Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes.

Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.

Microscale advection governs microbial growth and oxygen consumption in macroporous aggregates.

Most microbial life on Earth is found in localized microenvironments that collectively exert a crucial role in maintaining ecosystem health and influencing global biogeochemical cycles. In many habitats such as biofilms in aquatic systems, bacterial flocs in activated sludge, periphyton mats, or particles sinking in the ocean, these microenvironments experience sporadic or continuous flow. Depending on their microscale structure, pores and channels through the microenvironments permit localized flow that shifts the relative importance of diffusive and advective mass transport. How this flow alters nutrient supply, facilitates waste removal, drives the emergence of different microbial niches, and impacts the overall function of the microenvironments remains unclear. Here, we quantify how pores through microenvironments that permit flow can elevate nutrient supply to the resident bacterial community using a microfluidic experimental system and gain further insights from coupled population-based and computational fluid dynamics simulations. We find that the microscale structure determines the relative contribution of advection vs diffusion, and even a modest flow through a pore in the range of 10 µm s-1 can increase the carrying capacity of a microenvironment by 10%. Recognizing the fundamental role that microbial hotspots play in the Earth system, developing frameworks that predict how their heterogeneous morphology and potential interstitial flows change microbial function and collectively alter global scale fluxes is critical.IMPORTANCEMicrobial life is a key driver of global biogeochemical cycles. Similar to the distribution of humans on Earth, they are often not homogeneously distributed in nature but occur in dense clusters that resemble microbial cities. Within and around these clusters, diffusion is often assumed as the sole mass-transfer process that dictates nutrient supply and waste removal. In many natural and engineered systems such as biofilms in aquatic environments, aggregates in bioremediation, or flocs in wastewater treatment plants, these clusters are exposed to flow that elevates mass transfer, a process that is often overlooked. In this study, we show that advective fluxes can increase the local growth of bacteria in a single microenvironment by up to 50% and shape their metabolism by disrupting localized anoxia or supplying nutrients at different rates. Collectively, advection-enhanced mass transport may thus regulate important biogeochemical transformations in both natural and engineered environments.

An interdisciplinary and application-oriented approach to teach microfluidics.

Microfluidics is a relatively novel interdisciplinary research area with broad applications in chemistry, physics, material science, and biology. Despite the rapid growth of the field, students' exposure to microfluidic technologies is still limited and often insufficient to appreciate the advantages over other commonly used technologies. To this end, we designed a five-day course, "Microfluidics for microbial ecology," in which students with very different backgrounds learn the basics of microfluidic technologies and sample a range of applications in microbial ecology. The course was created for Master and Ph.D. students interested in applying microfluidics to their research and, therefore, followed an application-oriented approach. The presentation of critical aspects of fluid flow phenomena at the microscale and an outline of the advantages and constraints of the technology provide students with the background to design and perform microfluidics-based experiments. In order to improve the effectiveness of learning in a class with diverse interests and backgrounds, two active learning exercises were implemented. The first comprised the design of an individualized microfluidics experiment in parallel with the lectures: students were guided to apply each module to their personalized application and discuss it in groups. The second was a group experimental activity, in which students jointly set up, performed, analyzed, and presented a microfluidics-based experiment. Given the multidisciplinary teaching context, the course was able to foster common conceptual ground and promote discussion among students. This application-oriented approach built upon experimental activities and in-class discussion is well suited to promote learning in a technology-related subject such as microfluidics.

Healthy and diseased in vitro models of vascular systems.

Irregular hemodynamics affects the progression of various vascular diseases, such atherosclerosis or aneurysms. Despite the extensive hemodynamics studies on animal models, the inter-species differences between humans and animals hamper the translation of such findings. Recent advances in vascular tissue engineering and the suitability of in vitro models for interim analysis have increased the use of in vitro human vascular tissue models. Although the effect of flow on endothelial cell (EC) pathophysiology and EC-flow interactions have been vastly studied in two-dimensional systems, they cannot be used to understand the effect of other micro- and macro-environmental parameters associated with vessel wall diseases. To generate an ideal in vitro model of the vascular system, essential criteria should be included: 1) the presence of smooth muscle cells or perivascular cells underneath an EC monolayer, 2) an elastic mechanical response of tissue to pulsatile flow pressure, 3) flow conditions that accurately mimic the hemodynamics of diseases, and 4) geometrical features required for pathophysiological flow. In this paper, we review currently available in vitro models that include flow dynamics and discuss studies that have tried to address the criteria mentioned above. Finally, we critically review in vitro fluidic models of atherosclerosis, aneurysm, and thrombosis.

PhenoChip: A single-cell phenomic platform for high-throughput photophysiological analyses of microalgae.

