Lattice‐Boltzmann modeling of contaminant degradation by chemotactic bacteria: Exploring the formation and movement of bacterial bands

Abstract

[1] We developed a three-dimensional Lattice-Boltzmann (LB) model to simulate the biodegradation of a dissolved substrate, toward which bacteria exhibit chemotaxis. The model was verified by comparing simulations to capillary assay experiments performed elsewhere. In these assays, a capillary containing an aqueous solution, with initially uniformly distributed dissolved naphthalene, was dipped into a reservoir containing Pseudomonas putida, a microorganism that exhibits chemotaxis to naphthalene. These experiments were also performed with additional glass beads present in the capillary and reservoir. The simulations show that a fraction of the bacteria separates from the reservoir to form a band that moves with constant speed into the capillary while metabolizing the naphthalene. We also used the LB model to explore band formation in a porous medium under groundwater flow conditions. If a bacterial slug is injected, two bacterial bands form; one moves upstream and the other moves downstream. The magnitudes of the two band velocities, as measured relative to the pore water velocity, are identical. Bacteria injected in excess are advected downstream in a fluid parcel containing no substrate. Our simulations suggest that the bioremediation of a contaminant plume in groundwater can potentially be enhanced by the injection of chemotactic bacteria. We also derived a correlation that predicts the number of bacteria in a band that separates from a semi-infinite bacterial slug in a domain containing substrate that is initially uniformly distributed. This correlation allows estimation of the optimal number of bacteria that needs to be added to a substrate-filled domain, such that the number of bacteria in the band is maximum while simultaneously avoiding the injection of excess bacteria that do not make it into the band.

Transverse Bacterial Migration Induced by Chemotaxis in a Packed Column with Structured Physical Heterogeneity

“…Groundwater flow usually drives bacteria to transport through highly conductive regions of the subsurface, leaving the pollutants trapped within low permeable zones without treatment , . Chemotaxis, the ability of bacteria to sense chemical gradients and migrate preferentially toward regions with high chemoattractant concentrations, is considered to enhance bioremediation by directing microorganisms toward closer contact with the residual contaminants in less conductive zones in aquifers − .…”

Pore‐Scale Numerical and Experimental Investigation of Colloid Retention at the Secondary Energy Minimum

“…Berry et al (2004) used a mesoscopic approach known as smoothed particle hydrodynamics to study contaminant transport and deposition in a complex two‐dimensional porous flow. Very recently, the lattice‐Boltzmann approach has been applied to simulate pore‐scale flow in realistic three‐dimensional porous media to help quantify the transport and retention of colloids and contaminants in complex systems (e.g., Li et al, 2010; Long and Hilpert, 2008, 2009; Long et al, 2010).…”

Understanding the joint impacts of soil architecture and microbial dynamics on soil functions: Insights derived from microscale models

“…The majority of studies that have tried to reproduce experimental conditions consider idealised geometries such as micromodels (e.g., Borer et al, 2018Borer et al, , 2019Centler et al, 2011), packs of spherical grains (e.g., Gharasoo et al, 2012;Peszynska et al, 2016) and in a few cases repacked soils (e.g., Babey et al, 2017;Monga et al, 2014). Assessment of microscale models on experimental microfluidic devices, as advocated by Smercina et al (2021), appears promising since biodiversity and the movement of microbes can be easily controlled and monitored (e.g., Long & Hilpert, 2008). For example, Borer et al (2019) were able to reconcile contradictory results between their microscale model and experiments carried out on microfluidic devices by introducing more complex metabolic pathways in their biological module.…”