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

Biofilm formation in xenobiotic-degrading microorganisms

The increased presence of xenobiotics affects living organisms and the environment at large on a global scale. Microbial degradation is effective for the removal of xenobiotics from the ecosystem. In natural habitats, biofilms are formed by single or multiple populations attached to biotic/abiotic surfaces and interfaces. The attachment of microbial cells to these surfaces is possible via the matrix of extracellular polymeric substances (EPSs). However, the molecular machinery underlying the development of biofilms differs depending on the microbial species. Biofilms act as biocatalysts and degrade xenobiotic compounds, thereby removing them from the environment. Quorum sensing (QS) helps with biofilm formation and is linked to the development of biofilms in natural contaminated sites. To date, scant information is available about the biofilm-mediated degradation of toxic chemicals from the environment. Therefore, we review novel insights into the impact of microbial biofilms in xenobiotic contamination remediation, the regulation of biofilms in contaminated sites, and the implications for large-scale xenobiotic compound treatment.

Optimal transport of active particles induced by substrate concentration oscillations

We show the existence of a stochastic resonant regime in the transport of active colloidal particles under confinement. The periodic addition of substrate to the system causes the spectral amplification to exhibit a maximum for an optimal noise level value. The consequence of this is that particles can travel longer distances with lower fuel consumption. The stochastic resonance phenomenon found allows the identification of optimal scenarios for the transport of active particles, enabling them to reach regions that are otherwise difficult to access, and may therefore find applications in transport in cell membranes and tissues for medical treatments and soil remediation.

Predicting bacterial transport through saturated porous media using an automated machine learning model

Escherichia coli, as an indicator of fecal contamination, can move from manure-amended soil to groundwater under rainfall or irrigation events. Predicting its vertical transport in the subsurface is essential for the development of engineering solutions to reduce the risk of microbiological contamination. In this study, we collected 377 datasets from 61 published papers addressing E. coli transport through saturated porous media and trained six types of machine learning algorithms to predict bacterial transport. Eight variables, including bacterial concentration, porous medium type, median grain size, ionic strength, pore water velocity, column length, saturated hydraulic conductivity, and organic matter content were used as input variables while the first-order attachment coefficient and spatial removal rate were set as target variables. The eight input variables have low correlations with the target variables, namely, they cannot predict target variables independently. However, using the predictive models, input variables can effectively predict the target variables. For scenarios with higher bacterial retention, such as smaller median grain size, the predictive models showed better performance. Among six types of machine learning algorithms, Gradient Boosting Machine and Extreme Gradient Boosting outperformed other algorithms. In most predictive models, pore water velocity, ionic strength, median grain size, and column length showed higher importance than other input variables. This study provided a valuable tool to evaluate the transport risk of E.coli in the subsurface under saturated water flow conditions. It also proved the feasibility of data-driven methods that could be used for predicting other contaminants' transport in the environment.

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.

Hydrobiological Mechanism Controlling the Synergistic Effects of Unsaturated Flow and Soil Organic Matter on the Degradation of Emerging Organic Contaminants in Soils

Hydrology is a key factor influencing microbial degradation of emerging organic contaminants (EOCs) in soils, but the underlying mechanisms are not clear. In this study, biotic and abiotic column experiments were performed to investigate the removal and degradation of five EOCs in soils with different soil organic matter (SOM) contents under saturated and unsaturated flow conditions. In biotic experiments, 54-90% of bisphenol A (BPA) and 9-22% of ibuprofen (IBU) were removed from the aqueous phase of saturated columns due to adsorption and biodegradation. The biodegradation removed 26-65% of BPA and 1-22% of IBU. Decreasing soil pore water saturation from 100 to 80% increased BPA removal to 97-100% and IBU removal to 42-43% due to increased biodegradation (67-81% for BPA and 36-39% for IBU). No significant removal of BPA and IBU was observed in SOM-removed soils under saturated and unsaturated flow conditions. The desaturation did not influence sorptive losses of BPA (<27%) and IBU (<7%), suggesting their negligible adsorption at air-water interfaces but increased biodegradation of BPA and IBU sorbed at SOM-water interfaces. The study shows that soil drying and SOM can synergistically degrade BPA and IBU but have no effect on recalcitrant carbamazepine, tetracycline, and ciprofloxacin.

