Bacterial chemotaxis toward a NAPL source within a pore-scale microfluidic chamber

Dimensionless Parameters Define Criteria for Optimal Flow Velocity in Enhancing Chemotactic Response toward Residual Contaminants in Porous Media

Chemotactic bacteria may overcome challenges posed by nonaqueous-phase liquid (NAPL) contaminants of low solubility in groundwater and limited bioavailability in tight pores by preferentially migrating to NAPL sources. We explored the transport of chemotactic bacteria to NAPL ganglia at varying pore water velocities in a dual-permeability microfluidic device and using computer-simulated solutions of transport equations. In our experiments, bacteria exhibited a chemotactic response toward NAPL ganglia at the junctures of low- and high-permeability regions (i.e., micropockets), and the extent of retention initially increased with velocity and then decreased at the highest velocity. A dimensional analysis revealed that maximum accumulations occurred at moderate values of the Péclet number P e c = v m d p χ o ∼10 in our system. We also found that accumulation dynamics in micropockets can be represented by a logistic equation incorporating convection and chemotaxis time scales τ f = L i v f and τ che = l a 2 χ o , respectively. By analyzing seven literature studies on chemotaxis, we identified an exposure time scale to chemicals τ exp = d p v f that was useful for evaluating the chemotaxis efficiency. Our study provided unique insights into the effect of fluid flow on chemotaxis in porous media by demonstrating that increasing the fluid velocity to some extent can promote chemotaxis. The dimensionless parameters inform the design of efficient bioremediation strategies for contaminated porous media.

Pore-scale visualization of LNAPL displacement by chemical agents in heterogeneous groundwater system

The remediation of light non-aqueous phase liquids (LNAPLs) from groundwater remains a critical environmental challenge, particularly in heterogeneous aquifers. Existing remediation techniques often struggle with low-permeability zones, limiting their effectiveness. In this study, we developed and validated a microfluidic platform to simulate heterogeneous porous media and evaluate the performance of four chemical agents, including the green bio-solvent Cyrene. Cyrene demonstrated superior efficiency, achieving a 30-45 % increase in oil removal compared to conventional agents, particularly in low-permeability zones. The platform enabled real-time visualization of pore-scale displacement processes, while the gray value method quantified residual oil saturation (Sor), and results demonstrated that permeability and pore structure significantly affect displacement efficiency. These findings highlight the scalability and environmental advantages of Cyrene for groundwater remediation and provide new insights into displacement mechanisms in complex subsurface systems.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals

In this review, selected examples are presented to demonstrate how microfluidic approaches can be utilized for investigating microbial life from deep geological environments, both from practical and fundamental perspectives. Beginning with the definition of the deep underground biosphere and the conventional experimental techniques employed for these studies, the use of microfluidic systems for accessing critical parameters of deep life in geological environments at the microscale is subsequently addressed (high pressure, high temperature, low volume). Microfluidics can simulate a range of environmental conditions on a chip, enabling rapid and comprehensive studies of microbial behavior and interactions in subsurface ecosystems, such as simulations of porous systems, interactions among microbes/microbes/minerals, and gradient cultivation. Transparent microreactors allow real-time, noninvasive analysis of microbial activities (microscopy, Raman spectroscopy, FTIR microspectroscopy, etc.), providing detailed insights into biogeochemical processes and facilitating pore-scale analysis. Finally, the current challenges and opportunities to expand the use of microfluidic methodologies for studying and monitoring the deep biosphere in real time under deep underground conditions are discussed.

Effects of mono- and multicomponent nonaqueous-phase liquid on the migration and retention of pollutant-degrading bacteria in porous media

The successful implementation of in-situ bioremediation of nonaqueous-phase liquid (NAPL) contamination in soil-groundwater systems is greatly influenced by the migration performance of NAPL-degrading bacteria. However, the impact and mechanisms of NAPL on the migration/retention of pollutant-degrading bacteria remain unclear. This study investigated the migration/retention performance of A. lwoffii U1091, a strain capable of degrading diesel while producing surfactants, in porous media without and with the presence of mono- and multicomponent NAPL (n-dodecane and diesel) under environmentally relevant conditions. The results showed that under all examined conditions (5 and 50 mM NaCl solution at flow rates of 4 and 8 m/d), the presence of n-dodecane/diesel in porous media could reduce the migration and enhance retention of A. lwoffii in quartz sand columns. Moreover, comparing with mutlicomponent NAPLs of n-dodecane, the monocomponent NAPLs (diesel) exhibited a greater reduction effect on the retention of A. lwoffii in porous media. Through systemically investigating the potential mechanisms via tracer experiment, visible chamber experiment, and theoretical calculation, we found that the reduction in porosity, repulsive forces and movement speeds, the presence of stagnant flow zones in porous media, particularly the biosurfactants generated by A. lwoffii contributed to the enhanced retention of bacteria in NAPL-contaminated porous media. Moreover, owing to presence of the greater amount of hydrophilic components in diesel than in n-dodecane, the available binding sites for the adsorption of bacteria were lower in diesel, resulting in the slightly decreased retention of A. lwoffii in porous media containing diesel than n-dodecane. This study demonstrated that comparing with porous media without NAPL contamination, the retention of strain capable of degrading NAPL in porous media with NAPL contamination was enhanced, beneficial for the subsequent biodegradation of NAPL.

