Consideration of soil as a living ecosystem offers the potential for innovative and sustainable solutions to geotechnical problems. This is a new paradigm for many in geotechnical engineering. Realising the potential of this paradigm requires a multidisciplinary approach that embraces biology and geochemistry to develop techniques for beneficial ground modification. This paper assesses the progress, opportunities, and challenges in this emerging field. Biomediated geochemical processes, which consist of a geochemical reaction regulated by subsurface microbiology, currently being explored include mineral precipitation, gas generation, biofilm formation and biopolymer generation. For each of these processes, subsurface microbial processes are employed to create an environment conducive to the desired geochemical reactions among the minerals, organic matter, pore fluids, and gases that constitute soil. Geotechnical applications currently being explored include cementation of sands to enhance bearing capacity and liquefaction resistance, sequestration of carbon, soil erosion control, groundwater flow control, and remediation of soil and groundwater impacted by metals and radionuclides. Challenges in biomediated ground modification include upscaling processes from the laboratory to the field, in situ monitoring of reactions, reaction products and properties, developing integrated biogeochemical and geotechnical models, management of treatment by-products, establishing the durability and longevity/reversibility of the process, and education of engineers and researchers.

Consideration of soil as a living ecosystem offers the potential for innovative and sustainable solutions to geotechnical problems. This is a new paradigm for many in geotechnical engineering. Realising the potential of this paradigm requires a multidisciplinary approach that embraces biology and geochemistry to develop techniques for beneficial ground modification. This paper assesses the progress, opportunities, and challenges in this emerging field. Biomediated geochemical processes, which consist of a geochemical reaction regulated by subsurface microbiology, currently being explored include mineral precipitation, gas generation, biofilm formation and biopolymer generation. For each of these processes, subsurface microbial processes are employed to create an environment conducive to the desired geochemical reactions among the minerals, organic matter, pore fluids, and gases that constitute soil. Geotechnical applications currently being explored include cementation of sands to enhance bearing capacity and liquefaction resistance, sequestration of carbon, soil erosion control, groundwater flow control, and remediation of soil and groundwater impacted by metals and radionuclides. Challenges in biomediated ground modification include upscaling processes from the laboratory to the field, in situ monitoring of reactions, reaction products and properties, developing integrated biogeochemical and geotechnical models, management of treatment by-products, establishing the durability and longevity/reversibility of the process, and education of engineers and researchers.

Specimens of silica sand treated via enzyme induced carbonate precipitation (EICP) showed surprisingly high strength at a relatively low carbonate content when non-fat powdered milk was included in the treatment solution. EICP is a biologically-based soil improvement technique that uses free urease enzyme to catalyze the hydrolysis of urea in an aqueous solution, producing carbonate ions and alkalinity that in the presence of calcium cations leads to precipitation of calcium carbonate. The strength achieved at less than 1.4% carbonate content via a single cycle of treatment was unprecedented compared to results reported in the literature from both EICP and microbially induced carbonate precipitation (MICP). Scanning electron microscope images show that in the specimens treated with the solution containing powdered milk the carbonate precipitate was concentrated at interparticle contacts. The impact of these results include reductions in the concentration of substrate and enzyme required to achieve a target compressive strength, reduction in the undesirable ammonium chloride by-product, and, depending on the desired strength, reduction in the number of cycles of EICP treatment. These advantages enhance the potential for development of a sustainable method of soil improvement via hydrolysis of urea.

Wind tunnel tests show that enzyme-induced carbonate precipitation (EICP) holds promise as a method for mitigation of fugitive dust emissions. Fugitive dust (wind-blown fine-grained soil) is a significant environmental problem in semi-arid and arid environments. Conventional methods for fugitive dust control, including the application of water, salt, or synthetic polymers, are either ineffective in arid climates, limited to short-term stabilisation, or very expensive. EICP employs hydrolysis of urea (ureolysis), a process catalysed by the urease enzyme, to precipitate calcium carbonate (CaCO3) in the presence of calcium ions. Urease is a widely occurring enzyme found in many plants and microorganisms. Wind tunnel experiments were conducted to evaluate the use of a topically applied EICP solution containing plant-derived urease to stabilise soil against fugitive dust emission. Three different soils were tested: a native Arizona silty sand, a uniform medium-grained silica sand and fine sand-sized mine tailings from southern Arizona. The wind tunnel tests established the treatment concentrations at which EICP was more effective in suppressing fugitive dust than specimens prepared by either thoroughly wetting the soil or treatment with a salt–urea solution. These tests demonstrate the potential of EICP treatment as a means of mitigating fugitive dust emissions.

Microbially induced calcium carbonate precipitation (MICP) is attracting increasing attention as a sustainable means of soil improvement. While there are several possible MICP mechanisms, microbial denitrification has the potential to become one of the preferred methods for MICP because complete denitrification does not produce toxic byproducts, readily occurs under anoxic conditions, and potentially has a greater carbonate yield per mole of organic electron donor than other MICP processes. Denitrification may be preferable to ureolytic hydrolysis, the MICP process explored most extensively to date, as the byproduct of denitrification is benign nitrogen gas, while the chemical pathways involved in hydrolytic ureolysis processes produce undesirable and potentially toxic byproducts such as ammonium (NH 4 + ). This thesis focuses on bacterial denitrification and presents preliminary results of bench-scale laboratory experiments on denitrification as a candidate calcium carbonate precipitation mechanism.The bench-scale bioreactor and column tests, conducted using the facultative anaerobic bacterium Pseudomonas denitrificans, show that calcite can be precipitated from calcium-rich pore water using denitrification. Experiments also explore the potential for reducing environmental impacts and lowering costs associated with denitrification by reducing the total dissolved solids in the reactors and columns, optimizing the chemical matrix, and addressing the loss of free calcium in the form of calcium phosphate precipitate from the pore fluid.ii The potential for using MICP to sequester radionuclides and metal contaminants that are migrating in groundwater is also investigated. In the sequestration process, divalent cations and radionuclides are incorporated into the calcite structure via substitution, forming low-strontium calcium carbonate minerals that resist dissolution at a level similar to that of calcite. Work by others using the bacterium Sporosarcina pasteurii has suggested that in-situ sequestration of radionuclides and metal contaminants can be achieved through MICP via hydrolytic ureolysis. MICP through bacterial denitrification seems particularly promising as a means for sequestering radionuclides and metal contaminants in anoxic environments due to the anaerobic nature of the process and the ubiquity of denitrifying bacteria in the subsurface.iii ACKNOWLEDGMENTS I am deeply grateful for the assistance and guidance provided by my committee members Dr. Edward Kavazanjian, Dr. Bruce Rittmann, and Dr.Everett Shock. I would like extend a special thanks to Dr. Kavazanjian for all his efforts including the countless hours spent providing a deeper and broader understanding of geotechnical engineering that can only come from fruitful years of academic work bolstered by equally impressive years in industry. I would also like to thank Dr. Rittmann for allowing me the opportunity to work and train in his laboratory, and affording me much needed guidance. As a pioneer in his field, Dr. Rittmann has provided me wi...