On the calculation of the elastic modulus of a biofilm streamer

A microfluidic platform for characterizing the structure and rheology of biofilm streamers

Biofilm formation is the most successful survival strategy for bacterial communities. In the biofilm lifestyle, bacteria embed themselves in a self-secreted matrix of extracellular polymeric substances (EPS), which acts as a shield against mechanical and chemical insults. When ambient flow is present, this viscoelastic scaffold can take a streamlined shape, forming biofilm filaments suspended in flow, called streamers. Streamers significantly disrupt the fluid flow by causing rapid clogging and affect transport in aquatic environments. Despite their relevance, the structural and rheological characterization of biofilm streamers is still at an early stage. In this work, we present a microfluidic platform that allows the reproducible growth of biofilm streamers in controlled physico-chemical conditions and the characterization of their biochemical composition, morphology, and rheology in situ. We employed isolated micropillars as nucleation sites for the growth of single biofilm streamers under the continuous flow of a diluted bacterial suspension. By combining fluorescent staining of the EPS components and epifluorescence microscopy, we were able to characterize the biochemical composition and morphology of the streamers. Additionally, we optimized a protocol to perform hydrodynamic stress tests in situ, by inducing controlled variations of the fluid shear stress exerted on the streamers by the flow. Thus, the reproducibility of the formation process and the testing protocol make it possible to perform several consistent experimental replicates that provide statistically significant information. By allowing the systematic investigation of the role of biochemical composition on the structure and rheology of streamers, this platform will advance our understanding of biofilm formation.

Layered viscoelastic properties of granular biofilms

Granular biofilms are dense spherical complex biological systems composed mainly of multi-microbial cells, water, and extracellular polymeric substances (EPS). They facilitate efficient purification and settling of activated sludge in wastewater treatment processes. The viscoelastic properties of these complex biofilm systems are important characteristics that control their growth and dictate how they respond to hydrodynamic forces and chemical stimuli. However, the viscoelastic properties of granular biofilms are poorly understood. In this paper, we study granular biofilms' viscoelastic properties using optical coherence elastography (OCE), a nondestructive method that integrates optical coherence tomography (OCT) with elastic wave propagation. While quantitative viscoelastic characterization of granular biofilms is challenging due to their heterogeneous properties, we show that elastic waves are suitable for this purpose. First, we employ guided elastic waves in a thin section of a granular biofilm to reveal a two-layered profile for the viscoelastic properties. Next, we utilize circumferential elastic waves that propagate near the surface of a non-sectioned spherical biofilm to quantify the layered system's viscoelastic properties. To the best of our knowledge, this work is the first quantitative study that characterizes the layered viscoelastic properties of granular biofilms. The measurement approach may provide a platform to study the interplay between the viscoelastic properties and other characteristics of granular biofilms such as the complex microbial system, morphology, and oxygen distribution.

Biofilm compressibility in ultrafiltration: A relation between biofilm morphology, mechanics and hydraulic resistance

Poroelastic fluid-structure interaction models were coupled to experimental data to determine the effects of biofilm spatial distribution of mechanical and hydraulic properties on the biofilm hydraulic resistance and compressibility in membrane filtration processes. Biofilms were cultivated on ultrafiltration membranes for 20 and 30 days under high (0.28 bar) and low (0.06 bar) transmembrane pressure (TMP), in dead-end filtration mode. Subsequently, biofilms were subjected to a compression/relaxation cycles by step-wise TMP changes. Structural deformation of biofilms during compression was observed in-situ using optical coherence tomography. Experimental results show that the observed increase in the biofilm hydraulic resistance during compression is not necessarily accompanied by a detectable biofilm thickness reduction. A dual-layer biofilm model with a dense base and porous top layer could explain these observed results. Because porosity controls indirectly the mechanical response of biofilms under compression, results could be described without assuming a gradient in mechanical properties within the biofilm. The biofilm surface roughness did not significantly influence the water flux in this study. However, the fraction of biofilm base layer directly exposed to bulk liquid could be a good indicator in the determination of water flux. The main implications of this study for the design and operation of low-pressure membrane systems (e.g., MF and UF with fouling layer being the main filtration resistance) lays in the selection of favorable operational TMP and biofilm morphology.