Lab on a chip for a low-carbon future

Transitioning our society to a sustainable future, with low or net-zero carbon emissions to the atmosphere, will require a wide-spread transformation of energy and environmental technologies. In this perspective article, we describe how lab-on-a-chip (LoC) systems can help address this challenge by providing insight into the fundamental physical and geochemical processes underlying new technologies critical to this transition, and developing the new processes and materials required. We focus on six areas: (I) subsurface carbon sequestration, (II) subsurface hydrogen storage, (III) geothermal energy extraction, (IV) bioenergy, (V) recovering critical materials, and (VI) water filtration and remediation. We hope to engage the LoC community in the many opportunities within the transition ahead, and highlight the potential of LoC approaches to the broader community of researchers, industry experts, and policy makers working toward a low-carbon future.

Chemotaxis along local chemical gradients enhanced bacteria dispersion and PAH bioavailability in a heterogenous porous medium

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous, EPA-designated priority pollutants for soil and groundwater, remaining recalcitrant to bioremediation because of limited bioavailability. In this work, we used naphthalene as a model PAH and soil bacteria Pseudomonas putida G7 to investigate the potential role of chemotaxis to enhance access to PAHs in heterogenous porous media. To this aim, we conducted transport experiments and numerical simulations with chemotactic bacteria and naphthalene trapped within a non-aqueous phase liquid (NAPL) mainly in low permeable areas of a dual-permeability microfluidic device. Microscopic imaging showed higher accumulations of chemotactic bacteria, about eight times that of nonchemotactic bacteria, at the junctures between high and low permeability regions. Pore-scale simulations for fluid flow and naphthalene revealed that the junctures are stagnant areas of fluid flow, which generated strong and temporally persistent naphthalene gradients. The landscape and densities of bacterial accumulation at the junctures were strongly regulated by flow profiles and naphthalene gradients especially those transverse to flow. We conducted macroscale simulations using convective dispersion equations with an added chemotactic velocity to account for directed migration toward naphthalene. Simulated results showed good consistency with experiments and pore-scale simulation as normalized bacterial accumulation per mm of NAPL was 7.80, 7.84 and 7.71 mm^-1 for experiments, pore-scale and macroscale simulations, respectively. Macroscale simulations indicated that in the absence of grain-boundary restrictions associated with the pore structure bacterial dispersion needed to be increased by 50 % to account for the interplay between chemotactic response and naphthalene gradients at the pore-scale level. Our work details the mechanism of pore-scale chemotaxis in enhancing bioavailability of PAHs and its impact on biomass retention at the system level, which provides a potential solution toward more efficient bioremediation for contaminants such as PAHs with limited bioavailability.

Numerical Simulation of the Enrichment of Chemotactic Bacteria in Oil-Water Two-Phase Transfer Fields of Heterogeneous Porous Media

Oil pollution in soil-groundwater systems is difficult to remove, and a large amount of residual oil is trapped in the low permeable layer of the heterogeneous aquifer. Aromatic hydrocarbons in oil have high toxicity and low solubility in water, which are harmful to the ecological environment. Chemotactic degrading bacteria can perceive the concentration gradient of non-aqueous phase liquid (NAPL) pollutants in the groundwater environment, and enrich and proliferate around the pollutants, thus achieving a more efficient and thorough remediation effect. However, the existing theoretical models are relatively simple. The physical fields of oil–water two-phase flow and oil-phase solute convection and diffusion in water are not coupled, which further restricts the accuracy of studies on bacterial chemotaxis to NAPL. In this study, geometric models based on the actual microfluidic experimental study were constructed. Based on the phase field model, diffusion convection equation and chemotaxis velocity equation, the effects of heterogeneity of porous media, wall wettability and groundwater flow rate on the residual oil and the concentration distribution of chemotaxis bacteria were studied. Under all of the simulation conditions, the residual oil in the high permeable area was significantly lower than that in the low permeable area, and the wall hydrophilicity enhanced the water flooding effect. Chemotactic bacteria could react to the concentration gradient of pollutants dissolved into water in the oil phase, and enrich near the oil–water interface with high concentration of NAPL, and the density of chemotactic bacteria at the oil–water interface can be up to 1.8–2 times higher than that in the water phase at flow rates from 1.13 to 6.78 m/d.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Chemotaxis Increases the Retention of Bacteria in Porous Media with Residual NAPL Entrapment

