Abiotic streamers in a microfluidic system

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.

The structural role of bacterial eDNA in the formation of biofilm streamers

Streamers, filamentous bacterial biofilms formed in flowing systems, are ubiquitous in natural and artificial environments, where they cause clogging of devices and spreading of infections. Despite their impact, little is known about the nature and properties of streamers and their response to fluid flow. Here, we uncover the specific contribution of bacterial secreted extracellular DNA and exopolysaccharide Pel, two important components in Pseudomonas aeruginosa biofilms, to the formation and the mechanical properties of the streamers. We then show how this knowledge can be used to control biofilm streamer formation, both to inhibit or to promote it.

Across diverse habitats, bacteria are mainly found as biofilms, surface-attached communities embedded in a self-secreted matrix of extracellular polymeric substances (EPS), which enhance bacterial recalcitrance to antimicrobial treatment and mechanical stresses. In the presence of flow and geometric constraints such as corners or constrictions, biofilms can take the form of long, suspended filaments (streamers), which bear important consequences in industrial and clinical settings by causing clogging and fouling. The formation of streamers is thought to be driven by the viscoelastic nature of the biofilm matrix. Yet, little is known about the structural composition of streamers and how it affects their mechanical properties. Here, using a microfluidic platform that allows growing and precisely examining biofilm streamers, we show that extracellular DNA (eDNA) constitutes the backbone and is essential for the mechanical stability of Pseudomonas aeruginosa streamers. This finding is supported by the observations that DNA-degrading enzymes prevent the formation of streamers and clear already formed ones and that the antibiotic ciprofloxacin promotes their formation by increasing the release of eDNA. Furthermore, using mutants for the production of the exopolysaccharide Pel, an important component of P. aeruginosa EPS, we reveal an concurring role of Pel in tuning the mechanical properties of the streamers. Taken together, these results highlight the importance of eDNA and of its interplay with Pel in determining the mechanical properties of P. aeruginosa streamers and suggest that targeting the composition of streamers can be an effective approach to control the formation of these biofilm structures.

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.

Mapping the local viscosity of non-Newtonian fluids flowing through disordered porous structures

Flow of non-Newtonian fluids through topologically complex structures is ubiquitous in most biological, industrial and environmental settings. The interplay between local hydrodynamics and the fluid’s constitutive law determines the distribution of flow paths. Consequently the spatial heterogeneity of the viscous resistance controls mass and solute transport from the micron to the meter scale. Examples range from oil recovery and groundwater engineering to drug delivery, filters and catalysts. Here we present a new methodology to map the spatial variation of the local viscosity of a non-Newtonian fluid flowing through a complex pore geometry. We use high resolution image velocimetry to determine local shear rates. Knowing the local shear rate in combination with a separate measurement of the fluid’s constitutive law allows to quantitatively map the local viscosity at the pore scale. Our experimental results—which closely match with three-dimensional numerical simulations—demonstrate that the exponential decay of the longitudinal velocity distributions, previously observed for Newtonian fluids, is a function of the spatial heterogeneity of the local viscosity. This work sheds light on the relationship between hydraulic properties and the viscosity at the pore scale, which is of fundamental importance for predicting transport properties, mixing, and chemical reactions in many porous systems.

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.

Effect of microchannel structure and fluid properties on non-inertial particle migration

In this work, we investigate the influence of channel structure and fluid rheology on non-inertial migration of non-Brownian polystyrene beads. Particle migration in this regime can be found in biomedical, chemical, environmental and geological applications. However, the effect of fluid rheology on particle migration in porous media remains to be clearly understood. Here, we isolate the effects of elasticity and shear thinning by comparing a Newtonian fluid, a purely elastic (Boger) fluid, and a shear-thinning elastic fluid. To mimic the complexity of geometries in real-world application, a random porous structure is created through a disordered arrangement of cylindrical pillars in the microchannel. Experiments are repeated in an empty channel and in channels with an ordered arrangement of pillars, and the similarities and differences in the observed particle focusing are analyzed. It is found that elasticity drives the particles away from the channel walls in an empty microchannel. Notably, particle focusing is unaffected by curved streamlines in an ordered porous microchannel and particles stay away from pillars in elastic fluids. Shear-thinning is found to reduce the effect of focusing and a broader region of particle concentration is observed. It is also noteworthy that the rheological characteristics of the fluid are not important for the particle distribution in a randomly arranged pillared microchannel and particles have a uniform distribution for all suspending fluids. Moreover, discussion on the current discrepancy in the literature about the equilibrium positions of the particles in a channel is extended by analyzing the results obtained in the current experiments.

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.