Metal contamination in groundwater aquifers poses risks to human health as well as other life forms. Previous laboratory experiments have demonstrated that bacteria found in geologic settings like aquifers are likely to adsorb metal contaminants and attenuate metal migration. However, as bacteria can also migrate through the groundwater aquifer a better understanding of the combined effect of these two processes is required. The aim of this laboratory study was to a) explore the affinity bacteria exhibit towards metals and porous media of varying composition, b) investigate the effect of mineral and solution composition on the bacterial filtration and c) use the combined data to predict the impact of microbes on metal mobility in porous media. Pantoea Agglomerans was used as a model bacterium while column materials consisted of quartz sand and iron-oxide coated sand (IOCS). Bacteria were characterised using potentiometric titrations to identify the type and concentration of sites present on their bacterial wall. Particular attention was paid to the effect of kinetics of proton and metal adsorption due to the variable contact times that solutions have with bacteria in columns. It was found that increasing the contact time between cell surfaces and protons during potentiometric titrations resulted in less reproducible results. This was due to the release of cell exudates under high pH conditions rather than cell death. Exudates were also found to adsorb protons. Moreover, zinc adsorption onto cell surfaces is higher after 60 to 90 minutes of contact time, while there is a decline in adsorption for longer contact times due to release of cell exudates in the solution. Stability constants for the adsorption of zinc onto cell surface sites, quartz and IOCS materials were determined through batch adsorption experiments, providing a mechanistic explanation of the adsorption process. Reactive transport models incorporating kinetics and surface complexation are developed to describe zinc movement through packed columns. Batch kinetic studies showed that significant Zn sorption to IOCS takes place gradually during the first two hours of contact time. Adsorption continues to take place at a slower rate for an additional 10 hours. This kinetic effect is manifested also during flow-through experiments (column dimensions: length 0.12 m, diameter 0.025 m) with a Darcian velocity 6.1·10-3 cm s-1, which is comparable to natural groundwater flow rates through sand porous media. A pseudo-second order kinetic adsorption model is combined with a numerical advection dispersion model for the first time to predict Zn transport. Model output results are of mixed quality as the model cannot successfully describe contaminant arrival time and breakthrough curve shape simultaneously. Moreover, a mechanistic surface complexation reactive transport model is capable of predicting Zn sorption under varying pH conditions demonstrating the versatility of mechanistic models. However, these models do not account for kinetics and therefore they are not intended to fit the dispersion of the contaminant due to kinetic effects of adsorption. Experiments in mixed zinc/cell systems demonstrate that transport through IOCS is dominated by the adsorption to the porous medium. This is consistent with the batch surface complexation predictions for the system. Adsorption to bacteria is reversible and zinc is stripped from the cells and redistributed onto the IOCS. Adsorption onto cells becomes significant and plays a role in mobile metal speciation only once the column is saturated with zinc.

Cyanobacteria, also known as blue-green algae for a long time, are the most ancient and problematic bloom-forming phylum on earth. An alert levels framework has been established by World Health Organization(WHO) to prevent the potential harmful cyanobacterial blooms. Normally, low cyanobacteria levels are found in surface water. 2000 cyanobacterial cells/mL and 100,000 cyanobacterial cells/mL are established for WHO Alert Level 1 and 2, respectively. However, eutrophication, climate change and other factors may promote the spread of cyanobacteria and increase the occurrence of harmful cyanobacterial blooms in water on a global scale. Hence, a rapid real time cyanobacteiral monitoring system is required to protect public health from the cyanotoxins produced by toxic cyanobacterial species. Current methods to control or prevent the development of harmful cyanobacterial blooms are either expensive, time consuming or not effective in the long term. The best method to control the blooms is to prevent the formation of the blooms at the very beginning. Although emerging advanced autofluorescence-based sensors, imaging flow cytometry applications, and remote sensing have been utilized for rapid real-time enumeration and classification of cyanobacteria, the need to accurately monitor low-level cyanobacterial species in water remains unsolved. Microflow cytometry has been employed as a functional cell analysis technique in past decades, and it can provide real-time, accurate results. The autofluorescence of cyanobacterial pigments can be used for determination and counting of cyanobacterial density in water. A pre-concentration system of an automated cyanobacterial concentration and recovery system (ACCRS) based on tangential flow filtration and back-flushing technique was applied to reduce the sample assay volume and increase the concentration of target cells for further cell capture and detection. In this project, a microflow cytometry platform with a microfluidic device and an automated pre-concentration system was established to monitor cyanobacteria and provide early warning alerts for potential harmful blooms. In this work, quantification of low-level cyanobacterial samples (∼ 5 cyanobacterial cells/mL) in water has been achieved by using a microflow cytometer together with a pre-concentration system (ACCRS). Meanwhile, this platform can also provide early warning alerts for potential harmful cyanobacterial blooms at least 15 days earlier before reaching WHO Alert Level 1. Results have shown that this platform can be applied for rapid determination of cyanobacteria and early warning alerts can be triggered for authorities to protect the public and the environment. / Thesis / Doctor of Engineering (DEng) / Harmful cyanobacterial blooms have been a rising risk to the public heath across the world in recent decades. Alert levels of cyanobacteria in water has also been established. In this case, a rapid on-side monitoring system for cyanobacteria is required. In this thesis, a microflow cytometer platform combined with a bacterial concentration and recovery system was built to quickly monitor the relatively low level of cyanobacteria for early warning alerts. A pre-enrichment system based on tangential flow filtration and back-flushing technique was applied to increase the concentration levels of microbial samples and a microfluidic device capable of collecting phycocyanin fluorescence was designed to count cyanobacterial cells. The limit of quantification for cyanobacterial concentration based on the microflow cytometry platform was as low as ∼ 5 cells/mL. We can claim that the microflow cytometry platform can provide useful early warning alerts for the decision-makers to control the potential harmful cyanobacterial blooms at the very early stage and protect the aquatic animals and public health.