Chemotaxis has the potential to decrease the persistence of nonaqueous phase liquid (NAPL) contaminants in aquifers by allowing pollutant-degrading bacteria to move toward sources of contamination and thus influence dissolution. This experimental study investigated the migratory response of chemotactic bacteria to a distribution of residual NAPL ganglia entrapped within a laboratory-scale sand column under continuous-flow at a superficial velocity of 0.05 cm/min. Naphthalene dissolved in a model NAPL 2,2,4,4,6,8,8-heptamethylnonane partitioned into the aqueous phase to create localized chemoattractant gradients throughout the column. A pulse mixture of equal concentrations of Pseudomonas putida G7, a strain chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a nonchemotactic mutant, was introduced to the column and effluent bacterial concentrations were measured with time. Breakthrough curves (BTCs) for the two strains were noticeably different upon visual inspection. Differences in BTCs (compared to nonchemotactic controls) were quantified in terms of percent recovery and were statistically significant ( p < 0.01). Chemotaxis reduced percent recovery in the effluent by 45% thereby increasing the population of bacteria that were retained within the column in the vicinity of residual NAPL contaminants. An increase in flow rate to a superficial velocity of 0.25 cm/min did not diminish cell retention associated with the chemotactic effect.

Modeling Transport of Chemotactic Bacteria in Granular Media with Distributed Contaminant Sources

Chemotaxis has the potential to improve bioremediation strategies by enhancing the transport of pollutant-degrading bacteria to the source of contamination, leading to increased pollutant accessibility and biodegradation. This computational study extends work reported previously in the literature to include predictions of chemotactic bacterial migration in response to multiple localized contaminant sources within porous media. An advection-dispersion model, in which chemotaxis was represented explicitly as an additional advection-like term, was employed to simulate the transport of bacteria within a sand-packed column containing a distribution of chemoattractant sources. Simulation results provided insight into attractant and bacterial distributions within the column. In particular, it was found that chemotactic bacteria exhibited a distinct biased migration toward contaminant sources that resulted in a 30% decrease in cell recovery, and concomitantly an enhanced retention within the sand column, compared to the nonchemotactic control. Model results were consistent with experimental observations. Parametric studies were conducted to provide insight into the influence of chemotaxis parameters on bacterial migration and cell percent recovery. The model results provide a better understanding of the effect of chemotaxis on bacterial transport in response to distributed contaminant sources.

Enhanced Retention of Chemotactic Bacteria in a Pore Network with Residual NAPL Contamination

Nonaqueous-phase liquid (NAPL) contaminants are difficult to eliminate from natural aquifers due, in part, to the heterogeneous structure of the soil. Chemotaxis enhances the mixing of bacteria with contaminant sources in low-permeability regions, which may not be readily accessible by advection and dispersion alone. A microfluidic device was designed to mimic heterogeneous features of a contaminated groundwater aquifer. NAPL droplets (toluene) were trapped within a fine pore network, and bacteria were injected through a highly conductive adjacent macrochannel. Chemotactic bacteria (Pseudomonas putida F1) exhibited greater accumulation near the pore network at 0.5 m/day than both the nonchemotactic control and the chemotactic bacteria at a higher groundwater velocity of 5 m/day. Chemotactic bacteria accumulated in the vicinity of NAPL droplets, and the accumulation was 15% greater than a nonchemotactic mutant. Indirect evidence showed that chemotactic bacteria were retained within the contaminated low-permeability region longer than nonchemotactic bacteria at 0.25 m/day. This retention was diminished at 5 m/day. Numerical solutions of the bacterial-transport equations were consistent with the experimental results. Because toluene is degraded by P. putida F1, the accumulation of chemotactic bacteria around NAPL sources is expected to increase contaminant consumption and improve the efficiency of bioremediation.

