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Microbial Conlonization in Confined Chaotic Mixtures

Project description

3D imaging of subsurface bacterial habitats

Bacteria that reside under the surface of the earth play an instrumental role in biogeochemical cycles. They have also been exploited for bioremediation and the management of water resources. The EU-funded MicroMix project is interested to study the natural environment and community dynamics of subsurface bacteria. Researchers are working under the hypothesis that nutrient distribution in these habitats follows a chaotic rather than homogeneous pattern. They have built a novel bioreactor system for imaging the chemical landscapes and bacterial colonies in 3D porous media such as those encountered in the natural habitat of subsurface bacteria. Results will unveil important aspects of bacterial growth and colonisation under different conditions.


Subsurface bacteria represent a fundamental, yet poorly known, component of the Earth’s biosphere. These communities are key in biogeochemical cycles and in a range of problems in Environmental and Geosciences, ranging from water resources management and bioremediation, to CO2 sequestration and geothermal energy. Until recently, the opacity of 3D porous media-the natural habitat of subsurface bacteria-had prevented in situ and in vivo imaging of bacterial dynamics in such environments. Recent experimental and theoretical breakthroughs at the host institution have led to the discovery that flows in natural porous media are chaotic in nature. Since chaotic mixing is known to yield and sustain strong chemical gradients at micro-scale, this discovery challenges the assumption of homogeneous nutrient distributions, broadly-used in current models of subsurface microbial processes. The goal of MicroMix is thus to explore the effect of chaotic mixing on bacterial growth and colonization in 3D porous media under positive stimuli (WP1: mixing-limited nutrient resources) and negative stimuli (WP2: antibiotic source, nutrient rerouting by bioclogging). To do so, we will develop a novel bioreactor system, primarily based upon coupling high-resolution Laser Induced Fluorescence and optical index matching, which will allow us to obtain the first joint imaging of chemical landscapes and bacterial colonies in 3D porous media. The project builds upon the combined expertise of the ER in the field of biomicrofluidics, of the supervisor in mixing dynamics, and of the secondment supervisor on biofilm dynamics in porous media. Through a detailed career development plan, a tailored training program and access to key experimental facilities and scientific networks, MicroMix will ensure an efficient re-integration of the ER and place him at the forefront of research on environmental fluid dynamics.


Net EU contribution
€ 196 707,84

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Bretagne Bretagne Ille-et-Vilaine
Activity type
Higher or Secondary Education Establishments
Total cost
€ 196 707,84