Matching Items (9)
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- All Subjects: Biogeochemistry
- Creators: Kavazanjian, Edward
- Creators: Anbar, Ariel D
- Resource Type: Text
Description
Humans have dramatically increased phosphorus (P) availability in terrestrial and aquatic ecosystems. As P is often a limiting nutrient of primary production, changes in its availability can have dramatic effects on ecosystem processes. I examined the effects of calcium carbonate (CaCO3) deposition, which can lower P concentrations via coprecipitation of phosphate, on P availability in two systems: streams in the Huachuca Mountains, Arizona, and a stream, Río Mesquites, in Cuatro Ciénegas, México. Calcium carbonate forms as travertine in the former and within the microbialites of the latter. Despite these differences, CaCO3 deposition led to lowered P availability in both systems. By analyzing a three-year dataset of water chemistry from the Huachuca Mountain streams, I determined that P concentrations were negatively related to CaCO3 deposition rates. I also discovered that CaCO3 was positively correlated with nitrogen concentrations, suggesting that the stoichiometric effect of CaCO3 deposition on nutrient availability is due not only to coprecipitation of phosphate, but also to P-related constraints on biotic nitrogen uptake. Building from these observations, bioassays of nutrient limitation of periphyton growth suggest that P limitation is more prevalent in streams with active CaCO3 deposition than those without. Furthermore, when I experimentally reduced rates of CaCO3 deposition within one of the streams by partial light-exclusion, areal P uptake lengths decreased, periphyton P content and growth increased, and periphyton nutrient limitation by P decreased. In Río Mesquites, CaCO3 deposition was also associated with P limitation of microbial growth. There, I investigated the consequences of reductions in CaCO3 deposition with several methods. Calcium removal led to increased concentrations of P in the microbial biomass while light reductions decreased microbial biomass and chemical inhibition had no effect. These results suggest that CaCO3 deposition in microbialites does limit biological uptake of P, that photoautotrophs play an important role in nutrient acquisition, and, combined with other experimental observations, that sulfate reduction may support CaCO3 deposition in the microbialite communities of Río Mesquites. Overall, my results suggest that the effects of CaCO3 deposition on P availability are general and this process should be considered when managing nutrient flows across aquatic ecosystems.
ContributorsCorman, Jessica R. (Author) / Elser, James J (Thesis advisor) / Anbar, Ariel D (Committee member) / Childers, Daniel L. (Committee member) / Grimm, Nancy (Committee member) / Souza, Valeria (Committee member) / Arizona State University (Publisher)
Created2015
Description
Molybdenum (Mo) is a key trace nutrient for biological assimilation of nitrogen, either as nitrogen gas (N2) or nitrate (NO3-). Although Mo is the most abundant metal in seawater (105 nM), its concentration is low (<5 nM) in most freshwaters today, and it was scarce in the ocean before 600 million years ago. The use of Mo for nitrogen assimilation can be understood in terms of the changing Mo availability through time; for instance, the higher Mo content of eukaryotic vs. prokaryotic nitrate reductase may have stalled proliferation of eukaryotes in low-Mo Proterozoic oceans. Field and laboratory experiments were performed to study Mo requirements for NO3- assimilation and N2 fixation, respectively. Molybdenum-nitrate addition experiments at Castle Lake, California revealed interannual and depth variability in plankton community response, perhaps resulting from differences in species composition and/or ammonium availability. Furthermore, lake sediments were elevated in Mo compared to soils and bedrock in the watershed. Box modeling suggested that the largest source of Mo to the lake was particulate matter from the watershed. Month-long laboratory experiments with heterocystous cyanobacteria (HC) showed that <1 nM Mo led to low N2 fixation rates, while 10 nM Mo was sufficient for optimal rates. At 1500 nM Mo, freshwater HC hyperaccumulated Mo intercellularly, whereas coastal HC did not. These differences in storage capacity were likely due to the presence in freshwater HC of the small molybdate-binding protein, Mop, and its absence in coastal and marine cyanobacterial species. Expression of the mop gene was regulated by Mo availability in the freshwater HC species Nostoc sp. PCC 7120. Under low Mo (<1 nM) conditions, mop gene expression was up-regulated compared to higher Mo (150 and 3000 nM) treatments, but the subunit composition of the Mop protein changed, suggesting that Mop does not bind Mo in the same manner at <1 nM Mo that it can at higher Mo concentrations. These findings support a role for Mop as a Mo storage protein in HC and suggest that freshwater HC control Mo cellular homeostasis at the post-translational level. Mop's widespread distribution in prokaryotes lends support to the theory that it may be an ancient protein inherited from low-Mo Precambrian oceans.
