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The adsorption behaviour of micro-organisms during the initial attachment stage of biofilm formation affects subsequent stages. The available area for attachment and the chemophysical properties of a surface affect microbial attachment performance. This study focused on the initial attachment behaviour of Klebsiella aerogenes on monazite by measuring the ratio of planktonic against sessile subpopulations (P:S ratio), and the potential role of extracellular DNA (eDNA). eDNA production, effects of physicochemical properties of the surface, particle size, total available area for attachment, and the initial inoculation size on the attachment behaviour were tested. K. aerogenes attached to monazite immediately after exposure to the ore; however, the P:S ratio significantly (p = 0.05) changed in response to the particle size, available area, and inoculation size. Attachment occurred preferentially on larger-sized (~50 µm) particles, and either decreasing the inoculation size or increasing the available area further promoted attachment. Nevertheless, a portion of the inoculated cells always remained in a planktonic state. K. aerogenes produced lower eDNA in response to the changed surface chemical properties when monazite was replaced by xenotime. Using pure eDNA to cover the monazite surface significantly (p ≤ 0.05) hindered bacterial attachment due to the repulsive interaction between the eDNA layer and bacteria.

Microbial attachment and biofilm formation is a ubiquitous behaviour of microorganisms and is the most crucial prerequisite of contact bioleaching. Monazite and xenotime are two commercially exploitable minerals containing rare earth elements (REEs). Bioleaching using phosphate solubilizing microorganisms is a green biotechnological approach for the extraction of REEs. In this study, microbial attachment and biofilm formation of Klebsiella aerogenes ATCC 13048 on the surface of these minerals were investigated using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM). In a batch culture system, K. aerogenes was able to attach and form biofilms on the surface of three phosphate minerals. The microscopy records showed three distinctive stages of biofilm development for K. aerogenes commencing with initial attachment to the surface occurring in the first minutes of microbial inoculation. This was followed by colonization of the surface and formation of a mature biofilm as the second distinguishable stage, with progression to dispersion as the final stage. The biofilm had a thin-layer structure. The colonization and biofilm formation were localized toward physical surface imperfections such as cracks, pits, grooves and dents. In comparison to monazite and xenotime crystals, a higher proportion of the surface of the high-grade monazite ore was covered by biofilm which could be due to its higher surface roughness. No selective attachment or colonization toward specific mineralogy or chemical composition of the minerals was detected. Finally, in contrast to abiotic leaching of control samples, microbial activity resulted in extensive microbial erosion on the high-grade monazite ore.

The porosity in minerals contributes to enhanced permeability for fluid flow in natural systems and engineering processes. Porosity can be created by fluid-mediated mineral replacement reactions. Such reaction-induced porosity can evolve with time, yet the mechanisms and kinetics of porosity creation and evolution remain poorly understood. This thesis presents experimental investigations on the creation and evolution of mineral porosity in two model replacement reactions, i.e., the replacement of calcite by gypsum and anhydrite with a positive volume change and the replacement of pentlandite by violarite and millerite with a negative volume change. These replacement reactions were conducted under mildly acidic hydrothermal conditions for up to 18 months, and the mineralogy, microstructure and porosity of the reaction products were quantitatively analysed by powder X-ray diffraction, (ultra) small-angle neutron scattering, high resolution scanning electron microscopy, focused-ion beam scanning electron microscopy, and X-ray micro-tomography. The results showed that porosity creation and evolution are highly dependent on mineral systems and reaction conditions. In the calcite-gypsum-anhydrite mineral system, the experiments at 25-60 °C produced intragranular nanopores in gypsum replacing calcite. Because of the positive volume change, gypsum overgrowth also occurred on the grain surface, and the gypsum in the overgrowth region contained intergranular micropores. Porosity coarsening was rapid (a few weeks) in the replacement region, leading to the formation of micro-voids in the core of gypsum grains. The replacement reaction was sensitive to temperature. When the experiments were conducted at a higher temperature of 220 °C, anhydrite was formed instead of gypsum. Porosity evolution in anhydrite was different when compared to gypsum at lower temperatures. In the pentlandite-violarite-millerite mineral system, only replacement occurred, likely because the negative volum