Interactive removal of bacterial and viral particles during transport through low-cost filtering materials

Pathogen filtration is critically important for water sanitation. However, it is a big challenge to balance removal efficiency and filtering material cost. In this study, we quantified the removal processes of a bacterial strain Escherichia coli 652T7 and a model bacteriophage MS2 (ATCC 15597-B1) during their transport through columns containing iron filings (IF), calcined magnesite (CM), natural ore limestone (OL) or corn stalk biochar (BC) under saturated flow conditions. Experimental results showed that 99.98, 79.55, 63.79, and 62.59% of injected E. coli 652T7 and 98.78, 92.26, 68.79, and 69.82% of injected MS2 were removed by IF, CM, OL, and BC, respectively. The differences in removal percentage were attributed to the disparities of the microorganisms and filtering materials in surface function groups, surface charges, and surface morphology. Transport modeling with advection-dispersion equation (ADE) and interaction energy calculation with extended Derjaguin, Landau, Verwey, and Overbeek (XDLVO) model indicated that E. coli 652T7 and MS2 were mostly removed via irreversible attachment. In IF columns, E. coli 652T7 promoted the transport of MS2 but not vice versa. In CM columns, MS2 facilitated the transport of E. coli 652T7 and vice versa at a less extent. Such changes were a combined result of attachment site competition, steric effect, and mechanical straining. We found that the sum of the removal percentages of the two microorganisms in their respective transport experiments were similar to those calculated from their co-transport experiments. This result suggests that the removals were mainly limited by the attachment sites in the filtering materials.

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.

Can dispersal be leveraged to improve microbial inoculant success?

Microorganisms have long been isolated from soils to develop microbial inoculants, with the goal of spiking them into new soils to augment target functions. However, establishment can be sporadic, and we assume that inoculants simply arrive at their destination. Here, we posit a need for integrating dispersal into inoculant development and deployment. We argue that consideration for an inoculant's dispersal ability, whether via active (e.g., chemotaxis) or passive (e.g., attachment to other organisms) means, and including methods of deployment that allow multiple establishment attempts could help increase the predictability of inoculant success. Dispersal can influence many key aspects of in-field survival, including the ability to escape stressors, seek favorable colonization sites, facilitate multiple establishment attempts, and engage in multikingdom interactions.

Synergistic effects of unsaturated flow and soil organic matter on retention and transport of PPCPs in soils

This study examines the effects of soil organic matter (SOM) and water content on the transport of five selected pharmaceutical and personal care products (PPCPs, ibuprofen, carbamazepine, bisphenol A, tetracycline, and ciprofloxacin) in four natural soils with different SOM contents. Batch isotherm experiment results showed that SOM effect was very significant for positively charged tetracycline and ciprofloxacin (>99% adsorption, no desorption), relatively significant for non-dissociated carbamazepine and bisphenol A (17-57% adsorption, 6-71% desorption) and insignificant for negatively charged ibuprofen (4-8% adsorption, 60-87% desorption) in the soils. Transport results showed that neither tetracycline nor ciprofloxacin moved through the saturated and unsaturated soil columns, demonstrating their very limited mobility in soils as a result of significant electrostatic attraction independent of SOM and water conditions. Overall, higher SOM content and lower water content were favorable to the retention of ibuprofen, carbamazepine and bisphenol A in the soils. Breakthrough of ibuprofen, carbamazepine and bisphenol A was 100% (both saturated and unsaturated), 94% (saturated)-97% (unsaturated) and 85% (saturated)-90% (unsaturated) in SOM-removed soils; however only 78% (saturated)-57% (unsaturated), 93% (saturated)-67% (unsaturated), 11% (saturated)-0% (unsaturated) in the SOM-high soils. The effect of water content was not significant in the SOM-removed soils. The SOM could increase the kinetic (type 2) adsorption of PPCPs at the solid-water interface (SWI), and the air phase could increase the instantaneous (type 1) adsorption of PPCPs at the air-water interface (AWI). This result suggests that lowering water content could greatly enhance the adsorption of PPCPs that had high affinities to soils and vice versa. This study provides an important implication that AWI and SWI might have a nonlinear relationship in promoting the adsorption and reducing the mobility of PPCPs under unsaturated flow conditions.