ContributorsGlass, Jennifer (Author) / Anbar, Ariel D (Thesis advisor) / Shock, Everett L (Committee member) / Jones, Anne K (Committee member) / Hartnett, Hilairy E (Committee member) / Elser, James J (Committee member) / Fromme, Petra (Committee member) / Arizona State University (Publisher)
Created2011
Description
In many natural systems aqueous geochemical conditions dictate the reaction pathways of organic compounds. Geologic settings that span wide ranges in temperature, pressure, and composition vastly alter relative reaction rates and resulting organic abundances. The dependence of organic reactions on these variables contributes to planetary-scale nutrient cycling, and suggests that relative abundances of organic compounds can reveal information about inaccessible geologic environments, whether from the terrestrial subsurface, remote planetary settings, or even the distant past (if organic abundances are well preserved). Despite their relevance to planetary modeling and exploration, organic reactions remain poorly characterized under geochemically relevant conditions, especially in terms of their reaction kinetics, mechanisms, and equilibria.
In order to better understand organic transformations in natural systems, the reactivities of oxygen- and nitrogen-bearing organic functional groups were investigated under experimental hydrothermal conditions, at 250°C and 40 bar. The model compounds benzylamine and α-methylbenzylamine were used as analogs to environmentally relevant amines, ultimately elucidating two dominant deamination mechanisms for benzylamine, SN1 and SN2, and a single SN1 mechanism for deamination of α-methylbenzylamine. The presence of unimolecular and bimolecular mechanisms has implications for temperature dependent kinetics, indicating that Arrhenius rate extrapolation is currently unreliable for deamination.
Hydrothermal experiments with benzyl alcohol, benzylamine, dibenzylamine, or tribenzylamine as the starting material indicate that substitution reactions between these compounds (and others) are reversible and approach metastable equilibrium after 72 hours. These findings suggest that relative ratios of organic compounds capable of substitution reactions could be targeted as tracers of inaccessible geochemical conditions.
Metastable equilibria for organic reactions were investigated in a natural low-temperature serpentinizing continental system. Serpentinization is a water-rock reaction which generates hyperalkaline, reducing conditions. Thermodynamic calculations were performed for reactions between dissolved inorganic carbon and hydrogen to produce methane, formate, and acetate. Quantifying conditions that satisfy equilibrium for these reactions allows subsurface conditions to be predicted. These calculations also lead to hypotheses regarding active microbial processes during serpentinization.
In order to better understand organic transformations in natural systems, the reactivities of oxygen- and nitrogen-bearing organic functional groups were investigated under experimental hydrothermal conditions, at 250°C and 40 bar. The model compounds benzylamine and α-methylbenzylamine were used as analogs to environmentally relevant amines, ultimately elucidating two dominant deamination mechanisms for benzylamine, SN1 and SN2, and a single SN1 mechanism for deamination of α-methylbenzylamine. The presence of unimolecular and bimolecular mechanisms has implications for temperature dependent kinetics, indicating that Arrhenius rate extrapolation is currently unreliable for deamination.
Hydrothermal experiments with benzyl alcohol, benzylamine, dibenzylamine, or tribenzylamine as the starting material indicate that substitution reactions between these compounds (and others) are reversible and approach metastable equilibrium after 72 hours. These findings suggest that relative ratios of organic compounds capable of substitution reactions could be targeted as tracers of inaccessible geochemical conditions.
Metastable equilibria for organic reactions were investigated in a natural low-temperature serpentinizing continental system. Serpentinization is a water-rock reaction which generates hyperalkaline, reducing conditions. Thermodynamic calculations were performed for reactions between dissolved inorganic carbon and hydrogen to produce methane, formate, and acetate. Quantifying conditions that satisfy equilibrium for these reactions allows subsurface conditions to be predicted. These calculations also lead to hypotheses regarding active microbial processes during serpentinization.
ContributorsRobinson, Kirtland J (Author) / Shock, Everett L (Thesis advisor) / Herckes, Pierre (Committee member) / Hartnett, Hilairy E (Committee member) / Anbar, Ariel D (Committee member) / Arizona State University (Publisher)
Created2017
Description
This dissertation details an attempt to experimentally evaluate the Giroud et al. (1995) concentration factors for geomembranes loaded in tension perpendicular to a seam by laboratory measurement. Field observations of the performance of geomembrane liner systems indicates that tears occur at average strains well below the yield criteria. These observations have been attributed, in part, to localized strain concentrations in the geomembrane loaded in tension in a direction perpendicular to the seam. Giroud et al. (1995) has presented theoretical strain concentration factors for geomembrane seams loaded in tension when the seam is perpendicular to the applied tensile strain. However, these factors have never been verified. This dissertation was prepared in fulfillment of the requirements for graduation from Barrett, the Honors College at Arizona State University. The work described herein was sponsored by the National Science Foundation as a part of a larger research project entitled "NEESR: Performance Based Design of Geomembrane Liner Systems Subject to Extreme Loading." The work is motivated by geomembrane tears observed at the Chiquita Canyon landfill following the 1994 Northridge earthquake. Numerical analysis of the strains in the Chiquita Canyon landfill liner induced by the earthquake indicated that the tensile strains, were well below the yield strain of the geomembrane material. In order to explain why the membrane did fail, strain concentration factors due to bending at seams perpendicular to the load in the model proposed by Giroud et al. (1995) had to be applied to the geomembrane (Arab, 2011). Due to the localized nature of seam strain concentrations, digital image correlation (DIC) was used. The high resolution attained with DIC had a sufficient resolution to capture the localized strain concentrations. High density polyethylene (HDPE) geomembrane samples prepared by a leading geomembrane manufacturer were used in the testing described herein. The samples included both extrusion fillet and dual hot wedge fusion seams. The samples were loaded in tension in a standard triaxial test apparatus. to the seams in the samples including both extrusion fillet and dual hot wedge seams. DIC was used to capture the deformation field and strain fields were subsequently created by computer analysis.