Nondestructive characterization of soft materials and biofilms by measurement of guided elastic wave propagation using optical coherence elastography

Biofilms are soft multicomponent biological materials composed of microbial communities attached to surfaces. Despite the crucial relevance of biofilms to diverse industrial, medical, and environmental applications, the mechanical properties of biofilms are understudied. Moreover, most of the available techniques for the characterization of biofilm mechanical properties are destructive. Here, we detail a model-based approach developed to characterize the viscoelastic properties of soft materials and bacterial biofilms based on experimental data obtained using the nondestructive dynamic optical coherence elastography (OCE) technique. The model predicted the frequency- and geometry-dependent propagation velocities of elastic waves in a soft viscoelastic plate supported by a rigid substratum. Our numerical calculations suggest that the dispersion curves of guided waves recorded in thin soft plates by the dynamic OCE technique are dominated by guided waves, whose phase velocities depend on the viscoelastic properties and plate thickness. The numerical model was validated against experimental measurements in agarose phantom samples with different thicknesses and concentrations. The model was then used to interpret guided wave dispersion curves obtained by the OCE technique in bacterial biofilms developed in a rotating annular reactor, which allowed the quantitative characterization of biofilm shear modulus and viscosity. This study is the first to employ measurements of elastic wave propagation to characterize biofilms, and it provides a novel framework combining a theoretical model and an experimental approach for studying the relationship between the biofilm internal physical structure and mechanical properties.

Effect of biofilm structural deformation on hydraulic resistance during ultrafiltration: A numerical and experimental study

Biofilm formation in membrane systems negatively impacts the filtration system performances. This study evaluated how biofilm compression driven by permeate flow increases the hydraulic resistance and leads to reduction in permeate flux. We analysed the effect of biofilm compression on hydraulic resistance and permeate flux through computational models supported by experimental data. Biofilms with homogeneous surface structure were subjected to step-wise changes in flux and transmembrane pressure during compression and relaxation tests. Biofilm thickness under applied forces was measured non-invasively in-situ using optical coherence tomography (OCT). A numerical model of poroelasticity, which couples water flow through the biofilm with biofilm mechanics, was developed to correlate the structural deformation with biofilm hydraulics (permeability and resistance). The computational model enabled extracting mechanical and hydrological parameters corresponding to the experimental data. Homogeneous biofilms under elevated compression forces experienced a significant reduction in thickness while only a slight increase in resistance was observed. This shows that hydraulic resistance of homogeneous biofilms was affected more by permeability decrease due to pore closure than by a decrease in thickness. Both viscoelastic and elastoplastic models could describe well the permanent biofilm deformation. However, for biofilms under study, a simpler elastic model could also be used due to the small irreversible deformations. The elastic moduli fitting the measured data were in agreement with other reported values for biofilm under compression. Biofilm stiffening under larger flow-driven compression forces was observed and described numerically by correlating inversely the elastic modulus with biofilm porosity. The importance of this newly developed method lies in estimation of accurate biofilm mechanical parameters to be used in numerical models for both membrane filtration system and biofouling cleaning strategies. Such model can ultimately be used to identify optimal operating conditions for membrane system subjected to biofouling.

Towards standardized mechanical characterization of microbial biofilms: analysis and critical review

Developing reliable anti-biofilm strategies or efficient biofilm-based bioprocesses strongly depends on having a clear understanding of the mechanisms underlying biofilm development, and knowledge of the relevant mechanical parameters describing microbial biofilm behavior. Many varied mechanical testing methods are available to assess these parameters. The mechanical properties thus identified can then be used to compare protocols such as antibiotic screening. However, the lack of standardization in both mechanical testing and the associated identification methods for a given microbiological goal remains a blind spot in the biofilm community. The pursuit of standardization is problematic, as biofilms are living structures, i.e., both complex and dynamic. Here, we review the main available methods for characterizing the mechanical properties of biofilms through the lens of the relationship linking experimental testing to the identification of mechanical parameters. We propose guidelines for characterizing biofilms according to microbiological objectives that will help the reader choose an appropriate test and a relevant identification method for measuring any given mechanical parameter. The use of a common methodology for the mechanical characterization of biofilms will enable reliable analysis and comparison of microbiological protocols needed for improvement of engineering process and screening.

Recent advances in studying single bacteria and biofilm mechanics

Bacterial biofilms correspond to surface-associated bacterial communities embedded in hydrogel-like matrix, in which high cell density, reduced diffusion and physico-chemical heterogeneity play a protective role and induce novel behaviors. In this review, we present recent advances on the understanding of how bacterial mechanical properties, from single cell to high-cell density community, determine biofilm tri-dimensional growth and eventual dispersion and we attempt to draw a parallel between these properties and the mechanical properties of other well-studied hydrogels and living systems.