Chemotaxis Increases the Residence Time of Bacteria in Granular Media Containing Distributed Contaminant Sources

The use of chemotactic bacteria in bioremediation has the potential to increase access to, and the biotransformation of, contaminant mass within the subsurface. This laboratory-scale study aimed to understand and quantify the influence of chemotaxis on the residence times of pollutant-degrading bacteria within homogeneous treatment zones. Focus was placed on a continuous-flow sand-packed column in which a uniform distribution of naphthalene crystals created distributed sources of dissolved-phase contaminant. A 10 mL pulse of Pseudomonas putida G7, which is chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a nonchemotactic mutant strain, were simultaneously introduced into the sand-packed column at equal concentrations. Breakthrough curves obtained from experiments conducted with and without naphthalene were used to quantify the effect of chemotaxis on transport parameters. In the presence of the chemoattractant, longitudinal dispersion of PpG7 increased by a factor of 3, and percent recovery decreased by 43%. In contrast, PpG7 Y1 transport was not influenced by the presence of naphthalene. The results imply that pore-scale chemotaxis responses are evident at an interstitial velocity of 1.8 m/day, which is within the range of typical groundwater flow. Within the context of bioremediation, chemotaxis may work to enhance bacterial residence times in zones of contamination, thereby improving treatment.

Swimming Motility Reduces Deposition to Silica Surfaces

The transport and fate of bacteria in porous media is influenced by physicochemical and biological properties. This study investigated the effect of swimming motility on the attachment of cells to silica surfaces through comprehensive analysis of cell deposition in model porous media. Distinct motilities were quantified for different strains using global and cluster-based statistical analyses of microscopic images taken under no-flow condition. The wild-type, flagellated strain DJ showed strong swimming as a result of the actively swimming subpopulation whose average speed was 25.6 μm/s; the impaired swimming of strain DJ77 was attributed to the lower average speed of 17.4 μm/s in its actively swimming subpopulation; and both the nonflagellated JZ52 and chemically treated DJ cells were nonmotile. The approach and deposition of these bacterial cells were analyzed in porous media setups, including single-collector radial stagnation point flow cells (RSPF) and two-dimensional multiple-collector micromodels under well-defined hydrodynamic conditions. In RSPF experiments, both swimming and nonmotile cells moved with the flow when at a distance ≥20 μm above the collector surface. Closer to the surface, DJ cells showed both horizontal and vertical movement, limiting their contact with the surface, while chemically treated DJ cells moved with the flow to reach the surface. These results explain how wild-type swimming reduces attachment. In agreement, the deposition in micromodels was also lowest for DJ compared with those for DJ77 and JZ52. Wild-type swimming specifically reduced deposition on the upstream surfaces of the micromodel collectors. Conducted under environmentally relevant hydrodynamic conditions, the results suggest that swimming motility is an important characteristic for bacterial deposition and transport in the environment.

Quantitative analysis of chemotaxis towards toluene by Pseudomonas putida in a convection-free microfluidic device

Chemotaxis has been shown to be beneficial for the migration of soil-inhabiting bacteria towards industrial chemical pollutants, which they degrade. Many studies have demonstrated the importance of this microbial property under various circumstances; however, few quantitative analyses have been undertaken to measure the two essential parameters that characterize the chemotaxis of bioremediation bacteria: the chemotactic sensitivity coefficient χ(0) and the chemotactic receptor constant K(c). The main challenge to determine these parameters is that χ(0) and K(c) are coupled together in non-linear mathematical models used to evaluate them. In this study we developed a method to accurately measure these parameters for Pseudomonas putida in the presence of toluene, an important pollutant in groundwater contamination. Our approach uses a multilayer microfluidic device to expose bacteria to a convection-free linear chemical gradient of toluene that is stable over time. The bacterial distribution within the gradient is measured in terms of fluorescence intensity, and is then used to fit the parameters Kc and χ(0) with mathematical models. Critically, bacterial distributions under chemical gradients at two different concentrations were used to solve for both parameters independently. To validate the approach, the chemotaxis parameters of Escherichia coli strains towards α-methylaspartate were experimentally derived and were found to be consistent with published results from related work.

