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abstract: The potential of using bio-geo-chemical processes for applications in geotechnical engineering has been widely explored in order to overcome the limitation of traditional ground improvement techniques. Biomineralization via urea hydrolysis, referred to as Microbial or Enzymatic Induced Carbonate Precipitation (MICP/EICP), has been shown to increase soil strength by stimulating precipitation of calcium carbonate minerals, bonding soil particles and filling the pores. Microbial Induced Desaturation and Precipitation (MIDP) via denitrification has also been studied for its potential to stabilize soils through mineral precipitation, but also through production of biogas, which can mitigate earthquake induced liquefaction by desaturation of the soil. Empirical relationships have been established, which relate the amount of products of these biochemical processes to the engineering properties of treated soils. However, these engineering properties may vary significantly depending on the biomineral and biogas formation mechanism and distribution patterns at pore-scale. This research focused on the pore-scale characterization of biomineral and biogas formations in porous media. The pore-scale characteristics of calcium carbonate precipitation via EICP and biogenic gas formation via MIDP were explored by visual observation in a transparent porous media using a microfluidic chip. For this purpose, an imaging system was designed and image processing algorithms were developed to analyze the experimental images and detect the nucleation and growth of precipitated minerals and formation and migration mechanisms of gas bubbles within the microfluidic chip. Statistical analysis was performed based on the processed images to assess the evolution of biomineral size distribution, the number of precipitated minerals and the porosity reduction in time. The resulting images from the biomineralization study were used in a numerical simulation to investigate the relation between the mineral distribution, porosity-permeability relationships and process efficiency. By comparing biogenic gas production with abiotic gas production experiments, it was found that the gas formation significantly affects the gas distribution and resulting degree of saturation. The experimental results and image analysis provide insight in the kinetics of the precipitation and gas formation processes and their resulting distribution and related engineering properties. / Dissertation/Thesis / Doctoral Dissertation Civil, Environmental and Sustainable Engineering 2019

Yes / Cementitious composites are generally brittle and develop considerable tension cracks, resulting in corrosion of steel reinforcement and compromising structural durability. With careful selection and treatment, some kinds of bacteria are able to precipitate calcium carbonate and ‘heal’ cracks in cementitious composites through their metabolism, namely bacterial activity. It is envisioned that the bacterial technology-enabled cementitious composites could have great potential for engineering applications such as surface treatment, crack repair and self-healing construction material. This paper presents the state-of-the-art development of bacterial technology-enabled cementitious composites from the following aspects: mechanisms of bacterial induced calcium carbonate precipitation; methods of applying bacteria into cementitious composites; mechanical properties, durability and their influencing factors; various applications; cost effective analysis and prospect. The paper concludes with an outline of some future opportunities and challenges in the application of bacterial technology-enabled cementitious composites in construction. / National Science Foundation of China (51578110) and the Fundamental Research Funds for the Central Universities in China (DUT18GJ203).

The Proterozoic Espanola Formation (Huronian Sequence) was studied at Geneva Lake, Ontario, 45 miles north-west of Sudbury. A major lithological change exists in the Espanola Formation between this area and the type section on the north shore of Lake Huron, 75 miles to the south. Unusually pure (95 percent) microcrystalline limestones and dolostones occur in almost equal abundance to the calcareous siltstones which are the characteristic lithology of the formation in its type section. The existence and position of a fine grained deposit such as the Espanola in a stratigraphic sequence which consists mostly of glacial and periglacial deposits is unusual. It is suggested that this fine-grained deposit was an integral part of a cycle of deposition resulting from glacial advance and retreat and that its sedimentary basin was created by marine transgression in response to a glacial retreat. Spatial distribution of the Espanola Formation suggests that its sedimentary basin may have consisted of at least three environmental zones. At least one of these zones may represent a glacial melt-water lake. A microfossil search was carried out with negative results. This made speculation necessary in determining the origin of the calcareous fraction of the Espanola Formation. A mechanism is suggested whereby calcium carbonate is precipitated inorganically, as a result of photosynthesis by anaerobic bacteria. This mechanism can be observed in the present. If it is true, then the Espanola Formation may represent a time marker for the first presence of free oxygen in the atmosphere. / Thesis / Bachelor of Science (BSc)