High-contrast Brillouin and Raman micro-spectroscopy for simultaneous mechanical and chemical investigation of microbial biofilms

Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample. The correlative Raman and Brillouin investigation evidences the role of both extracellular polymeric substances and of hydration water in inducing a marked local softening of the biofilm.

Cellulose effects on morphology and elasticity of Vibrio fischeri biofilms

Cellulose effects on Vibrio fischeri biofilm morphology were tested for the wild-type and two of its isogenic mutants that either exhibit increased cellulose production or do not produce cellulose at all. Confocal laser scanning microscopy imaging of each biofilm revealed that total sessile volume increases with cellulose expression, but the size of colonies formed with cellulose was smaller, creating a more diffuse biofilm. These morphological differences were not attributed to variations in bacterial deposition, extracellular polymeric substances affinity to the surface or bacterial growth. A positive correlation was found between cellulose expression, Young's (elastic) modulus of the biofilm analyzed with atomic force microscope and shear modulus of the related extracellular polymeric substances layers analyzed with quartz crystal microbalance with dissipation monitoring. Cellulose production also correlated positively with concentrations of extracellular DNA. A significant negative correlation was observed between cellulose expression and rates of diffusion through the extracellular polymeric substances. The difference observed in biofilm morphology is suggested as a combined result of cellulose and likely extracellular DNA (i) increasing biofilm Young's modulus, making shear removal more difficult, and (ii) decreased diffusion rate of nutrients and wastes into and out of the biofilm, which effectively limits colony size.

Modeling of Mesoscale Variability in Biofilm Shear Behavior

Formation of bacterial colonies as biofilm on the surface/interface of various objects has the potential to impact not only human health and disease but also energy and environmental considerations. Biofilms can be regarded as soft materials, and comprehension of their shear response to external forces is a key element to the fundamental understanding. A mesoscale model has been presented in this article based on digitization of a biofilm microstructure. Its response under externally applied shear load is analyzed. Strain stiffening type behavior is readily observed under high strain loads due to the unfolding of chains within soft polymeric substrate. Sustained shear loading of the biofilm network results in strain localization along the diagonal direction. Rupture of the soft polymeric matrix can potentially reduce the intercellular interaction between the bacterial cells. Evolution of stiffness within the biofilm network under shear reveals two regimes: a) initial increase in stiffness due to strain stiffening of polymer matrix, and b) eventual reduction in stiffness because of tear in polymeric substrate.

Biomechanical Analysis of Infectious Biofilms

The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.

Interplay of physical mechanisms and biofilm processes: review of microfluidic methods

Bacteria in natural and artificial environments often reside in self-organized, integrated communities known as biofilms. Biofilms are highly structured entities consisting of bacterial cells embedded in a matrix of self-produced extracellular polymeric substances (EPS). The EPS matrix acts like a biological 'glue' enabling microbes to adhere to and colonize a wide range of surfaces. Once integrated into biofilms, bacterial cells can withstand various forms of stress such as antibiotics, hydrodynamic shear and other environmental challenges. Because of this, biofilms of pathogenic bacteria can be a significant health hazard often leading to recurrent infections. Biofilms can also lead to clogging and material degradation; on the other hand they are an integral part of various environmental processes such as carbon sequestration and nitrogen cycles. There are several determinants of biofilm morphology and dynamics, including the genotypic and phenotypic states of constituent cells and various environmental conditions. Here, we present an overview of the role of relevant physical processes in biofilm formation, including propulsion mechanisms, hydrodynamic effects, and transport of quorum sensing signals. We also provide a survey of microfluidic techniques utilized to unravel the associated physical mechanisms. Further, we discuss the future research areas for exploring new ways to extend the scope of the microfluidic approach in biofilm studies.

On the mechanics of bacterial biofilms on non-dissolvable surgical sutures: a laser scanning confocal microscopy-based finite element study

Biofilms are bacterial communities encapsulated within a self-secreted extracellular polymeric substance and are responsible for a wide range of chronic medical device related infections. Understanding and addressing the conditions that lead to the attachment and detachment of biofilms from biomedical surfaces (orthopaedic implants, sutures, intravenous catheters, cardio-vascular stents) has the potential to identify areas of the device that might be more prone to infection and predict how and when biofilms might dislodge. In this study, an integrated software methodology was devised to create image-based microscopic finite element models of real biofilm colonies of Staphylococcus aureus attached to a fragment of surgical suture. The goal was to predict how deformation of the suture may lead to the potential detachment of biofilm colonies by solving the equations of continuum mechanics using the finite element method for various loading cases. Tension, torsion and bending of the biomaterial structure were simulated, demonstrating that small strains in the suture can produce surface shear stresses sufficient to trigger the sliding of biofilms over the suture surface. Applications of this technique to other medical devices are discussed.

