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

Microfluidic Study on Green Remediation of Nonaqueous Phase Liquid (NAPL) Contamination in Heterogeneous Groundwater Systems Using Dihydrolevoclucosenone (Cyrene)

One of the primary challenges in conventional remediation of nonaqueous phase liquid (NAPL) contamination in groundwater is the heterogeneous nature of the groundwater system. Conventional remediation agents are often carried away by groundwater flow in high-permeability layers, making it difficult to access NAPL contaminants in low-permeability layers and are prone to generate secondary contamination. This study explores the use of dihydrolevoclucosenone (Cyrene), a bioderived green solvent, as an alternative to traditional remediating agents for NAPL remediation. Through microfluidic experiments and accompanying numerical modeling, we demonstrate that Cyrene enhances the dissolution and mobilization of NAPL contaminants, particularly in low-permeability zones, achieving residual NAPL reductions of up to 80% compared with water and Tween 80 solutions. These findings underscore Cyrene's dual environmental benefits as an eco-friendly solvent for both treating solid waste (e.g., stalks) and for NAPL remediation, paving the way for sustainable and green solutions in environmental management.

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.

Microbial chemotaxis in degradation of xenobiotics: Current trends and opportunities

Chemotaxis, the directed movement of microbes in response to chemical gradients, plays a crucial role in the biodegradation of xenobiotics, such as pesticides, industrial chemicals, and pharmaceuticals, which pose significant environmental and health risks. Emerging trends in genomics, proteomics, and synthetic biology have advanced our understanding and control of these processes, thereby enabling the development of engineered microorganisms with tailored chemotactic responses and degradation capabilities. This process plays an essential physiological role in processes, such as surface sensing, biofilm formation, quorum detection, pathogenicity, colonization, symbiotic interactions with the host system, and plant growth promotion. Field applications have demonstrated the potential of bioremediation for cleaning contaminated environments. Therefore, it helps to increase the bioavailability of pollutants and enables bacteria to access distantly located pollutants. Despite considerable breakthroughs in decoding the regulatory mechanisms of bacterial chemotaxis, there are still gaps in knowledge that need to be resolved to harness its potential for sensing and degrading pollutants in the environment. This review covers the role of bacterial chemotaxis in the degradation of xenobiotics present in the environment, focusing on chemotaxis-based bacterial and microfluidic biosensors for environmental monitoring. Finally, we highlight the current challenges and future perspectives for developing more effective and sustainable strategies to mitigate the environmental impact of xenobiotics.

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.

Microfluidic approaches in microbial ecology

Microbial life is at the heart of many diverse environments and regulates most natural processes, from the functioning of animal organs to the cycling of global carbon. Yet, the study of microbial ecology is often limited by challenges in visualizing microbial processes and replicating the environmental conditions under which they unfold. Microfluidics operates at the characteristic scale at which microorganisms live and perform their functions, thus allowing for the observation and quantification of behaviors such as growth, motility, and responses to external cues, often with greater detail than classical techniques. By enabling a high degree of control in space and time of environmental conditions such as nutrient gradients, pH levels, and fluid flow patterns, microfluidics further provides the opportunity to study microbial processes in conditions that mimic the natural settings harboring microbial life. In this review, we describe how recent applications of microfluidic systems to microbial ecology have enriched our understanding of microbial life and microbial communities. We highlight discoveries enabled by microfluidic approaches ranging from single-cell behaviors to the functioning of multi-cellular communities, and we indicate potential future opportunities to use microfluidics to further advance our understanding of microbial processes and their implications.

Risk reductions during pyrene biotransformation and mobilization in a model plant-bacteria-biochar system

The productive application of motile microorganisms for degrading hydrophobic contaminants in soil is one of the most promising processes in modern remediation due to its sustainability and low cost. However, the incomplete biodegradation of the contaminants and the formation of the intermediary metabolites in the process may increase the toxicity in soil during bioremediation, and motile inoculants may mobilize the pollutants through biosorption. Therefore, controlling these factors should be a fundamental part of soil remediation approaches. The aim of this study was to evaluate the sources of risk associated with the cometabolism-based transformation of ¹⁴C-labeled pyrene by inoculated Pseudomonas putida G7 and identify ways to minimize risk. Our model scenario examined the increase in bioaccessibility to a distant source of contamination facilitated by sunflower (Helianthus annuus L.) roots. A biochar trap for mobilized pollutant metabolites and bacteria has also been employed. The experimental design consisted of pots filled with a layer of sand with ¹⁴C-labeled pyrene (88 mg kg^-1) as a contamination focus located several centimeters from the inoculation point. Half of the pots included a biochar layer at the bottom. The pots were incubated in a greenhouse with sunflower plants and P. putida G7 bacteria. Pots with sunflower plants showed a higher biodegradation of pyrene, its mobilization as metabolites through the percolate and the roots, and bacterial mobilization toward the source of contamination, also resulting in increased pyrene transformation. In addition, the biochar layer efficiently reduced the concentrations of pyrene metabolites collected in the leachates. Therefore, the combination of plants, motile bacteria and biochar safely reduced the risk caused by the biological transformation of pyrene.

