In seawater, drinking is a fundamental part of the osmoregulatory strategy for teleost fish, and presents a unique challenge. The intestine has an established role in osmoregulation, and its ability to effectively absorb fluid from imbibed seawater is crucial to compensating for water losses to the surrounding hyperosmotic environment. Alongside solute-linked water transport (driven by NaCl cotransport), intestinal bicarbonate (HCO3-) secretion also benefits fluid absorption directly (via apical Cl-/HCO3- exchange), and indirectly through the formation of calcium carbonate (CaCO3) thus removing the osmotic influence of Ca2+ within the gut fluid. For the European flounder (Platichthys flesus), elevated luminal Ca2+ has proven to be a specific, potent stimulator of HCO3- secretion both in vitro and in vivo where these actions are presumably modulated by an extracellular Ca2+-sensing receptor (CaR). The focus of this work was to learn more about how intestinal HCO3- secretion is regulated, the role of Ca2+, and more specifically the CaR. To achieve this, in vitro ‘gut sac’ experiments investigated how luminal Ca2+ influenced HCO3- secretion, and associated ion and fluid transport. Contrary to expectation, increasing Ca2+ from 5 to 20 mM did not stimulate HCO3- secretion. In an attempt to elucidate the role of CaCO3 precipitation in fluid absorption, and further explore the physiological implications of HCO3- secretion, the intestine was perfused in vivo with salines containing varying concentrations of Ca2+ (10, 40 and 90 mM). The production and secretion of HCO3-, in addition to CaCO3 formation increased accordingly with Ca2+, and was associated with a dramatic 25 % rise in the fraction of fluid absorbed by the gut. Additional in vitro experiments, utilising the Ussing chamber, helped establish some of the characteristics of intestinal HCO3- secretion by the euryhaline killifish (Fundulus heteroclitus), but was unresponsive to elevated mucosal Ca2+. Further attempts to potentiate the activity of the CaR, and application of the receptor agonists gadolinium (Gd3+) and neomycin, failed to produce responses consistent with the effect of Ca2+ observed previously, either in vitro or in vivo. With no evidence supporting a direct role for an extracellular, intestinal CaR in HCO3- secretion it was argued that secretion would be principally regulated by two factors, the ability of the epithelia to generate high levels of intracellular HCO3- and the rate of CaCO3 formation.

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.

No description available.

<p>Modern microbialites and microbial mats are the focus of ongoing research as they provide an opportunity to understand microbial-mineral interactions during carbonate precipitation and the generation of biosignatures that can inform our interpretation of the geological record. This study determined the natural abundance isotopic compositions ([13]C, [14]C) of the primary carbon pools and microbial communities associated with modern freshwater microbialites located in Pavilion Lake and in carbonate rich microbial mats on the nearby Cariboo Plateau in British Columbia, Canada. </p> <p> Natural abundance [14]C analysis of carbon pools associated with the Pavilion Lake microbialites demonstrated that structures were actively growing and that groundwater carbon inputs to the lake and microbialites were minimal. Rather, ambient dissolved inorganic carbon (DIC) was the primary carbon source for both microbial communities and recent carbonate. </p> <p> Isotopic enrichment of calcium carbonate within microbial communities associated with the microbialites was identified as a biosignature of microbial photosynthetic influence driving precipitation. Elevated oxygen concentrations and pH within the microenvironment of small, sporadic nodular microbial surface communities was concurrent with in situ precipitation of carbonate with δ[13]C values higher than predicted abiotic values and δ[13]C of bulk organic matter and phospholipid fatty acids (PLFA) that were consistent with a photosynthetically dominated community. Elevated carbonate δ[13]C values were also noted in the thin surface microbial mat recovered from shallow (11m) microbialites. These samples showed increased biomass during summer sampling periods as compared to deeper samples, consistent with expected high rates of photosynthetic activity due to higher light levels and temperature at these depths. These results contrast other recent studies of modern microbialite systems that identified biosignatures of heterotrophic influences on precipitation of carbonates. PLFA profiles demonstrated that the surface microbial mat community consisting of both photosynthetic and heterotrophic microbes was stable over seasonal and spatial changes in light and temperature. However, changes in microbial biomass with depth and season indicated that microbial activity and growth plays an important role in the development of isotopic biosignatures. </p> <p> Biosignatures of high levels of photosynthetic activity were also observed in carbonate, rich microbial mats that exhibited undersaturated p CO2 concentrations during the summer and DIC δ[13]C values enriched above values predicted for isotopic equilibrium with atmospheric CO2. Seasonal and annual shifts in the balance of heterotrophy and autotrophy in the lakes and microenvironment of the mat accounted for observed variations in DIC and associated carbonate δ[13]C values. In contrast to other organic rich microbial mats, bulk organic δ[13]C values were not enriched and the systems did not show evidence of CO2 limitation. Rather, these results indicated that low bulk organic δ[13]C values and large isotopic discriminations can exist under conditions of high DIC concentrations and carbonate content that provide a non limiting carbon source to replenish photosynthetic drawdown. </p> / Thesis / Doctor of Philosophy (PhD)