Nonlinear deformation and localized failure of bacterial streamers in creeping flows

Mesoscopic ring element growth and deformation induced biofilm streamer evolution in microfluidic channels

In a fluid environment, biofilms usually form and grow into streamers attached to solid surfaces. Existing research on single streamers studied their formation and failure modes. In the experiment on biofilm growth in a microfluidic channel, we found that rings composed of bacteria and an extracellular matrix are important elements on a mesoscopic scale. In the fluid environment, the failure of these ring elements causes damage to streamers. We simulated the growth and deformation of the ring structure in the micro-channel using multi-agent simulation and fluid-structure coupling of a porous elastic body. Based on this, we simulated the biofilm evolution involving multi-ring deformation, which provides a new length scale to study the biofilm streamer dynamics in fluid environments.

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.

Impact of rheological properties on bacterial streamer formation

Bacterial biofilms, which can be found wherever there is water and a substrate, can cause chronic infections and clogging of industrial flow systems. Despite intensive investigation of the dynamics and rheological properties of biofilms, the impact of their rheological properties on streamer growth remains unknown. We numerically simulated biofilm growth in a pillar-flow and investigated the effects of rheological properties of a filamentous flow-shaped biofilm, called a 'streamer', on its formation by varying the viscoelasticity. The flow-field is assumed to be a Stokes flow and is solved by a boundary element method. A Maxwell model is used for extracellular matrix-mediated streamer growth to express the fluidity of streamer formations. Both high elastic modulus and viscosity are needed for streamer formation, and high viscosity promotes streamer growth at low cell concentrations. Our findings are consistent with experimental observations and can explain the relationship between the cell concentrations and viscosity at which streamers form.

Bacterial streamers as colloidal systems: Five grand challenges

Bacteria can thrive in biofilms, which are intricately organized communities with cells encased in a self-secreted matrix of extracellular polymeric substances (EPS). Imposed hydrodynamic stresses can transform this active colloidal dispersion of bacteria and EPS into slender thread-like entities called streamers. In this perspective article, the reader is introduced to the world of such deformable 'bacteria-EPS' composites that are a subclass of the generic flow-induced colloidal structures. While bacterial streamers have been shown to form in a variety of hydrodynamic conditions (turbulent and creeping flows), its abiotic analogues have only been demonstrated in low Reynolds number (Re < 1) particle-laden polymeric flows. Streamers are relevant to a variety of situations ranging from natural formations in caves and river beds to clogging of biomedical devices and filtration membranes. A critical review of the relevant biophysical aspects of streamer formation phenomena and unique attributes of its material behavior are distilled to unveil five grand scientific challenges. The coupling between colloidal hydrodynamics, device geometry and streamer formation are highlighted.

Hydrodynamics and surface properties influence biofilm proliferation

A biofilm is an interface-associated colloidal dispersion of bacterial cells and excreted polymers in which microorganisms find protection from their environment. Successful colonization of a surface by a bacterial community is typically a detriment to human health and property. Insight into the biofilm life-cycle provides clues on how their proliferation can be suppressed. In this review, we follow a cell through the cycle of attachment, growth, and departure from a colony. Among the abundance of factors that guide the three phases, we focus on hydrodynamics and stratum properties due to the synergistic effect such properties have on bacteria rejection and removal. Cell motion, whether facilitated by the environment via medium flow or self-actuated by use of an appendage, drastically improves the survivability of a bacterium. Once in the vicinity of a stratum, a single cell is exposed to near-surface interactions, such as van der Waals, electrostatic and specific interactions, similarly to any other colloidal particle. The success of the attachment and the potential for detachment is heavily influenced by surface properties such as material type and topography. The growth of the colony is similarly guided by mainstream flow and the convective transport throughout the biofilm. Beyond the growth phase, hydrodynamic traction forces on a biofilm can elicit strongly non-linear viscoelastic responses from the biofilm soft matter. As the colony exhausts the means of survival at a particular location, a set of trigger signals activates mechanisms of bacterial release, a life-cycle phase also facilitated by fluid flow. A review of biofilm-relevant hydrodynamics and startum properties provides insight into future research avenues.