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.

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.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Towards a digital twin for characterising natural source zone depletion: A feasibility study based on the Bemidji site

Natural source zone depletion (NSZD) of light non-aqueous phase liquids (LNAPLs) may be a valid long-term management option at petroleum impacted sites. However, its future long-term reliability needs to be established. NSZD includes partitioning, biotic and abiotic degradation of LNAPL components plus multiphase fluid dynamics in the subsurface. Over time, LNAPL components are depleted and those partitioning to various phases change, as do those available for biodegradation. To accommodate these processes and predict trends and NSZD over decades to centuries, for the first time, we incorporated a multi-phase multi-component multi-microbe non-isothermal approach to representatively simulate NSZD at field scale. To validate the approach we successfully mimic data from the LNAPL release at the Bemidji site. We simulate the entire depth of saturated and unsaturated zones over the 27 years of post-release measurements. The study progresses the idea of creating a generic digital twin of NSZD processes and future trends. Outcomes show the feasibility and affordability of such detailed computational approaches to improve decision-making for site management and restoration strategies. The study provided a basis to progress a computational digital twin for complex subsurface systems.

Anaerobic bacterial responses to carbonaceous materials and implications for contaminant transformation: Cellular, metabolic, and community level findings

Carbonaceous materials (CM) enhance the abundance and activity of bacteria capable of persistent organic (micro)pollutant (POP) degradation. This review synthesizes anaerobic bacterial responses to minimally modified CM in non-fuel cell bioremediation applications at three stages: attachment, metabolism, and biofilm genetic composition. Established relationships between biological behavior and CM surface properties are identified, but temporal relationships are not well understood, making it difficult to connect substratum properties and "pioneer" bacteria with mature microorganism-CM systems. Stark differences in laboratory methodology at each temporal stage results in observational, but not causative, linkages as system complexity increases. This review is the first to critically examine relationships between material and cellular properties with respect to time. The work highlights critical knowledge gaps that must be addressed to accurately predict microorganism-CM behavior and to tailor CM properties for optimized microbial activity, critical frontiers in establishing this approach as an effective bioremediation strategy.

Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media

The fate and transport of bacteria in porous media are essential for bioremediation and water quality control. However, the influence of biological activities like extracellular electron transfer (EET) and swimming motility toward granular media on cell transport remains unknown. Here, electroactive bacteria with higher Fe(III) reduction abilities were found to demonstrate greater retention in ferrihydrite-coated sand. Increasing the concentrations of the electron donor (1-10 mM lactate), shuttle (0-50 μM anthraquinone-2,6-disulfonate), and acceptor (ferrihydrite, MnO₂, or biochar) under flow conditions significantly reduced Shewanella oneidensis MR-1's mobility through redox-active porous media. The deficiency of EET ability or flagellar motion and inhibition of intracellular proton motive force, all of which are essential for energy taxis, enhanced MR-1's transport. It was proposed that EET could facilitate MR-1 to sense, tactically move toward, and attach on redox-active media surface, eventually improving its retention. Positive linear correlations were established among parameters describing MR-1's energy taxis ability (relative taxis index), cell transport behavior (dispersion coefficient and relative change of effluent percentage), and redox activity of media surface (reduction potential or electron-accepting rate), providing novel insights into the critical impacts of bacterial microscale motility on macroscale cell transport through porous media.

Phytoremediation of cadmium-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization in the Solanum nigrum L. rhizosphere

Microbe-assisted phytoremediation for Cd-polluted soil is being regarded increasingly. However, the availability of microbes that can collaborate with Cd-hyperaccumulators effectively has become one of bottlenecks restricting the remediation efficiency. A siderophore-producing bacterium (Y16; Enterobacter cloacae) isolated from the rhizospheric soil of Cd-hyperaccumulator Solanum nigrum L. was identified by 16S rRNA gene sequencing and biochemical analysis, and then used for analyzing microbial chemotaxis, carbon source utilization, and insoluble P/Cd mobilization capacities. Besides, a soil-pot trial was performed to underlie the phytoremediation mechanism of Cd-polluted soil assisted by D-gluconate-enhanced Enterobacter cloacae colonization (DEYC) in the Solanum nigrum L. rhizosphere. Results displayed that D-gluconate was an effective chemoattractant and carbon source strengthening Y16 colonization, and Y16 exhibited strong abilities to mobilize insoluble P/Cd in shake flask by extracellular acidification (p < 0.05). In the soil-pot trial, DEYC observably enhanced soil Cd phytoextraction by Solanum nigrum L., and increased microbial diversity according to alpha- and beta-diversity analysis (p < 0.05). Taxonomic distribution and co-occurrence network analysis suggested that DEYC increased relative abundances of dominant microbial taxa associated with soil acidification (Acidobacteria-6), indoleacetic acid secretion (Ensifer adhaerens), soil fertility improvement (Flavisolibacter, Bdellovibrio bacteriovorus, and Candidatus nitrososphaera), and insoluble Cd mobilization (Massilia timonae) at different classification levels. Importantly, COGs analysis further shown that DEYC aroused the up-regulation of key genes related to chemotactic motility, carbon fixation, TCA cycle, and propanoate metabolism. These results indicated that DEYC drove the rhizospheric enrichment of pivotal microbial taxa directly or indirectly involved in soil Cd mobilization, meanwhile distinctly promoted plant growth for accumulating more mobilizable Cd. Therefore, Y16 could be used as bio-inoculants for assisting phytoremediation of Cd-polluted soil.

