Periodic Reporting for period 4 - BEBOP (Bacterial biofilms in porous structures: from biomechanics to control)
Période du rapport: 2023-07-01 au 2024-12-31
Bacteria-driven biotechnology is a powerful approach for engineering porous materials and processes across industries. This project focused on two key ideas: 1) precise control of the properties of porous systems can be obtained by exploiting bacteria and their remarkable capabilities; 2) porous media, with their high surface-to-volume ratios and complex structures, could be a major part of bacterial synthetic biology, serving as a scaffold enabling controlled, large-scale sessile microorganism cultivation.
The main scientific obstacle to precise control of such processes was the lack of understanding of complex biophysical mechanisms in complex porous structures, even in the case of single-strain biofilms. We hypothesized that deeper insight into the fundamentals of biofilm biomechanics and physical ecology in porous media would provide a novel theoretical basis for engineering and control.
Our first objective was to unravel the interactions between fluid flow, transport phenomena, and biofilms within connected multiscale heterogeneous structures. We developed novel microfluidic platforms integrated with online instrumentation, advanced imaging, and multi-scale modeling approaches, achieving accurate measurements in controlled conditions and detailed characterization of the spatio-temporal dynamics of biofilm development and bacterial ecology in porous media flows.
The second scientific objective was to create the primary building blocks toward a control theory of bacteria in porous media. Through a combination of experiments and mathematical modeling, we identified key variables governing biomass dynamics and global porous media properties. We also developed a novel porous micro-bioreactor technology that makes it possible to test new control strategies, e.g. bacterial predators or quorum-sensing inhibition, in a miniaturized system.
This work advances the field by developing microfluidic methods and multi-scale modeling approaches for studying biologically active porous media, while revealing fundamental new physics governing flow-biofilm interactions. These advances will enable applications in wastewater processing, soil bioremediation, and self-regulating construction materials, while providing a pathway from synthetic biology proof-of-concept to production.
The main scientific obstacle to precise control of such processes was the lack of understanding of complex biophysical mechanisms in complex porous structures, even in the case of single-strain biofilms. We hypothesized that deeper insight into the fundamentals of biofilm biomechanics and physical ecology in porous media would provide a novel theoretical basis for engineering and control.
Our first objective was to unravel the interactions between fluid flow, transport phenomena, and biofilms within connected multiscale heterogeneous structures. We developed novel microfluidic platforms integrated with online instrumentation, advanced imaging, and multi-scale modeling approaches, achieving accurate measurements in controlled conditions and detailed characterization of the spatio-temporal dynamics of biofilm development and bacterial ecology in porous media flows.
The second scientific objective was to create the primary building blocks toward a control theory of bacteria in porous media. Through a combination of experiments and mathematical modeling, we identified key variables governing biomass dynamics and global porous media properties. We also developed a novel porous micro-bioreactor technology that makes it possible to test new control strategies, e.g. bacterial predators or quorum-sensing inhibition, in a miniaturized system.
This work advances the field by developing microfluidic methods and multi-scale modeling approaches for studying biologically active porous media, while revealing fundamental new physics governing flow-biofilm interactions. These advances will enable applications in wastewater processing, soil bioremediation, and self-regulating construction materials, while providing a pathway from synthetic biology proof-of-concept to production.
Completed developments (much of this work has been published in journals and presented in conferences)
- We have developed a UV-C LED-based technique for controlling bacterial distribution in PDMS microfluidic devices, enabling precise spatial control of colonization for extended periods. This approach has been validated through publication in Biomicrofluidics and featured by Fluigent.
- We have developed diverse microfluidic platforms from PDMS-glass chips to stereolithography 3D-printed devices with integrated functionality (published in Lab on a Chip), alongside advanced on-chip microscopy techniques for network-scale measurements and biofilm mechanical characterization.
- We have developed a modular micromodel platform for studying bacterial biofilm formation in porous media flows, integrating additive manufacturing with microfluidic control systems. This versatile system enables investigation of biofilm dynamics in 3D environments (published in Lab on a Chip).
- We have developed complementary theoretical frameworks: a network theory approach for biofilm development in porous media, and a stochastic modeling framework for growth and sloughing dynamics in channel flows (published in eLife).
- We have characterized how flow-bacterial interactions govern P. aeruginosa dynamics in microchannels, revealing how nutrient gradients and growth-detachment competition drive clogging dynamics and hydraulic resistance fluctuations (published in eLife).
- We have demonstrated that hydrodynamic interactions create nonlocal effects driving dynamics in porous media biofilms, validated with P. aeruginosa and S. aureus (manuscript under evaluation).
- We have used individual-based models to investigate bacterial dynamics in dense populations, revealing key insights into bacterial competition mechanisms (published in Nature Communications).
Promising directions
- We have investigated functionalized gold nanoparticles as X-ray tomography contrast agents for visualizing biofilm development in opaque porous media, with promising initial results pending optimization.
- We have investigated how physical obstacles influence bacterial mixing through modeling and microfluidic experiments, with implications for ecological interactions.