Photosynthetic microorganisms are key players in aquatic ecosystems with strong potential for bioenergy production, yet their systematic selection at the single-cell level for improved productivity or stress resilience ("phenotyping") has remained largely inaccessible. To facilitate the phenotyping of microalgae and cyanobacteria, we developed "PhenoChip," a platform for the multiparametric photophysiological characterization and selection of unicellular phenotypes under user-controlled physicochemical conditions. We used PhenoChip to expose single cells of the coral symbiont Symbiodinium to thermal and chemical treatments and monitor single-cell photophysiology via chlorophyll fluorometry. This revealed strain-specific thermal sensitivity thresholds and distinct pH optima for photosynthetic performance, and permitted the identification of single cells with elevated resilience toward rising temperature. Optical expulsion technology was used to collect single cells from PhenoChip, and their propagation revealed indications of transgenerational preservation of photosynthetic phenotypes. PhenoChip represents a versatile platform for the phenotyping of photosynthetic unicells relevant to biotechnology, ecotoxicology, and assisted evolution.

Generating Controlled, Dynamic Chemical Landscapes to Study Microbial Behavior.

We demonstrate a method for the generation of controlled, dynamic chemical pulses-where localized chemoattractant becomes suddenly available at the microscale-to create micro-environments for microbial chemotaxis experiments. To create chemical pulses, we developed a system to introduce amino acid sources near-instantaneously by photolysis of caged amino acids within a polydimethylsiloxane (PDMS) microfluidic chamber containing a bacterial suspension. We applied this method to the chemotactic bacterium, Vibrio ordalii, which can actively climb these dynamic chemical gradients while being tracked by video microscopy. Amino acids, rendered biologically inert ('caged') by chemical modification with a photoremovable protecting group, are uniformly present in the suspension but not available for consumption until their sudden release, which occurs at user-defined points in time and space by means of a near-UV-A focused LED beam. The number of molecules released in the pulse can be determined by a calibration relationship between exposure time and uncaging fraction, where the absorption spectrum after photolysis is characterized by using UV-Vis spectroscopy. A nanoporous polycarbonate (PCTE) membrane can be integrated into the microfluidic device to allow the continuous removal by flow of the uncaged compounds and the spent media. A strong, irreversible bond between the PCTE membrane and the PDMS microfluidic structure is achieved by coating the membrane with a solution of 3-aminopropyltriethoxysilane (APTES) followed by plasma activation of the surfaces to be bonded. A computer-controlled system can generate user-defined sequences of pulses at different locations and with different intensities, so as to create resource landscapes with prescribed spatial and temporal variability. In each chemical landscape, the dynamics of bacterial movement at the individual scale and their accumulation at the population level can be obtained, thereby allowing the quantification of chemotactic performance and its effects on bacterial aggregations in ecologically relevant environments.

Bacterial maze runners reveal hidden diversity in chemotactic performance.

Chemotaxis allows microorganisms to exploit gradients in chemical stimuli to find nutrient resources and hosts or escape noxious substances. Thus, the life of individual microbes in their natural environments is a continual sequence of decisions based on the perceived chemical gradients. However, it has remained unclear to what extent the chemotaxis properties vary among cells of one species, and whether there is a spectrum of different 'decision makers' within populations of bacteria. In our recent study (Salek, Carrara et al., Nature Communications 10 (1), 1877), we combine microfluidic experiments with mathematical modeling to demonstrate that even in clonal populations, bacteria are individuals with different abilities to climb chemical gradients.

Bacterial chemotaxis in a microfluidic T-maze reveals strong phenotypic heterogeneity in chemotactic sensitivity.

Many microorganisms have evolved chemotactic strategies to exploit the microscale heterogeneity that frequently characterizes microbial habitats. Chemotaxis has been primarily studied as an average characteristic of a population, with little regard for variability among individuals. Here, we adopt a classic tool from animal ecology - the T-maze - and implement it at the microscale by using microfluidics to expose bacteria to a sequence of decisions, each consisting of migration up or down a chemical gradient. Single-cell observations of clonal Escherichia coli in the maze, coupled with a mathematical model, reveal that strong heterogeneity in the chemotactic sensitivity coefficient exists even within clonal populations of bacteria. A comparison of different potential sources of heterogeneity reveals that heterogeneity in the T-maze originates primarily from the chemotactic sensitivity coefficient, arising from a distribution of pathway gains. This heterogeneity may have a functional role, for example in the context of migratory bet-hedging strategies.

Intermittent turbulence in flowing bacterial suspensions.

Dense suspensions of motile bacteria, possibly including the human gut microbiome, exhibit collective dynamics akin to those observed in classic, high Reynolds number turbulence with important implications for chemical and biological transport, yet this analogy has remained primarily qualitative. Here, we present experiments in which a dense suspension of Bacillus subtilis bacteria was flowed through microchannels and the velocity statistics of the flowing suspension were quantified using a recently developed velocimetry technique coupled with vortex identification methods. Observations revealed a robust intermittency phenomenon, whereby the average velocity profile of the suspension fluctuated between a plug-like flow and a parabolic flow profile. This intermittency is a hallmark of the onset of classic turbulence and Lagrangian tracking revealed that it here originates from the presence of transient vortices in the active, collective motion of the bacteria locally reinforcing the externally imposed flow. These results link together two entirely different manifestations of turbulence and show the potential of the microfluidic approach to mimic the environment characteristic of certain niches of the human microbiome.