Biophysical methods to quantify bacterial behaviors at oil-water interfaces

Motivated by the need for improved understanding of physical processes involved in bacterial biodegradation of catastrophic oil spills, we review biophysical methods to probe bacterial motility and adhesion at oil-water interfaces. This review summarizes methods that probe bulk, average behaviors as well as local, microscopic behaviors, and highlights opportunities for future work to bridge the gap between biodegradation and biophysics.

Surface-Adsorbed Contaminants Mediate the Importance of Chemotaxis and Haptotaxis for Bacterial Transport Through Soils

Chemotaxis and haptotaxis are important biological mechanisms that influence microbial movement toward concentrated chemoattractants in mobile liquids and along immobile surfaces, respectively. This study investigated their coupled effect, as induced by naphthalene (10 mg L⁻¹), on the transport and retention of two pollutant-degrading bacteria, Pseudomonas fluorescens 5RL (Pf5RL) and Pseudomonas stutzeri DQ1 (PsDQ1), in quartz sand and natural soil. The results demonstrated that PsDQ1 was not chemotactic, whereas Pf5RL was chemotactic at 25°C but not at 4°C due to the restricted movement. In a quartz sand column, haptotaxis did not play a role in increasing the transport of Pf5RL as compared with chemotaxis. Compared with a naphthalene-free soil column, Pf5RL broke through naphthalene-presaturated soil columns to reach a stable effluent concentration 0.5 pore volumes earlier due to advective chemotaxis occurring behind the plume front in the bulk solution. Pf5RL also demonstrated greater retention (e.g., a doubled rate of attachment and a one-third smaller breakthrough percentage) due to along-surface haptotaxis and near-surface chemotaxis occurring in less mobile water near the soil surface. However, both chemotaxis and haptotaxis were weakened when Pf5RL co-transported with naphthalene due to reduced adsorption of naphthalene on the soil. This study suggests that surface adsorption of naphthalene can mediate the relative importance of advective chemotaxis (facilitating initial breakthrough), near-surface chemotaxis (increasing bacterial collision), and haptotaxis (increasing bacterial residence time).

Natural source zone depletion of LNAPL: A critical review supporting modelling approaches

Natural source zone depletion (NSZD) of light non-aqueous phase liquids (LNAPLs) includes partitioning, transport and degradation of LNAPL components. NSZD is being considered as a site closure option during later stages of active remediation of LNAPL contaminated sites, and where LNAPL mass removal is limiting. To ensure NSZD meets compliance criteria and to design enhanced NSZD actions if required, residual risks posed by LNAPL and its long term behaviour require estimation. Prediction of long-term NSZD trends requires linking physicochemical partitioning and transport processes with bioprocesses at multiple scales within a modelling framework. Here we expand and build on the knowledge base of a recent review of NSZD, to establish the key processes and understanding required to model NSZD long term. We describe key challenges to our understanding, inclusive of the dominance of methanogenic or aerobic biodegradation processes, the potentially changeability of rates due to the weathering profile of LNAPL product types and ages, and linkages to underlying bioprocesses. We critically discuss different scales in subsurface simulation and modelling of NSZD. Focusing on processes at Darcy scale, 36 models addressing processes of importance to NSZD are investigated. We investigate the capabilities of models to accommodate more than 20 subsurface transport and transformation phenomena and present comparisons in several tables. We discuss the applicability of each group of models for specific site conditions.

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.

Theoretical Insight into the Biodegradation of Solitary Oil Microdroplets Moving through a Water Column

In the aftermath of oil spills in the sea, clouds of droplets drift into the seawater column and are carried away by sea currents. The fate of the drifting droplets is determined by natural attenuation processes, mainly dissolution into the seawater and biodegradation by oil-degrading microbial communities. Specifically, microbes have developed three fundamental strategies for accessing and assimilating oily substrates. Depending on their affinity for the oily phase and ability to proliferate in multicellular structures, microbes might either attach to the oil surface and directly uptake compounds from the oily phase, or grow suspended in the aqueous phase consuming solubilized oil, or form three-dimensional biofilms over the oil–water interface. In this work, a compound particle model that accounts for all three microbial strategies is developed for the biodegradation of solitary oil microdroplets moving through a water column. Under a set of educated hypotheses, the hydrodynamics and solute transport problems are amenable to analytical solutions and a closed-form correlation is established for the overall dissolution rate as a function of the Thiele modulus, the Biot number and other key parameters. Moreover, two coupled ordinary differential equations are formulated for the evolution of the particle size and used to investigate the impact of the dissolution and biodegradation processes on the droplet shrinking rate.

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.