Modelling mechanical characteristics of microbial biofilms by network theory

In this contribution, we present a constitutive model to describe the mechanical behaviour of microbial biofilms based on classical approaches in the continuum theory of polymer networks. Although the model is particularly developed for the well-studied biofilms formed by mucoid Pseudomonas aeruginosa strains, it could easily be adapted to other biofilms. The basic assumption behind the model is that the network of extracellular polymeric substances can be described as a superposition of worm-like chain networks, each connected by transient junctions of a certain lifetime. Several models that were applied to biofilms previously are included in the presented approach as special cases, and for small shear strains, the governing equations are those of four parallel Maxwell elements. Rheological data given in the literature are very adequately captured by the proposed model, and the simulated response for a series of compression tests at large strains is in good qualitative agreement with reported experimental behavior.

Effect of shear stress and growth conditions on detachment and physical properties of biofilms

Detachment is one of the major processes determining the physical structure and microbial functionalities of biofilms. To predict detachment, it is necessary to take the mechanical properties of the biofilm and the effect of both hydrodynamic and growth conditions into account. In this work, experiments were conducted with biofilms developed under various shear stresses and with various substrate natures. In addition, two cases were considered in order to differentiate between the effect of hydrodynamic factors and growth factors: the biofilms were directly grown under the targeted shear stress (τ) condition or they were precultivated under very low shear stress (0.01 Pa) and then exposed to high shear stress in the range of 0.1-13 Pa. An exponential and asymptotic decrease of the biofilm thickness and mass with increasing τ was observed in both cases. On contrary density, expressed as the biofilm dry mass on a known substratum divided by the average thickness increased with τ. Denitrifying biofilms always showed greater thickness and density than oxic biofilms. These results showed the presence of a compact basal layer that resisted shear stresses as high as 13 Pa whatever the culture conditions. Above this basal layer, the cohesion was lower and depended on the shear stress applied during biofilm development. The application of shear stress to the biofilms resulted in both detachment and compression, but detachment prevailed for the upper part of the biofilms and compression prevailed for the basal layers. A model of biofilm structure underlying the stratified character of this aggregate is given in terms of density and cohesion.

Mass transfer enhancement in moving biofilm structures

Biofilms are layers of microbial cells growing on an interface and they can form highly complex structures adapted to a wide variety of environmental conditions. Biofilm streamers have a small immobile base attached to the support and a flexible tail elongated in the flow direction, which can vibrate in fast flows. Herein we report numerical results for the role of the periodical movement of biofilm streamers on the nutrient uptake and in general on the solute mass transfer enhancement due to flow-induced oscillations. We developed what to our knowledge is a novel two-dimensional fluid-structure interaction model coupled to unsteady solute mass transport and solved the model using the finite element method with a moving mesh. Results demonstrate that the oscillatory movement of the biofilm tail significantly increases the substrate uptake. The mass transfer coefficient is the highest in regions close to the streamer tip. The reason for substrate transfer enhancement is the increase in speed of tip movement relative to the surrounding liquid, thereby reducing the thickness of the mass transfer boundary layer. In addition, we show that the relative mass transfer enhancement in unsteady conditions compared with the rigid static structure is larger at higher flow velocities, and this relative increase favors a more flexible structure.

Quantifying the tensile strength of microbial mats grown over noncohesive sediments

