbial community is composed. Since these species are well characterised on a physiological and genomic level, their interactions can be studied in detail using of specialised techniques. The four first WP packages will be supported by a fifth WP where the experiments are in parallel, simulated in silico. This unique coupling of mathematical and experimental ecological theory development will permit us to test basic ecological theories on microbial communities

Figure 1: Overview of the different WPs and ecosystems that are considered. To test the ecological theories, experiments with increased complexity will be used from WP1 to WP4, and validated by in silico simulation in WP5 that will be carried out in parallel.

  • WP1: Simple, but high throughput approaches will be applied to test the effect of microbial community composition (richness, evenness, diversity, architecture, species characteristics…) on certain ecological phenomena (e.g. invasion, horizontal gene transfer, functionality). The experiments will be performed in small volume systems (designated as microcosms) that allow high throughput analysis of hundreds to thousands of experiments simultaneously. Experimental design and statistical analysis of these complex setups is crucial, and therefore in this WP, the integration of mathematical modelling with high-throughput microbial microcosm setups will be central.
  • WP2: High throughput methodologies will be used to study the influence of environmental stressors and/or stimuli on these model microbial communities. Resilience and robustness of the ecosystems in relation to the environmental changes will be examined.
  • WP 3: The model microbial communities will be inoculated in their natural, but sterile habitats. This will allow us to study specific abiotic properties of the studied ecosystems such as the occurrence of shear stress, heterogeneity, and gradient formation.
  • WP4: The theories developed in the first three WPs will be evaluated with existing microbial ecosystems and the natural endogenous microbial communities.
  • WP5: In silico synthetic ecosystems will be used to mathematically approach the same ecological questions. Accurate spatiotemporal modelling techniques will help to answer experimental hypotheses and elucidate mechanisms underlying the observed data. WP5 interacts with all other WPs among all partners in a two-way fashion: all partners will deliver data that can be used to parameterize and validate the models, but on the other hand the models will elucidate interesting experiments that add to the proof of the theory.