Aquifers are an important storage location and source of fresh groundwater. They may become polluted by a number of contaminants including mobile divalent radionuclides such as strontium-90 which is a byproduct of uranium fission. A method for remediating such divalent radionuclides is sequestration through co-precipitation into calcium carbonate. Calcium carbonate precipitation occurs naturally but can be enhanced by the use of ureolytic microorganisms living within the aquifer. The microbial enzyme urease cleaves ammonia from urea (added as a stimulant to the aquifer) increasing the pH and subsequently pushing the bicarbonate equilibrium towards precipitation. Laboratory experimentation is necessary to better predict field scale outcomes of remediation that is driven by ureolytic calcium carbonate co-precipitation. To aid in such laboratory experiments, I constructed two ureolytic organisms which contain green fluorescent protein (GFP) so that the location of the microbes in relation to media flow paths and precipitation can be viewed by microscopy in a 2- dimensional porous medium flow cell reactor. The reactor was operated with a parallel flow regime where the two influent media would not promote microbially induced calcium carbonate precipitation until they were mixed in the flow cell. A demonstration study compared the results of parallel flow and mixing in the reactor operated with and without one of the GFP-containing ureolytic organisms. The growth and precipitation of calcium carbonate within the reactor pore space altered flow paths to promote a wider mixing zone and a more widely distributed overall calcium carbonate precipitation pattern. This study will allow optimization of remediation efforts of contaminants such as strontium-90 in aquifers. / Graduation date: 2012

Microbial-Induced Calcium Carbonate (CaCO3) Precipitation (MICP) is a biological process in which microbial activities alter the surrounding aqueous environment and induce CaCO3 precipitation. Because the formed CaCO3 crystals can bond soil particles and improve the mechanical properties of soils such as strength, MICP has been explored for potential engineering applications such as soil stabilisation. However, it has been difficult to control and predict the properties of CaCO3 precipitates, thus making it very challenging to achieve homogeneous MICP-treated soils with the desired mechanical properties. This PhD study investigates MICP at both micro and macro scales to improve the micro-scale understandings of MICP which can be applied at the macro-scale for improving the homogeneity and mechanical properties of MICP-treated sand. A microfluidic chip which models a sandy soil matrix was designed and fabricated to investigate the micro-scale fundamentals of MICP. The first important finding was that, during MICP processes, phase transformation of CaCO3 can occur, which results in smaller and less stable CaCO3 crystals dissolving at the expense of growth of larger and more stable CaCO3 crystals. In addition, it was found that bacteria can aggregate after being mixed with cementation solution, and both bacterial density and the concentration of cementation solution affect the size of aggregates, which may consequently affect the transport and distribution of bacteria in a soil matrix. Furthermore, bacterial density was found to have a profound effect on both the growth kinetics and characteristics of CaCO3. A higher bacterial density resulted in a quicker formation of a larger amount of smaller crystals, whereas a lower bacterial density resulted in a slower formation of fewer but larger crystals. Based on the findings from micro-scale experiments, upscaling experiments were conducted on sandy soils to investigate the effect of injection interval on the strength of MICP treated soils and the effects of bacterial density and concentration of cementation solution on the uniformity of MICP treated soils. Increasing the interval between injections of cementation solution (from 4 h to 24 h) increased the average size of CaCO3 crystals and the resulting strength of MICP-treated sand. An optimised combination of bacterial density and cementation solution concentration resulted in a relative homogeneous distribution of CaCO3 content and suitable strength and stiffness of MICP-treated sand. This thesis study revealed that a microfluidic chip is a very useful tool to investigate the micro-scale fundamentals of MICP including the behaviour of bacteria and the process of CaCO3 precipitation. The optimised MICP protocols will be useful for improving the engineering performance of MICP-treated sandy soils such as uniformity and strength.