Should I stay or should I go? Spatio-temporal dynamics of bacterial biofilms in confined flows

  1. Massinissa Benbelkacem
  2. Gabriel Ramos
  3. Fatima El Garah
  4. Yara Abidine
  5. Christine Roques
  6. Yohan Davit

  • Curated by eLife

    eLife logo

    eLife assessment

    This important study integrates microfluidic experiments and mathematical modeling to investigate how flow dynamics and biofilm growth and detachment influence each other. Using Pseudomonas aeruginosa as a model organism, the study identifies several key effects and stages in biofilm development, albeit with some weaknesses in clearly defining the setup and some of their interpretations. The comparison between experimental results and theoretical models is convincing, providing a robust analysis of the biofilm's behavior under varying flow conditions. The findings will be helpful for researchers working on biofilms and their applications.

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

The vast majority of bacteria live in sessile biofilms that colonize the channels, pores and crevices of confined structures. Flow in these structures carries the nutrients necessary for growth, but also generates stresses and detachment from surfaces. Conversely, bacteria tend to occupy a large part of the available space and, in so doing, increase resistance to flow and modify transport properties. Although the importance of advective transport and hydrodynamic forces on bacteria is well known, the complex feedback effects that control development in confined geome-tries are much less understood. Here, we study how couplings between flow and bacterial development control the spatio-temporal dynamics of Pseudomonas aeruginosa in microchannel flows. We demonstrate that nutrient limitation drives the longitudinal distribution of biomass, while a competition between growth and flow-induced detachment controls the maximum clogging and the temporal dynamics. We find that successive cycles of sloughing and growth cause persistent fluctuations of the hydraulic resistance and prevent the system from ever reaching a true steady-state. Our results indicate that these self-sustained fluctuations are a signature effect of biofilm development in confined flows and could thus be a key component of the spreading of biofilms in infections, environmental processes and engineering applications. Consistent with the description of other bursting events, such as earthquakes or avalanches, we further show that the dynamics of sloughing can be described as a jump stochastic process with a gamma distribution of interevent times. This stochastic modeling approach opens the way towards a new quantitative approach to the characterization of the apparent randomness and irreproducibility of biofilm experiments in such systems.

Article activity feed

  1. Version published to 10.7554/elife.98292.1 on eLife
  2. Version published to 10.7554/elife.98292 on eLife
  3. eLife

    eLife assessment

    This important study integrates microfluidic experiments and mathematical modeling to investigate how flow dynamics and biofilm growth and detachment influence each other. Using Pseudomonas aeruginosa as a model organism, the study identifies several key effects and stages in biofilm development, albeit with some weaknesses in clearly defining the setup and some of their interpretations. The comparison between experimental results and theoretical models is convincing, providing a robust analysis of the biofilm's behavior under varying flow conditions. The findings will be helpful for researchers working on biofilms and their applications.

  4. eLife

    Reviewer #1 (Public Review):

    Summary:
    The paper investigates the interplay between fluid flow and biofilm development using Pseudomonas aeruginosa PAO1 in microfluidic channels. By combining experimental observations with mathematical modeling, the study identifies the significant impact of nutrient limitation and hydrodynamic forces on biofilm growth and detachment. The authors demonstrate that nutrient limitation drives the longitudinal distribution of biomass, while flow-induced detachment influences the maximum clogging and temporal dynamics. The study highlights that pressure buildup plays a critical role in biofilm detachment, leading to cyclic episodes of sloughing and regrowth. A stochastic model is used to describe the detachment process, capturing the apparent randomness of sloughing events. The findings offer insights into biofilm behavior during clogging and fouling, potentially relevant to infections, environmental processes, and engineering applications.

    Strengths:
    This paper demonstrates a strong integration of experimental work and mathematical modeling, providing a comprehensive understanding of biofilm dynamics in straight microfluidic channel. The simplicity of the microchannel geometry allows for accurate modeling, and the findings have the potential to be applied to more complex geometries. The detailed analysis of nutrient limitation and its impact on biofilm growth offers valuable insights into the conditions that drive biofilm formation. The model effectively describes biofilm development across different stages, capturing both initial growth and cyclic detachment processes. While cyclic pressure buildup has been studied previously, the incorporation of a stochastic model to describe detachment events is a novel and significant contribution, capturing the complexity and randomness of biofilm behavior. Finally, the investigation of pressure buildup and its role in cyclic detachment and regrowth enhances our understanding of the mechanical forces at play, making the findings applicable to a wide range of technological and clinical contexts.

    Weaknesses:
    The study achieves its primary goal of integrating experiments and modeling to understand the coupling between flow and biofilm growth and detachment in a microfluidic channel, but it should have highlighted the weaknesses of the methods. I list the ones that, in my opinion, are the main ones:

    • The study does not consider biofilm porosity, which could significantly affect the flow and forces exerted on the biofilm. Porosity could impact the boundary conditions, such as the no-slip condition, which should be validated experimentally.
    • The research suggests EPS development as a stage in biofilm growth but does not probe it using lectin staining. This makes it impossible to accurately assess the role of EPS in biofilm development and detachment processes.
    • While the force and flow are three-dimensional, the images are taken in two dimensions. The paper does not clearly explain how the 2D images are extrapolated to make 3D assessments, which could lead to inaccuracies.
    • Although the findings are tested using polysaccharide-deficient mutants, the results could have been analyzed in greater detail. A more thorough analysis would help to better understand the role of matrix composition on the stochastic model of detachment.

  5. eLife

    Reviewer #2 (Public Review):

    This manuscript develops well-controlled microfluidic experiments and mathematical modelling to resolve how the temporal development of P. aeruginosa biofilms is shaped by ambient flow. The experiment considers a simple rectangular channel on which a constant flow rate is applied and UV LEDs are used to confine the biofilm to a relatively small length of device. While there is often considerable geometrical complexity in confined environments and feedback between biofilm/flow (e.g. in porous media), these simplified conditions are much more amenable to analysis. A non-dimensional mathematical model that considers nutrient transport, biofilm growth and detachment is developed and used to interpret experimental data. Regimes with both gradual detachment and catastrophic sloughing are considered. The concentration of nutrients in the media is altered to resolve the effect of nutrient limitation. In addition, the role of a couple of major polysaccharide EPS components are explored with mutants, which leads results in line with previous studies.

    There has been a vast amount of experimental and modelling work done on biofilms, but relatively rarely are the two linked together so tightly as in this paper. Predictions on influence of the non-dimensional Damkohler number on the longitudinal distribution of biofilm and functional dependence of flow on the maximum amount of biofilm (phi_max) are demonstrated. The study reconfirms a number of previous works that showed the gradual detachment rate of biofilms scales with the square root of the shear stress. More challenging are the rapid biofilm detachment events where a large amount of biofilm is detached at once. These events occur are identified experimentally using an automated analysis pipeline and are fitted with probability distributions. The time between detachment events was fitted with a Gamma distribution and the amplitude of the detachment events was fitted with a log-normal distribution, however, it is not clear how good these fits are. Experimental data was then used as an input for a stochastic differential equation, but the output of this model is compared only qualitatively to that of the experiments. Overall, this paper does an admirable job of developing a well-constrained experiments and a tightly integrated mathematical framework through which to interpret them. However, the new insights this provides the underlying physical/biological mechanisms are relatively limited.

  6. Version published to 10.1101/2024.06.07.597893v1 on bioRxiv