A multiple-relaxation-time lattice-boltzmann model for bacterial chemotaxis: effects of initial concentration, diffusion, and hydrodynamic dispersion on traveling bacterial bands

Bacterial chemotaxis can enhance the bioremediation of contaminants in aqueous and subsurface environments if the contaminant is a chemoattractant that the bacteria degrade. The process can be promoted by traveling bands of chemotactic bacteria that form due to metabolism-generated gradients in chemoattractant concentration. We developed a multiple-relaxation-time (MRT) lattice-Boltzmann method (LBM) to model chemotaxis, because LBMs are well suited to model reactive transport in the complex geometries that are typical for subsurface porous media. This MRT-LBM can attain a better numerical stability than its corresponding single-relaxation-time LBM. We performed simulations to investigate the effects of substrate diffusion, initial bacterial concentration, and hydrodynamic dispersion on the formation, shape, and propagation of bacterial bands. Band formation requires a sufficiently high initial number of bacteria and a small substrate diffusion coefficient. Uniform flow does not affect the bands while shear flow does. Bacterial bands can move both upstream and downstream when the flow velocity is small. However, the bands disappear once the velocity becomes too large due to hydrodynamic dispersion. Generally bands can only be observed if the dimensionless ratio between the chemotactic sensitivity coefficient and the effective diffusion coefficient of the bacteria exceeds a critical value, that is, when the biased movement due to chemotaxis overcomes the diffusion-like movement due to the random motility and hydrodynamic dispersion.

Coupled effects of chemotaxis and growth on traveling bacterial waves

Traveling bacterial waves are capable of improving contaminant remediation in the subsurface. It is fairly well understood how bacterial chemotaxis and growth separately affect the formation and propagation of such waves. However, their interaction is not well understood. We therefore perform a modeling study to investigate the coupled effects of chemotaxis and growth on bacterial migration, and examine their effects on contaminant remediation. We study the waves by using different initial electron acceptor concentrations for different bacteria and substrate systems. Three types of traveling waves can occur: a chemotactic wave due to the biased movement of chemotactic bacteria resulting from metabolism-generated substrate concentration gradients; a growth/decay/motility wave due to a dynamic equilibrium between bacterial growth, decay and random motility; and an integrated wave due to the interaction between bacterial chemotaxis and growth. Chemotaxis hardly enhances the bacterial propagation if it is too weak to form a chemotactic wave or its wave speed is less than half of the growth/decay/motility wave speed. However, chemotaxis significantly accelerates bacterial propagation once its wave speed exceeds the growth/decay/motility wave speed. When convection occurs, it speeds up the growth/decay/motility wave but slows down or even eliminates the chemotactic wave due to the dispersion. Bacterial survival proves particularly important for bacterial propagation. Therefore we develop a conceptual model to estimate the speed of growth/decay/motility waves.

Recent developments in microfluidics-based chemotaxis studies

Microfluidic devices can better control cellular microenvironments compared to conventional cell migration assays. Over the past few years, microfluidics-based chemotaxis studies showed a rapid growth. New strategies were developed to explore cell migration in manipulated chemical gradients. In addition to expanding the use of microfluidic devices for a broader range of cell types, microfluidic devices were used to study cell migration and chemotaxis in complex environments. Furthermore, high-throughput microfluidic chemotaxis devices and integrated microfluidic chemotaxis systems were developed for medical and commercial applications. In this article, we review recent developments in microfluidics-based chemotaxis studies and discuss the new trends in this field observed over the past few years.

Chemotaxis migration and morphogenesis of living colonies

Development of forms in living organisms is complex and fascinating. Morphogenetic theories that investigate these shapes range from discrete to continuous models, from the variational elasticity to time-dependent fluid approach. Here a mixture model is chosen to describe the mass transport in a morphogenetic gradient: it gives a mathematical description of a mixture involving several constituents in mechanical interactions. This model, which is highly flexible can incorporate many biological processes but also complex interactions between cells as well as between cells and their environment. We use this model to derive a free-boundary problem easier to handle analytically. We solve it in the simplest geometry: an infinite linear front advancing with a constant velocity. In all the cases investigated here as the 3 D diffusion, the increase of mitotic activity at the border, nonlinear laws for the uptake of morphogens or for the mobility coefficient, a planar front exists above a critical threshold for the mobility coefficient but it becomes unstable just above the threshold at long wavelengths due to the existence of a Goldstone mode. This explains why sparsely bacteria exhibit dendritic patterns experimentally in opposition to other colonies such as biofilms and epithelia which are more compact. In the most unstable situation, where all the laws: diffusion, chemotaxis driving and chemoattractant uptake are linear, we show also that the system can recover a dynamic stability. A second threshold for the mobility exists which has a lower value as the ratio between diffusion coefficients decreases. Within the framework of this model where the biomass is treated mainly as a viscous and diffusive fluid, we show that the multiplicity of independent parameters in real biologic experimental set-up may explain varieties of observed patterns.