Analysis of fluid flow and wall shear stress patterns inside partially filled agitated culture well plates.

The appearance of highly resistant bacterial biofilms in both community and hospitals environments is a major challenge in modern clinical medicine. The biofilm structural morphology, believed to be an important factor affecting the behavioral properties of these "super bugs", is strongly influenced by the local hydrodynamics over the microcolonies. Despite the common use of agitated well plates in the biology community, they have been used rather blindly without knowing the flow characteristics and influence of the rotational speed and fluid volume in these containers. The main purpose of this study is to characterize the flow in these high-throughput devices to link local hydrodynamics to observed behavior in cell cultures. In this work, the flow and wall shear stress distribution in six-well culture plates under planar orbital translation is simulated using Computational Fluid Dynamics (CFD). Free surface, flow pattern and wall shear stress for two shaker speeds (100 and 200 rpm) and two volumes of fluid (2 and 4 mL) were investigated. Measurements with a non-intrusive optical shear stress sensor and High Frame-rate Particle Imaging Velocimetry (HFPIV) are used to validate CFD predictions. An analytical model to predict the free surface shape is proposed. Results show a complex three-dimensional flow pattern, varying in both time and space. The distribution of wall shear stress in these culture plates has been related to the topology of flow. This understanding helps explain observed endothelial cell orientation and bacterial biofilm distributions observed in culture dishes. The results suggest that the mean surface stress field is insufficient to capture the underlying dynamics mitigating biological processes.

Methicillin resistant Staphylococcus aureus adhesion to human umbilical vein endothelial cells demonstrates wall shear stress dependent behaviour.

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is an increasingly prevalent pathogen capable of causing severe vascular infections. The goal of this work was to investigate the role of shear stress in early adhesion events. METHODS: Human umbilical vein endothelial cells (HUVEC) were exposed to MRSA for 15-60 minutes and shear stresses of 0-1.2 Pa in a parallel plate flow chamber system. Confocal microscopy stacks were captured and analyzed to assess the number of MRSA. Flow chamber parameters were validated using micro-particle image velocimetry (PIV) and computational fluid dynamics modelling (CFD). RESULTS: Under static conditions, MRSA adhered to, and were internalized by, more than 80% of HUVEC at 15 minutes, and almost 100% of the cells at 1 hour. At 30 minutes, there was no change in the percent HUVEC infected between static and low flow (0.24 Pa), but a 15% decrease was seen at 1.2 Pa. The average number of MRSA per HUVEC decreased 22% between static and 0.24 Pa, and 37% between 0.24 Pa and 1.2 Pa. However, when corrected for changes in bacterial concentration near the surface due to flow, bacteria per area was shown to increase at 0.24 Pa compared to static, with a subsequent decline at 1.2 Pa. CONCLUSIONS: This study demonstrates that MRSA adhesion to endothelial cells is strongly influenced by flow conditions and time, and that MSRA adhere in greater numbers to regions of low shear stress. These areas are common in arterial bifurcations, locations also susceptible to generation of atherosclerosis.

The influence of flow cell geometry related shear stresses on the distribution, structure and susceptibility of Pseudomonas aeruginosa 01 biofilms.

The effects of non-uniform hydrodynamic conditions resulting from flow cell geometry (square and rectangular cross-section) on Pseudomonas aeruginosa 01 (PAO1) biofilm formation, location, and structure were investigated for nominally similar flow conditions using a combination of confocal scanning laser microscope (CSLM) and computational fluid dynamics (CFD). The thickness and surface coverage of PAO1 biofilms were observed to vary depending on the location in the flow cell and thus also the local wall shear stress. The biofilm structure in a 5:1 (width to height) aspect ratio rectangular flow cell was observed to consist mainly of a layer of bacterial cells with thicker biofilm formation observed in the flow cell corners. For square cross-section (1:1 aspect ratio) flow cells, generally thicker and more uniform surface coverage biofilms were observed. Mushroom shaped structures with hollow centers and wall breaks, indicative of 'seeding' dispersal structures, were found exclusively in the square cross-section tubes. Exposure of PAO1 biofilms grown in the flow cells to gentamicin revealed a difference in susceptibility. Biofilms grown in the rectangular flow cell overall exhibited a greater susceptibility to gentamicin compared to those grown in square flow cells. However, even within a given flow cell, differences in susceptibility were observed depending on location. This study demonstrates that the spanwise shear stress distribution within the flow cells has an important impact on the location of colonization and structure of the resultant biofilm. These differences in biofilm structure have a significant impact on the susceptibility of the biofilms grown within flow channels. The impact of flow modification due to flow cell geometry should be considered when designing flow cells for laboratory investigation of bacterial biofilms.