ContributorsAndresen, Jake Austin (Author) / Kavazanjian, Edward (Thesis director) / Gutierrez, Angel (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Two challenges in the implementation of enzyme induced carbonate precipitation(EICP) are the cost of enzyme and the variability of the enzyme. Urease enzyme costs
can be lowered drastically with the use of crude extract from plant materials, but
experience has shown variability in the source of the crude urease enzyme, the crude
urease enzyme extraction methods, and the concentration of the EICP solution can cause
significant variability in the efficacy of the EICP solution.
This thesis examines the variability in the efficacy of crude enzyme derived from
jack beans (Canavalia ensiformis) and sword beans (Canavalia gladiata), two of the
most commonly used sources of urease enzyme for EICP. The sources of variability
investigated herein include the crude extraction method (including the effect of the bean
husks on extraction) and different chemical constituent concentrations. These effects
were assessed using enzyme activity measurements and precipitation efficiency tests. The
activity tests were performed via spectrophotometry using Nessler's reagent. The
precipitation tests looked at the influence of chemical constituent concentrations of 0.67
M calcium chloride and 1 M urea with non-fat dry milk in the EICP solutions and a
higher concentration solution with chemical constituent concentrations of 2 M for both
calcium chloride and urea with non-fat dry milk. The high concentration solution was
selected based on preliminary testing results to maximize carbonate precipitation in one
cycle of treatment. Significant sources of a decline in activity (and increase in variation)
of the crude urease enzyme were found in extraction from sword beans with husks, high
chemical constituent concentrations, and juicing instead of cheesecloth filtration.
This thesis also examines the accuracy of commonly used correlation factors for
converting electrical conductivity to urease enzyme activity. Crude jack bean and sword
bean urease enzyme activity measurement via electrical conductivity was found to have a
correlation coefficient that differed from the previously reported correlation when
compared to activity measured via the more accurate spectrophotometry using Nessler’s
reagent measurements.
ContributorsPearson, Rayanna (Author) / Kavazanjian, Edward (Thesis advisor) / Khodadadi Tirkolaei, Hamed (Committee member) / Salifu, Emmanuel (Committee member) / Arizona State University (Publisher)
Created2022
Description
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.
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.
ContributorsKim, Daehyun (Author) / van Paassen, Leon (Thesis advisor) / Kavazanjian, Edward (Committee member) / Zapata, Claudia (Committee member) / Mahabadi, Nariman (Committee member) / Tao, Junliang (Committee member) / Jang, Jaewon (Committee member) / Arizona State University (Publisher)
Created2019
Description
Mantle derived basalts along the entirety of the Earth’s Mid-Ocean Ridge (MOR) spreading centers are continuously altered by seawater, allowing the hydrosphere to subsume energy and exchange mass with the deep, slowly cooling Earth. Compositional heterogeneities inherent to these basalts—the result of innumerable geophysical and geochemical processes in the mantel and crust—generate spatial variation in the equilibrium states toward which these water-rock environments cascade. This alteration results in a unique distribution of precipitate assemblages, hydrothermal fluid chemistries, and energetic landscapes among ecosystems rooted within and above the seafloor. The equilibrium states for the full range of basalt compositional heterogeneity present today are calculated over all appropriate temperatures and extents of reaction with seawater, along with the non-equilibrium mixtures generated when hydrothermal fluids mix back into seawater. These mixes support ancient and diverse ecosystems fed not by the energy of the sun, but by the geochemical energy of the Earth. Facilitated by novel, high throughout code, this effort has yielded a high-resolution compositional database that is mapped back onto all ridge systems. By resolving the chemical and energetic consequences of basalt-seawater interaction to sub-ridge scales, alteration features that are globally homogeneous can be distinguished from those that are locally unique, guiding future field observations with testable geochemical and biochemical predictions.
