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- All Subjects: Biogeochemistry
- Creators: Shock, Everett
- Creators: Kavazanjian, Edward
- Resource Type: Text
Description
This dissertation is presented in two sections. First, I explore two methods of using stable isotope analysis to trace environmental and biogeochemical processes. Second, I present two related studies investigating student understanding of the biogeochemical concepts that underlie part one. Fe and Hg are each biogeochemically important elements in their own way. Fe is a critical nutrient for phytoplankton, while Hg is detrimental to nearly all forms of life. Fe is often a limiting factor in marine phytoplankton growth. The largest source, by mass, of Fe to the open ocean is windblown mineral dust, but other more soluble sources are more bioavailable. To look for evidence of these non-soil dust sources of Fe to the open ocean, I measured the isotopic composition of aerosol samples collected on Bermuda. I found clear evidence in the fine size fraction of a non-soil dust Fe source, which I conclude is most likely from biomass burning. Widespread adoption of compact fluorescent lamps (CFL) has increased their importance as a source of environmental Hg. Isotope analysis would be a useful tool in quantifying this impact if the isotopic composition of Hg from CFL were known. My measurements show that CFL-Hg is isotopically fractionated, in a unique pattern, during normal operation. This fractionation is large and has a distinctive, mass-independent signature, such that CFL Hg can be uniquely identified from other sources. Misconceptions research in geology has been a very active area of research, but student thinking regarding the related field of biogeochemistry has not yet been studied in detail. From interviews with 40 undergraduates, I identified over 150 specific misconceptions. I also designed a multiple-choice survey (concept inventory) to measure understanding of these same biogeochemistry concepts. I present statistical evidence, based on the Rasch model, for the reliability and validity of this instrument. This instrument will allow teachers and researchers to easily quantify learning outcomes in biogeochemistry and will complement existing concept inventories in geology, chemistry, and biology.
ContributorsMead, Chris (Author) / Anbar, Ariel (Thesis advisor) / Semken, Steven (Committee member) / Shock, Everett (Committee member) / Herckes, Pierre (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2014
Description
In enzyme induced carbonate precipitation (EICP), calcium carbonate (CaCO3) precipitation is catalyzed by plant-derived urease enzyme. In EICP, urea hydrolyzes into ammonia and inorganic carbon, altering geochemical conditions in a manner that promotes carbonate mineral precipitation. The calcium source in this process comes from calcium chloride (CaCl2) in aqueous solution. Research work conducted for this dissertation has demonstrated that EICP can be employed for a variety of geotechnical purposes, including mass soil stabilization, columnar soil stabilization, and stabilization of erodible surficial soils. The research presented herein also shows that the optimal ratio of urea to CaCl2 at ionic strengths of less than 1 molar is approximately 1.75:1. EICP solutions of very high initial ionic strength (i.e. 6 M) as well as high urea concentrations (> 2 M) resulted in enzyme precipitation (salting-out) which hindered carbonate precipitation. In addition, the production of NH4+ may also result in enzyme precipitation. However, enzyme precipitation appeared to be reversible to some extent. Mass soil stabilization was demonstrated via percolation and mix-and-compact methods using coarse silica sand (Ottawa 20-30) and medium-fine silica sand (F-60) to produce cemented soil specimens whose strength improvement correlated with CaCO3 content, independent of the method employed to prepare the specimen. Columnar stabilization, i.e. creating columns of soil cemented by carbonate precipitation, using Ottawa 20-30, F-60, and native AZ soil was demonstrated at several scales beginning with small columns (102-mm diameter) and culminating in a 1-m3 soil-filled box. Wind tunnel tests demonstrated that surficial soil stabilization equivalent to that provided by thoroughly wetting the soil can be achieved through a topically-applied solution of CaCl2, urea, and the urease enzyme. The topically applied solution was shown to form an erosion-resistant CaCO3 crust on fine sand and silty soils. Cementation of erodible surficial soils was also achieved via EICP by including a biodegradable hydrogel in the stabilization solution. A dilute hydrogel solution extended the time frame over which the precipitation reaction could occur and provided improved spatial control of the EICP solution.
ContributorsHamdan, Nasser M (Author) / Kavazanjian Jr., Edward (Thesis advisor) / Rittmann, Bruce (Thesis advisor) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2015
Description
Biological soil crusts (BSCs) are critical components of arid and semiarid environments and provide the primary sources of bioavailable macronutrients and increase micronutrient availability to their surrounding ecosystems. BSCs are composed of a variety of microorganisms that perform a wide range of physiological processes requiring a multitude of bioessential micronutrients, such as iron, copper, and molybdenum. This work investigated the effects of BSC activity on soil solution concentrations of bioessential elements and examined the microbial production of organic chelators, called siderophores. I found that aluminum, vanadium, copper, zinc, and molybdenum were solubilized in the action of crusts, while nickel, zinc, arsenic, and zirconium were immobilized by crust activity. Potassium and manganese displayed behavior consistent with biological removal and mobilization, whereas phosphorus and iron solubility were dominated by abiotic processes. The addition of bioavailable nitrogen altered the effects of BSCs on soil element mobilization. In addition, I found that the biogeochemical activites of BSCs were limited by molybdenum, a fact that likely contributes to co-limitation by nitrogen. I confirmed the presence of siderophore producing microbes in BSCs. Siderophores are low-molecular weight organic compounds that are released by bacteria to increase element solubility and facilitate element uptake; siderophore production is likely the mechanism by which BSCs affect the patterns I observed in soil solution element concentrations. Siderophore producers were distributed across a range of bacterial groups and ecological niches within crusts, suggesting that siderophore production influences the availability of a variety of elements for use in many physiological processes. Four putative siderophore compounds were identified using electrospray ionization mass spectrometry; further attempts to characterize the compounds confirmed two true siderophores. Taken together, the results of my work provide information about micronutrient cycling within crusts that can be applied to BSC conservation and management. Fertilization with certain elements, particularly molybdenum, may prove to be a useful technique to promote BSC growth and development which would help prevent arid land degradation. Furthermore, understanding the effects of BSCs on soil element mobility could be used to develop useful biomarkers for the study of the existence and distribution of crust-like communities on ancient Earth, and perhaps other places, like Mars.