Biofilms in marine and fluvial environments can comprise strong bacterial and diatom mats covering large areas of the bed and act to bind sediments. In this case the bed material becomes highly resistant to shear stresses applied by the overlying fluid motion and detachment, when it does occur, is manifest in patches of biofilm of the order cm(2) being entrained into the flow. This article is the first to report tensile test data specific to the centimeter scale using moist biofilm/sediment composite materials; the strain (ε)-stress (σ) relationships permit quantification of the elasticity (Young's modulus, E) and cohesive strength of each specimen. Specifically, we compare the mechanical strength of cyanobacterial biofilm-only samples to that of biofilm cultured over sediment samples (glass beads or natural sands of d ~ 1 mm) for up to 8 weeks. The range of tensile strength (1,288-3,283 Pa) for composite materials was up to three times higher than previous tensile tests conducted at smaller scale on mixed culture biofilm [Ohashi et al. (1999) Water Sci Technol 39:261-268], yet of similar range to cohesive strength values recorded on return activated sludge flocs [RAS; Poppele and Hozalski (2003) J Microbiol Methods 55:607-615]. Composite materials were 3-6 times weaker than biofilm-only samples, indicating that adhesion to sediment grains is weaker than cohesion within the biofilm. Furthermore, in order to relate the tensile test results to the more common in-situ failure of bio-mats due to shear flow, controlled erosion experiments were conducted in a hydraulic flume with live fluid flow. Here, the fluid shear stress causing erosion was 3 orders of magnitude lower than tensile stress; this highlights both the problem of interpreting material properties measured ex-situ and the need for a better mechanistic model of bio-mat detachment.

Secondary flow as a mechanism for the formation of biofilm streamers

In most environments, such as natural aquatic systems, bacteria are found predominantly in self-organized sessile communities known as biofilms. In the presence of a significant flow, mature multispecies biofilms often develop into long filamentous structures called streamers, which can greatly influence ecosystem processes by increasing transient storage and cycling of nutrients. However, the interplay between hydrodynamic stresses and streamer formation is still unclear. Here, we show that suspended thread-like biofilms steadily develop in zigzag microchannels with different radii of curvature. Numerical simulations of a low-Reynolds-number flow around these corners indicate the presence of a secondary vortical motion whose intensity is related to the bending angle of the turn. We demonstrate that the formation of streamers is directly proportional to the intensity of the secondary flow around the corners. In addition, we show that a model of an elastic filament in a two-dimensional corner flow is able to explain how the streamers can cross fluid streamlines and connect corners located at the opposite sides of the channel.

Determination of biofilm mechanical properties from tensile tests performed using a micro-cantilever method

Recently, a micro-cantilever method was introduced for measuring the ultimate tensile strength of intact bacterial biofilms. Herein, is reported the analysis of the video files from the testing of a 4-day-old Staphylococcus epidermidis biofilm to determine the elastic modulus, toughness, and failure strain. Elastic modulus (1270+/-280 Pa) was within the range of previously reported values (17-6000 Pa). The high failure strains (240+/-16%) indicate the substantial ductility of bacterial biofilms. In addition, the toughness of the biofilm sample was determined from the area under the stress-strain plot (2.8+/-0.44 kJ m(-3)). Thus, it was demonstrated that the micro-cantilever test video files can be used for the determination of other mechanical property parameters besides ultimate tensile strength.

Applying the digital image correlation method to estimate the mechanical properties of bacterial biofilms subjected to a wall shear stress

A digital image correlation (DIC) method was applied to characterize the mechanical behavior of Pseudomonas aeruginosa biofilms in response to wall shear stress using digital video micrographs taken from biofilm flow cells. The appearance of the biofilm in the transmitted light photomicrographs presented a natural texture which was highly conducive to random encoding for DIC. The displacement fields were calculated for two biofilm specimens. The DIC method concurred with previous analysis showing that biofilms exhibit viscoelastic behavior, but had the advantage over simple length measurements of longitudinal strain that it could precisely measure local strains in length (x) and width (y) within biofilm clusters with a 2 mum resolution as a function of time and wall shear stress. It was concluded that DIC was more accurate at measuring elastic moduli than simple length measurements, but that time-lapse 3D images would enable even more accurate estimates to be performed.

Viscoelastic properties of Staphylococcus aureus and Staphylococcus epidermidis mono-microbial biofilms

The viscoelastic properties of mono‐microbial biofilms produced by ocular and reference staphylococcal strains were investigated. The microorganisms were characterized for their haemolytic activity and agr typing and the biofilms, grown on stainless steel surface under static conditions, were analysed by Confocal Laser Scanning Microscopy. Static and dynamic rheometric tests were carried out to determine the steady‐flow viscosity and the elastic and viscous moduli. The analysed biofilms showed the typical time‐dependent behaviour of viscoelastic materials with considerable elasticity and mechanical stability except for Staphylococcus aureus ATCC 29213 biofilm which showed a very fragile structure. In particular, S. aureus 6ME biofilm was more compact than other staphylococcal biofilms studied with a yield stress ranging between 2 and 3 Pa. The data obtained in this work could represent a starting point for developing new therapeutic strategies against biofilm‐associated infections, such as improving the drug effect by associating an antimicrobial agent with a biofilm viscoelasticity modifier.