ContributorsELY, TUCKER (Author) / Shock, Everett L (Thesis advisor) / Till, Christy B. (Committee member) / Walker, Sara I (Committee member) / Anbar, Ariel D (Committee member) / Hartnett, Hilairy E (Committee member) / Arizona State University (Publisher)
Created2020
Description
Water is a vital resource, and its protection is a priority world-wide. One widespread threat to water quality is contamination by chlorinated solvents. These dry-cleaning and degreasing agents entered the watershed through spills and improper disposal and now are detected in 4% of U.S. aquifers and 4.5-18% of U.S. drinking water sources. The health effects of these contaminants can be severe, as they are associated with damage to the nervous, liver, kidney, and reproductive systems, developmental issues, and possibly cancer. Chlorinated solvents must be removed or transformed to improve water quality and protect human and environmental health. One remedy, bioaugmentation, the subsurface addition of microbial cultures able to transform contaminants, has been implemented successfully at hundreds of sites since the 1990s. Bioaugmentation uses the bacteria Dehalococcoides to transform chlorinated solvents with hydrogen, H2, as the electron donor. At advection limited sites, bioaugmentation can be combined with electrokinetics (EK-Bio) to enhance transport. However, challenges for successful bioremediation remain. In this work I addressed several knowledge gaps surrounding bioaugmentation and EK-Bio. I measured the H2 consuming capacity of soils, detailed the microbial metabolisms driving this demand, and evaluated how these finding relate to reductive dechlorination. I determined which reactions dominated at a contaminated site with mixed geochemistry treated with EK-Bio and compared it to traditional bioaugmentation. Lastly, I assessed the effect of EK-Bio on the microbial community at a field-scale site. Results showed the H2 consuming capacity of soils was greater than that predicted by initial measurements of inorganic electron acceptors and primarily driven by carbon-based microbial metabolisms. Other work demonstrated that, given the benefits of some carbon-based metabolisms to microbial reductive dechlorination, high levels of H2 consumption in soils are not necessarily indicative of hostile conditions for Dehalococcoides. Bench-scale experiments of EK-Bio under mixed geochemical conditions showed EK-Bio out-performed traditional bioaugmentation by facilitating biotic and abiotic transformations. Finally, results of microbial community analysis at a field-scale implementation of EK-Bio showed that while there were significant changes in alpha and beta diversity, the impact of EK-Bio on native microbial communities was minimal.
ContributorsAltizer, Megan Leigh (Author) / Torres, César I (Thesis advisor) / Krajmalnik-Brown, Rosa (Thesis advisor) / Rittmann, Bruce E (Committee member) / Kavazanjian, Edward (Committee member) / Delgado, Anca G (Committee member) / Arizona State University (Publisher)
Created2020
Description
Urease, an amidohydrolase, is an essential ingredient in the emerging engineering technique of biocementation. When free urease enzyme is used this carbonate precipitation process is often referred to as enzyme induced carbonate precipitation (EICP). To date, most engineering applications of EICP have used commercially available powdered urease. However, the high cost of commercially available urease is a major barrier to adoption of engineering applications of EICP in practice. The objective of this dissertation was to develop a simple and inexpensive enzyme production technique using agricultural resources. The specific objectives of this dissertation were (i) to develop a simple extraction process to obtain urease from common agricultural resources and identify a preferred agricultural resource for further study, (ii) to reduce the cost of enzyme production by eliminating the use of a buffer, centrifugation, and dehusking of the beans during the extraction process, (iii) investigate the stability of the extracted enzyme both in solution and after reduction to a powder by lyophilization (freeze-drying), and (iv) to study the kinetics of the extracted enzyme.
The results presented in this dissertation confirmed that inexpensive crude extracts of urease from agricultural products, including jack beans, soybeans, and watermelon seeds, are effective at catalyzing urea hydrolysis for carbonate precipitation. Based upon unit yield, jack beans were identified as the preferred agricultural resource for urease extraction. Results also showed that the jack bean extract retained its activity even after replacing the buffer with tap water and eliminating acetone fractionation, centrifugation, and dehusking. It was also found that the lyophilized crude extract maintained its activity during storage for at least one year and more effectively than either the crude extract solution or rehydrated commercial urease. The kinetics of the extracted enzyme was studied to gain greater insight into the optimum concentration of urea in engineering applications of EICP. Results showed higher values for the half-saturation coefficient of the crude extract compared to the commercial enzymes.
The results presented in this dissertation demonstrate the potential for a significant reduction in the cost of applying EICP in engineering practice by mass production of urease enzyme via a simple extraction process.
ContributorsJavadi, Neda (Author) / Kavazanjian, Edward (Thesis advisor) / Khodadadi Tirkolaei, Hamed (Committee member) / Hamadan, Naser (Committee member) / Delgado, Anca (Committee member) / Arizona State University (Publisher)
Created2021