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

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.

Tuning chemotactic and diffusiophoretic spreading via hydrodynamic flows

The transport of microorganisms by chemotaxis is described by the same "log-sensing" response as colloids undergoing diffusiophoresis, despite their different mechanistic origins. We employ a recently-developed macrotransport theory to analyze the advective-diffusive transport of a chemotactic or diffusiophoretic colloidal species (both referred to as "colloids") in a circular tube under a steady pressure-driven flow (referred to as hydrodynamic flow) and transient solute gradient. First, we derive an exact solution to the log-sensing chemotactic/diffusiophoretic macrotransport equation. We demonstrate that a strong hydrodynamic flow can reduce spreading of solute-repelled colloids, by eliminating super-diffusion which occurs in an otherwise quiescent system. In contrast, hydrodynamic flows always enhance spreading of solute-attracted colloids. Second, we generalize the exact solution to show that the above tunable spreading phenomena by hydrodynamic flows persist quantitatively for decaying colloids, as may occur with cell death, for example. Third, we examine the spreading of chemotactic colloids by employing a more general model that captures a hallmark of chemotaxis, that log-sensing occurs only over a finite range of solute concentration. Apart from demonstrating for the first time the generality of the macrotransport theory to incorporate an arbitrary chemotactic flow model, we reveal via numerical solutions new regimes of anomalous spreading, which match qualitatively with experiments and are tunable by hydrodynamic flows. The results presented here could be employed to tailor chemotactic/diffusiophoretic colloid transport using hydrodynamic flows, which are central to applications such as oil recovery and bioremediation of aquifers.

Controlling pore-scale processes to tame subsurface biomineralization

Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.

Chemotactic migration of bacteria in porous media

Chemotactic migration of bacteria-their ability to direct multicellular motion along chemical gradients-is central to processes in agriculture, the environment, and medicine. However, current understanding of migration is based on studies performed in bulk liquid, despite the fact that many bacteria inhabit tight porous media such as soils, sediments, and biological gels. Here, we directly visualize the chemotactic migration of Escherichia coli populations in well-defined 3D porous media in the absence of any other imposed external forcing (e.g., flow). We find that pore-scale confinement is a strong regulator of migration. Strikingly, cells use a different primary mechanism to direct their motion in confinement than in bulk liquid. Furthermore, confinement markedly alters the dynamics and morphology of the migrating population-features that can be described by a continuum model, but only when standard motility parameters are substantially altered from their bulk liquid values to reflect the influence of pore-scale confinement. Our work thus provides a framework to predict and control the migration of bacteria, and active matter in general, in complex environments.

High-fidelity profiling and modeling of heterogeneity in wastewater systems using milli-electrode array (MEA): Toward high-efficiency and energy-saving operation

High energy consumption is a critical problem for wastewater treatment systems currently monitored using conventional "single point" probes and operated with manual or automatic open-loop control strategies, exhibiting significant time lag. This challenge is addressed in this study by profiling the variation of three critical water quality parameters (conductivity, temperature and pH) along the depth of a reactor at high spatiotemporal resolution in a real-time mode using flat thin milli-electrode array (MEA) sensors. The profiling accurately captured the heterogeneous status of the reactor under transient shocks (conductivity and pH) and slow lingering shock (temperature), providing an effective dataset to optimize the chemical dosage and energy requirement of wastewater treatment systems. Transient shock models were developed to validate the MEA profiles and calculate mass transfer coefficients. Monte Carlo simulation revealed high-resolution MEA profiling combined with fast closed-loop control strategies can save 59.50% of energy consumption (Temperature and oxygen consumption controls) and 45.29% of chemical dosage, and reach 16.28% performance improvement over the benchmark (defined with ideal conditions), compared with traditional "single-point" sensors that could only monitor the entire system through a single process state. This study demonstrated the capability of MEA sensors to profile reactor heterogeneity, visualize the variation of water quality at high resolution, provide complete datasets for accurate control, and ultimately lead to energy-saving operation with high resilience.

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.

Cotransport of biochar and Shewanella oneidensis MR-1 in saturated porous media: Impacts of electrostatic interaction, extracellular electron transfer and microbial taxis

Biochar widely applied to soil can influence microbial community composition and participate in extracellular electron transfer (EET). However, little is known about the cotransport behaviors of bacteria and biochar in aquifer and soil-water environments, which can affect the fate and application performance of biochar. In this study, we found that in comparison to their individual transport behaviors, the mobilities of cotransporting Shewanella oneidensis MR-1 and biochar colloid (BC) were significantly inhibited. The decreasing colloidal mobilities at higher ionic strengths signified the importance of electrostatic interaction between cell and BC in cotransport. Moreover, the less suppressed cotransport of BC and mutants defective of EET and the elevated inhibition effects on cotransport by adding exogenous electron donor suggested the importance of EET. Difference in cotransport behavior was also observed with BC having different redox states. Compared with oxidized BC, reduced BC with higher hydrophobicity led to easier aggregation with cell and higher retention in column. More importantly, MR-1 exhibited EET-dependent taxis towards biochar, which also contributed to the enhanced heteroaggregation and decreased mobilities of cell and biochar. Our results highlight that metabolic activities of microbes towards abiotic colloids cannot be neglected when assessing their transport behaviors, especially in subsurface environments abounded with redox-active inorganic particles and microbes performing extracellular respiration.