Section: Overall Objectives

Validate hypotheses and identify models with experimental data

Among our current collaborations and projects (ANR DIMIMOS, ANR DISCO, ARC VITELBIO, Agropolis Foundation BioInh, RNSC E-MICRAM), we have identified five experimental devices that we consider relevant for back and forth exchanges between models and real-world observations for the coming years.

1. Molecular fingerprints. The LBE at Narbonne is a world leader for one of these techniques, the SSCP (Single Strand Conformation Polymorphism) that allows to estimate the biodiversity of a microbial ecosystem and serve as a comparison instrument over time or between ecosystems. A similar kind of signal from the proteins expressions is also obtained within the ANR DIMIMOS with UMR MSE (Dijon).

2. Continuous cultures in chemostats. The chemostat device is the typical investigating device in microbiology. Spatial structures can be mimicked and controlled using interconnected chemostats. Because of contamination risks, experimentation in chemostat requires an adequate expertise which the LBE holds. We plan to launch new such experiments with microbial populations of interest for specialists of soil ecosystems, in collaboration with UMR Eco & Sols (Montpellier) and UMR Bioemco (Grignon).

3. Taylor-Couette reactors (with LBE Narbonne). These bioreactors are specifically designed for the culture of biofilms on coupons, that can be removed from the system for static analyses of biodiversity (SSCP) and microscopy. Experiments are already scheduled within a task of the ANR DISCO.

4. Flow-cell bioreactors (with Cemagref Antony). It consists in small capillary tubular reactors continuously fed by a pump, under a microscope that has been designed for a continuous acquisition of images. We aim to compare biofilm models with the information provide by theses images.

5. Micro-plates cultures (with UMR MSE Dijon and LBE Narbonne). It contains a hundred of small wells in each of which a microbial community is grown in batch on the available substrate. Optical density measurements allow one to monitor simultaneously the biomass growth in the wells. These devices are convenient to study the effects of different initial composition of the community under the same environmental conditions. We believe that it is also well suited to test neutral-like community models

Each measurement technique requires its own data analysis (filters, statistical analysis, image analysis...) to provide information that are relevant for the models. On the basis of these experimental observations, qualitative and quantitative validations of the models will be performed. Observers and image correlations are one of the techniques we are using.