Bacterial biomechanics-From individual behaviors to biofilm and the gut flora

Bacteria inhabit a variety of locations and play important roles in the environment and health. Our understanding of bacterial biomechanics has improved markedly in the last decade and has revealed that biomechanics play a significant role in microbial biology. The obtained knowledge has enabled investigation of complex phenomena, such as biofilm formation and the dynamics of the gut flora. A bottom-up strategy, i.e., from the cellular to the macroscale, facilitates understanding of macroscopic bacterial phenomena. In this Review, we first cover the biomechanics of individual bacteria in the bulk liquid and on surfaces as the base of complex phenomena. The collective behaviors of bacteria in simple environments are next introduced. We then introduce recent advances in biofilm biomechanics, in which adhesion force and the flow environment play crucial roles. We also review transport phenomena in the intestine and the dynamics of the gut flora, focusing on that in zebrafish. Finally, we provide an overview of the future prospects for the field.

Investigating fouling at the pore-scale using a microfluidic membrane mimic filtration system

The work investigates fouling in a microfluidic membrane mimic (MMM) filtration system for foulants such as polystyrene particles and large polymeric molecules. Our MMM device consists of a staggered arrangement of pillars which enables real-time visualization and analysis of pore-scale phenomena. Different fouling scenarios are investigated by conducting constant-pressure experiments. Fouling experiments are performed with three different types of foulants: polystyrene particle solution (colloidal fouling), polyacrylamide polymer solution (organic fouling) and a mixture of these two solutions (combined fouling). Four major categories of microscopic fouling are observed: cake filtration (upstream), pore blocking (inside the pores), colloidal aggregation (downstream) and colloidal streamer fouling (downstream). Our microfluidic experiments show that downstream colloidal aggregation and streamer fouling have a significant effect on overall membrane fouling which were not studied before.

Microfluidic bioanalytical flow cells for biofilm studies: a review

Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive experimental results include time-varying biofilm properties, structural and chemical heterogeneity, and especially their strong sensitivity to environmental cues. Therefore, in addition to judicious choice of measurement tools, a well-designed biofilm study requires strict control over experimental conditions, more so than most chemical studies. Due to excellent control over a host of physiochemical parameters, microfluidic flow cells have become indispensable in microbiological studies. Not surprisingly, the number of lab-on-chip studies focusing on biofilms and other microbiological systems with expanded analytical capabilities has expanded rapidly in the past decade. In this paper, we comprehensively review the current state of microfluidic bioanalytical research applied to bacterial biofilms and offer a perspective on new approaches that are expected to drive continued advances in this field.

Impact of bacterial streamers on biofouling of microfluidic filtration systems

We investigate the effect of biofouling in a microfluidic filtration system. The microfluidic platform consists of cylindrical microposts with a pore-spacing of 2 μm, which act as the filtration section of the device. One of our key findings is that there exists a critical pressure difference above which pronounced streamer formation is observed, which eventually leads to rapid clogging of the device with an accompanying exponential decrease in permeate flow. Moreover, when streamers do form, de-clogging of pores also occurs intermittently, which leads to small time scale fluctuations [O(10¹ s)] superimposed upon the large time scale [O(10² min)] clogging of the system. These de-clogging phenomena lead to a sharp increase in water permeation through the microfluidic filtration device but rates the water quality as biomass debris is transported in the permeate. Streamer-based clogging shares similarities with various fouling mechanisms typically associated with membranes. Finally, we also show that the pH of the feed strongly affects biofouling of the microfluidic filtration system.

Yield of reversible colloidal gels during flow start-up: release from kinetic arrest

Yield of colloidal gels during start-up of shear flow is characterized by an overshoot in shear stress that accompanies changes in network structure. Prior studies of yield of reversible colloidal gels undergoing strong flow model the overshoot as the point at which network rupture permits fluidization. However, yield under weak flow, which is of interest in many biological and industrial fluids shows no such disintegration. The mechanics of reversible gels are influenced by bond strength and durability, where ongoing rupture and re-formation impart aging that deepens kinetic arrest [Zia et al., J. Rheol., 2014, 58, 1121], suggesting that yield be viewed as release from kinetic arrest. To explore this idea, we study reversible colloidal gels during start-up of shear flow via dynamic simulation, connecting rheological yield to detailed measurements of structure, bond dynamics, and potential energy. We find that pre-yield stress grows temporally with the changing roles of microscopic transport processes: early time behavior is set by Brownian diffusion; later, advective displacements permit relative particle motion that stretches bonds and stores energy. Stress accumulates in stretched, oriented bonds until yield, which is a tipping point to energy release, and is passed with a fully intact network, where the loss of very few bonds enables relaxation of many, easing glassy arrest. This is immediately followed by a reversal to growth in potential energy during bulk plastic deformation and condensation into larger particle domains, supporting the view that yield is an activated release from kinetic arrest. The continued condensation of dense domains and shrinkage of network surfaces, along with a decrease in the potential energy, permit the gel to evolve toward more complete phase separation, supporting our view that yield of weakly sheared gels is a 'non-equilibrium phase transition'. Our findings may be particularly useful for industrial or other coatings, where weak, slow application via shear may lead to phase separation, inhibiting smooth distribution.