ContributorsNoonan, Kathryn Alexander (Author) / Hartnett, Hilairy (Thesis advisor) / Anbar, Ariel (Committee member) / Garcia-Pichel, Ferran (Committee member) / Shock, Everett (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
ContributorsMorrison, Keith D (Author) / Williams, Lynda B (Thesis advisor) / Williams, Stanley N (Thesis advisor) / Misra, Rajeev (Committee member) / Shock, Everett (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2015
Description
Lipids perform functions essential to life and have a variety of structures that are influenced by the organisms and environments that produced them. Lipids tend to resist degradation after cell death, leading to their widespread use as biomarkers in geobiology, though their interpretation is often tricky. Many lipid structures are shared among organisms and function in many geochemical conditions and extremes. I argue it is useful to interpret lipid distributions as a balance of functional necessity and energy cost. This work utilizes a quantitative thermodynamic framework for interpreting energetically driven adaptation in lipids.
Yellowstone National Park is a prime location to study biological adaptations to a wide range of temperatures and geochemical conditions. Lipids were extracted and quantified from thermophilic microbial communities sampled along the temperature (29-91°C) and chemical gradients of four alkaline Yellowstone hot springs. I observed that decreased alkyl chain carbon content, increased degree of unsaturation, and a shift from ether to ester linkage caused a downstream increase in the average oxidation state of carbon (ZC) I hypothesized these adaptations were selected because they represent cost-effective solutions to providing thermostable membranes.
This hypothesis was explored by assessing the relative energetic favorability of autotrophic reactions to form alkyl chains from known concentrations of dissolved inorganic species at elevated temperatures. I found that the oxidation-reduction potential (Eh) predicted to favor formation of sample-representative alkyl chains had a strong positive correlation with Eh calculated from hot spring water chemistry (R2 = 0.72 for the O2/H2O redox couple). A separate thermodynamic analysis of bacteriohopanepolyol lipids found that predicted equilibrium abundances of observed polar headgroup distributions were also highly correlated with Eh of the surrounding water (R2= 0.84). These results represent the first quantitative thermodynamic assessment of microbial lipid adaptation in natural systems and suggest that observed lipid distributions represent energetically cost-effective assemblages along temperature and chemical gradients.
Yellowstone National Park is a prime location to study biological adaptations to a wide range of temperatures and geochemical conditions. Lipids were extracted and quantified from thermophilic microbial communities sampled along the temperature (29-91°C) and chemical gradients of four alkaline Yellowstone hot springs. I observed that decreased alkyl chain carbon content, increased degree of unsaturation, and a shift from ether to ester linkage caused a downstream increase in the average oxidation state of carbon (ZC) I hypothesized these adaptations were selected because they represent cost-effective solutions to providing thermostable membranes.
This hypothesis was explored by assessing the relative energetic favorability of autotrophic reactions to form alkyl chains from known concentrations of dissolved inorganic species at elevated temperatures. I found that the oxidation-reduction potential (Eh) predicted to favor formation of sample-representative alkyl chains had a strong positive correlation with Eh calculated from hot spring water chemistry (R2 = 0.72 for the O2/H2O redox couple). A separate thermodynamic analysis of bacteriohopanepolyol lipids found that predicted equilibrium abundances of observed polar headgroup distributions were also highly correlated with Eh of the surrounding water (R2= 0.84). These results represent the first quantitative thermodynamic assessment of microbial lipid adaptation in natural systems and suggest that observed lipid distributions represent energetically cost-effective assemblages along temperature and chemical gradients.
ContributorsBoyer, Grayson Maxwell (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Herckes, Pierre (Committee member) / Arizona State University (Publisher)
Created2018
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
One goal of geobiochemistry is to follow geochemical energy supplies from the external environment to the inside of microbial cells. This can be accomplished by combining thermodynamic calculations of energy supplies from geochemical processes and energy demands for biochemical processes. Progress towards this goal is summarized here. A critique of all thermodynamic data for biochemical compounds involved in the citric acid cycle (CAC) and the formulation of metabolite properties allows predictions of the energy involved in each step of the cycle as well as the full forward and reverse cycles over wide ranges of temperature and pressure. These results allow evaluation of energy demands at the center of many microbial metabolic systems. Field work, sampling, and lab analyses from two low-temperature systems, a serpentinizing system, and a subglacial setting, provide the data used in these thermodynamic analyses of energy supplies. An extensive literature summary of microbial and molecular data from serpentinizing systems found is used to guide the evaluation and ranking of energy supplies used by chemolithoautotrophic microbes. These results constrain models of the distribution of microbial metabolisms throughout the low-temperature serpentinization systems in the Samail ophiolite in Oman (including locales of primary and subsequent alteration processes). Data collected from Robertson Glacier in Alberta, Canada, together with literature data from Lake Vida in Antarctica and bottom seawater, allowed thermodynamic analyses of low-temperature energy supplies in a glacial system. Results for 1460 inorganic redox reactions are used to fully inventory the geochemical energy sources that support the globally extensive cold biosphere.
ContributorsCanovas, Peter Anthony (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Sharp, Thomas (Committee member) / Tyburczy, James (Committee member) / Heimsath, Arjun (Committee member) / Arizona State University (Publisher)
Created2016
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
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