- We have started studying how predators and quorum sensing modulation influence colonization patterns in confined flows, pointing towards new approaches for controlling clogging.
- We have developed a UV-C LED-based technique for controlling bacterial distribution in PDMS microfluidic devices, enabling precise spatial control of colonization for extended periods. This approach has been validated through publication in Biomicrofluidics and featured by Fluigent.
- We have developed diverse microfluidic platforms from PDMS-glass chips to stereolithography 3D-printed devices with integrated functionality (published in Lab on a Chip), alongside advanced on-chip microscopy techniques for network-scale measurements and biofilm mechanical characterization.
- We have developed a modular micromodel platform for studying bacterial biofilm formation in porous media flows, integrating additive manufacturing with microfluidic control systems. This versatile system enables investigation of biofilm dynamics in 3D environments (published in Lab on a Chip).
- We have developed complementary theoretical frameworks: a network theory approach for biofilm development in porous media, and a stochastic modeling framework for growth and sloughing dynamics in channel flows (published in eLife).
- We have characterized how flow-bacterial interactions govern P. aeruginosa dynamics in microchannels, revealing how nutrient gradients and growth-detachment competition drive clogging dynamics and hydraulic resistance fluctuations (published in eLife).
- We have demonstrated that hydrodynamic interactions create nonlocal effects driving dynamics in porous media biofilms, validated with P. aeruginosa and S. aureus (manuscript under evaluation).
- We have used individual-based models to investigate bacterial dynamics in dense populations, revealing key insights into bacterial competition mechanisms (published in Nature Communications).
Promising directions
- We have investigated functionalized gold nanoparticles as X-ray tomography contrast agents for visualizing biofilm development in opaque porous media, with promising initial results pending optimization.
- We have investigated how physical obstacles influence bacterial mixing through modeling and microfluidic experiments, with implications for ecological interactions.
- We have started studying how predators and quorum sensing modulation influence colonization patterns in confined flows, pointing towards new approaches for controlling clogging.
Our project has significantly advanced the understanding of bacterial biofilm development in porous media through complementary experimental approaches and mathematical modeling. We have developed innovative experimental platforms, from advanced microfluidic devices to modular 3D printed micromodel systems, that enable detailed investigation of biofilm dynamics in controlled environments. Through these platforms, we have implemented microscopy techniques achieving precise measurements at network scale and characterization of biofilm mechanical properties.
We have achieved fundamental theoretical advances through multi-scale modeling approaches. Our stochastic framework reveals the physical mechanisms behind biofilm variability and sloughing events, while our network theory approach and individual-based models capture bacterial dynamics from single-cell to population scales. This theoretical work provides new tools for interpreting complex experimental observations and predicting biofilm behavior.
Our experimental findings have revealed fundamental mechanisms governing biofilm development in confined flows. We demonstrated that the interplay between nutrient gradients and flow-induced detachment controls biomass distribution, leading to the discovery of self-sustained fluctuations as an intrinsic characteristic of confined biofilm development. We also uncovered how nonlocal hydrodynamic interactions drive spatial-temporal dynamics and competition in porous media biofilms, providing new insights into bacterial adaptation strategies.
Building on these advances, our modular micromodel technology provides a versatile platform for rapidly testing new concepts in control engineering of bioclogging in porous media. Several promising research directions have also emerged from this project: new imaging approaches using functionalized nanoparticles as contrast agents, which could enable unprecedented visualization of biofilm development in opaque media, and biological control strategies in confined and porous media flows through predator-prey interactions and quorum sensing modulation.
Much of this work has been published in leading journals and presented at international conferences, establishing its significance in the field. These advances, combined with our fundamental understanding of flow-biofilm interactions, provide new perspectives for both theoretical microbial ecology and biotechnology applications.
We have achieved fundamental theoretical advances through multi-scale modeling approaches. Our stochastic framework reveals the physical mechanisms behind biofilm variability and sloughing events, while our network theory approach and individual-based models capture bacterial dynamics from single-cell to population scales. This theoretical work provides new tools for interpreting complex experimental observations and predicting biofilm behavior.
Our experimental findings have revealed fundamental mechanisms governing biofilm development in confined flows. We demonstrated that the interplay between nutrient gradients and flow-induced detachment controls biomass distribution, leading to the discovery of self-sustained fluctuations as an intrinsic characteristic of confined biofilm development. We also uncovered how nonlocal hydrodynamic interactions drive spatial-temporal dynamics and competition in porous media biofilms, providing new insights into bacterial adaptation strategies.
Building on these advances, our modular micromodel technology provides a versatile platform for rapidly testing new concepts in control engineering of bioclogging in porous media. Several promising research directions have also emerged from this project: new imaging approaches using functionalized nanoparticles as contrast agents, which could enable unprecedented visualization of biofilm development in opaque media, and biological control strategies in confined and porous media flows through predator-prey interactions and quorum sensing modulation.
Much of this work has been published in leading journals and presented at international conferences, establishing its significance in the field. These advances, combined with our fundamental understanding of flow-biofilm interactions, provide new perspectives for both theoretical microbial ecology and biotechnology applications.