Nano-Enabled Approaches to Chemical Imaging in Biosystems

Understanding and predicting how biosystems function require knowledge about the dynamic physicochemical environments with which they interact and alter by their presence. Yet, identifying specific components, tracking the dynamics of the system, and monitoring local environmental conditions without disrupting biosystem function present significant challenges for analytical measurements. Nanomaterials, by their very size and nature, can act as probes and interfaces to biosystems and offer solutions to some of these challenges. At the nanoscale, material properties emerge that can be exploited for localizing biomolecules and making chemical measurements at cellular and subcellular scales. Here, we review advances in chemical imaging enabled by nanoscale structures, in the use of nanoparticles as chemical and environmental probes, and in the development of micro- and nanoscale fluidic devices to define and manipulate local environments and facilitate chemical measurements of complex biosystems. Integration of these nano-enabled methods will lead to an unprecedented understanding of biosystem function.

Abiotic streamers in a microfluidic system

In this work, we report the phenomenon of formation of particle aggregates in the form of thin slender strings when a polyacrylamide (PAM) solution, laden with polystyrene (PS) beads is introduced into a microfluidic device containing an array of micropillars. PAM and a dilute solution of PS beads are introduced into the microfluidic channel through two separate inlets and localized particle aggregation is found to occur under certain flow regimes. The particle aggregates initially have a string-like morphology and are tethered at their ends to the micropillar walls, while the structure remains suspended in the fluid medium. Such a morphology inspired us to name these structures streamers. The flow regimes under which streamer formation is observed are quantified through state diagrams. We discuss the streamer formation time-scales and also show that streamer formation is likely the result of the flocculation of PS beads. Streamer formation has implications in investigating particle-laden complex flows through porous media.

Through thick and thin: a microfluidic approach for continuous measurements of biofilm viscosity and the effect of ionic strength

Continuous, non-intrusive measurements of time-varying viscosity of Pseudomonas sp. biofilms are made using a microfluidic method that combines video tracking with a semi-empirical viscous flow model. The approach uses measured velocity and height of tracked biofilm segments, which move under the constant laminar flow of a nutrient solution. Following a low viscosity growth stage, rapid thickening was observed. During this stage, viscosity increased by over an order of magnitude in less than ten hours. The technique was also demonstrated as a promising platform for parallel experiments by subjecting multiple biofilm-laden microchannels to nutrient solutions containing NaCl in the range of 0 to 34 mM. Preliminary data suggest a strong relationship between ionic strength and biofilm properties, such as average viscosity and rapid thickening onset time. The technique opens the way for a combinatorial approach to study the response of biofilm viscosity under well-controlled physical, chemical and biological growth conditions.

Dynamics of bacterial streamers induced clogging in microfluidic devices

Using a microfabricated porous media mimic platform, we investigated the clogging dynamics of bacterial biomass that accumulated in the device due to the formation of bacterial streamers. Particularly, we found the existence of a distinct clogging front which advanced via pronounced 'stick-slip' of the viscoelastic bacterial biomass over the solid surface of the micro pillar. Thus, the streamer, the solid surface, and the background fluidic media defined a clear three-phase front influencing these advancing dynamics. Interestingly, we also found that once the clogging became substantial, contrary to a static homogenous saturation state, the clogged mimic exhibited an instability phenomena marked by localized streamer breakage and failure leading to extended water channels throughout the mimic. These findings have implications for design and fabrication of biomedical devices and membrane-type systems such as porous balloon catheters, porous stents and filtration membranes prone to bacteria induced clogging as well as understanding bacterial growth and proliferation in natural porous media such as soil and rocks.