Bacterial transport in porous media

• Main Author: Teo, Ting Wei
• Other Authors: Marcos
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2022
• Subjects: Engineering::Mechanical engineering; Science::Physics
• Online Access: https://hdl.handle.net/10356/155633
• Institution: Nanyang Technological University

Bacteria are ubiquitous in our environment and play important roles in our ecosystem. The process of bacterial transportation often leads to modifications of the natural porous environment through phenomena such as biofilm formation and causes a reduction of permeability. It has been observed in various researches that bacterial cells are able to travel through large distance across a porous medium. The ability of bacterial cells travelling through large distance allows them to get deposited and attached onto surfaces, potentially increases the chances to start the cycle of biofilm formation, where planktonic cells can aggregate and secretes extracellular polymeric substance and releasing new planktonic cells into the environment and rapidly colonize the environment. While there is a vast research exploring the effects of bacterial biofilm on the alteration of permeability of the porous medium, little attention is given to the deposition of individual bacterial cells and the effects of distribution of porosity on the resultant spatial distribution of bacterial cells. The advent of lab-on-chip microfluidic technologies has enabled a myriad of new applications in biomedical, rapid sensing and detection of microorganism, and integration of multiple traditional laboratory procedures into an automated lab-on-a-chip system. Detection of bacteria by microfluidic systems has been demonstrated by means of electrochemical, nanoparticle based, and colorimetric detection, with significantly reduced footprint. Recently, a microfluidic platform “soil-on-a-chip” was coined to simulate complex soil environment and to investigate how organisms interact with soil environment. These soil-on-a-chip platforms offer precise spatiotemporal control on the microenvironments in terms of temperature, pH, gas composition, porosity and water saturation, which is essential for the understanding of soil organisms such as bacteria and fungi. Nonetheless, the effects of bacteria transport on the medium’s permeability, the dynamics such as the initiation and propagation of bacterial cells attaching onto the surfaces, preferential path and the mechanics of bacterial cells retention in the porous medium are yet to be fully explored. The quantification of the permeability of porous medium and the effects of bacteria contributing to the reduction of permeability may be investigated. In this thesis, I first developed a microfluidic device for the quantification of the permeability of any given porous medium using the direct and real time measurement of differential pressure between the upstream and downstream across the porous medium. With the developed pressure differential microfluidic chip, I investigated the effect of B. subtilis bacteria deposition on the porous chamber made up of packed polystyrene beads. The main findings obtained were as follows: (a) the average percentage of bacteria deposited is independent of the concentration of bacteria introduced; (b) more bacterial cells deposition is observed in regions with larger porosity. It has been shown that the infusion of DI water through the porous medium results in steady differential pressure (no presence of bacterial deposition) and the infusion of bacteria buffer indeed increases the differential pressure over the course of experiment; (c) based on a theoretical model developed, a slight positive correlation is determined on the spatial distribution of porosity and the resultant distribution of bacterial cells in the porous medium; (d) the estimated number of bacterial cells required to reduce 10% of the permeability is quantified to be as little as 1 × 107 cells. Subsequently, I developed a novel microfluidic device for the rapid estimation of bacteria concentration through filtration membrane and pressure differential measurements. We characterized the changes in pressure differential for samples with different concentrations of Escherichia coli bacteria relative to the start of experiment with only DI water flow. A total of 10 sets of experiments, each with six levels of bacteria buffer dilution is done to build a calibration curve for rapid bacteria estimation. Through the comprehensive experiments sets, I obtained a calibration curve for the relative pressure difference in relation to the sample bacterial concentration with a remarkable goodness of fit R2 of 0.9477 for E. coli bacterial concentration ranging from 106 to 108 CFU / mL. In other words, the device offers an inexpensive and rapid estimation of bacteria concentration in less than 30 minutes with an accuracy of up to 77.26 ± 18.88 %. Furthermore, the following findings were observed: (a) each filtration membrane has its own intrinsic property and inter-filtration membrane variability is present, causing the pressure differential measurement to varies; (b) the infusion of DI water is shown to achieve steady pressure differential while bacteria buffer increases the pressure differential; (c) deposition of bacterial cells on the filtration membrane causing a non-linear increment in pressure differential and the gradient discerns the concentration. Finally, I established an experimental protocol that allows visualization of bacterial cells transport through a porous medium and investigated the effects of bacteria transport in porous medium with the aim of studying the effects of spatial distribution of bacteria cells on the medium’s permeability and porosity. I investigated experimentally, (a) the porosity effect of the soil grains on the spatio-temporal distribution of bacteria, and (b) the effect of bacterial behaviors, such as swimming, hovering and aggregation, on the permeability of the porous medium matrix. Nafion particles are used and carefully matched refractive index can negate the boundaries of the porous medium, thus rendering a translucent medium that mimics the natural porous medium for bacterial observation. The preliminary results presented are in agreement with the work presented in the earlier section and can be refined further to investigate new phenomenon such as the effect of bacterial behaviors.