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Equipe de recherche MERE

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Microbial ecology for environmental preservation

Populations of cities and modern industrial techniques, particularly in agronomy, reject considerable quantities of chemicals (carbon, nitrogen, phosphorus) which are substrates (food) of choice for microorganisms. Direct rejection in nature of these products leads to uncontrolled growth of microorganisms perturbing the growth of more evolved forms of life. “Biological cleanup” (waste-water treatment) consists simply in reproducing this natural process in a controlled process in bioreactors (the “waste-water treatment plant”).

The study of biological waste-water treatment requires knowledge in a large number of domains, notably:


physics and chemistry of the environment,




microbial ecosystems,


process engineering,


automatic control,


mathematical and computer modeling,



Obviously, a small team like ours is not able to master this variety of research areas. Our expertise covers only the last three items, and we are used to having strong collaborationswith biologists and engineers. About one third of our publications is co-authored by such collaborators.

The transformation of pollution into biomass is performed in a microbial ecosystem. Thus, a good understanding of microbial ecology is essential. On the other hand, microbial ecosystems have an increasing importance in ecological theory. Microbial ecosystems present an interesting double feature:

They are small and therefore can be “observed” and `manipulated” in the laboratory;

Molecular biology methods have recently become available to measure microbial population sizes,

which makes them particularly attractive, see .

Our research focuses mainly on biodiversity: What are the mechanisms that explain the presence of a large number of species in microbial ecosystems? What are the functional consequences of biodiversity? We are working on mathematical models associated with these issues.

We strongly believe that good research is built upon a good knowledge of reality and, conversely, that good quality applications are based on the best available knowledge of current theories. That is why, along with its fundamental concerns, our team is involved in concrete activities ranging from simple technical helpsand participation in networks within the framework of national and international programs to the establishment and running of such networks. Most notably is our network TREASURE ( Treatment and Sustainable Reuse of Effluents in semi-arid climates) that includes participants from around the Mediterranean sea on a very specific development problem: Relevance of anaerobic digestion followed by membranes for water reuse for agriculture in semi-arid countries.

The industry of waste-water treatment is considered today as the first industry in terms of matter to be processed. Therefore, the design, the control and, in more general terms, the optimization of treatment processes are real challenges. One of our objectives is also to better understand these processes in order to optimize their functioning in the presence of uncertainties and of unknown and unmeasured external disturbances. To do so,

We approach the problems at two levels: the microscopic scale (the micro-organism) and the macroscopic one (the plant);

We use macroscopic modeling and control system science tools to develop new design rules, estimation techniques and control system that we calibrate on real biological pilot plants.

Our methodology starts with the development of mathematical models of the biological reactions and transports in the reactor. At this stage, we have very strong interactions with micro-biologists. Next, we analyze the model with the available mathematical tools or/and through computer simulations. We focus mainly on the effects of the spatial distribution of the biomass. This questioning can be understood at various scales.

At the macroscopic level, we compare the performances of various designs, from infinitely stirred reactors to purely non-mixed reactors through cascade of reactors;

At the microscopic level, we are interested in the growth process of the biomass, limitations caused by the diffusion of the substrate, and the role of the bio-films.

We are interested in fundamental questions of microbial ecology, like biodiversity of biomass, competition and predation, since they are at the roots of the understanding of biological waste-water treatment and, at the same time, we address very practical questions like the minimization of the size of the bioreactors.

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