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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
Aboveground net primary production (ANPP) is an important ecosystem process that, in drylands, is most frequently limited by water availability. Water availability for plants is in part controlled by the water holding capacity of soils. Available water holding capacity (AWHC) of soils is strongly influenced by soil texture and depth. This study drew upon localized rain gauge data and four data-sets of cover-line and biomass data to estimate ANPP and to determine annual precipitation (PPT). I measured soil depth to caliche and texture by layer of 112 plots across the four landscape units for which estimation of ANPP were available. A pedotransfer function was used to estimate AWHC from soil depth increments to depth of caliche measurements and texture analysis. These data were analyzed using simple and multivariate regression to test the effect of annual precipitation and available water holding capacity on aboveground net primary production. Soil texture remained constant among all plots (sandy loam) and depth to caliche varied from 15.16 cm to 189 cm. AWHC and the interaction term (PPT*AWHC) were insignificant (p=0.142, p=0.838) and annual PPT accounted for 18.4% of the variation in ANPP. The y-intercept was significantly different for ANPP ~ annual PPT when considering AWHC values either above or below 3 cm. Shrub ANPP was insensitive to precipitation regardless of AWHC (R2=-0.012, R2=0.014). Results from this study indicate that a model incorporating annual PPT and AWHC may not serve as a good predictor for ANPP at a site level where there is little variation in soil texture.
ContributorsWagner, Svenja K (Author) / Sala, Osvaldo E. (Thesis advisor) / Cease, Arianne (Committee member) / Hall, Sharon (Committee member) / Peters, Debra (Committee member) / Arizona State University (Publisher)
Created2019
Description
The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previous studies are well-characterized but within those trends is significant variability in single gene expression responses. I compare previous transcriptomics analyses with our protocol that limits the addition of bioavailable iron to growth media to identify consistent gene expression signals resulting from iron limitation. Second, I describe a novel method of improving the reliability of centroid-linkage clustering results. The size and complexity of modern sequencing datasets often prohibit constructing distance matrices, which prevents the use of many common clustering algorithms. Centroid-linkage circumvents the need for a distance matrix, but has the adverse effect of producing input-order dependent results. In this chapter, I describe a method of cluster edge counting across iterated centroid-linkage results and reconstructing aggregate clusters from a ranked edge list without a distance matrix and input-order dependence. Finally, I introduce dendritic heat maps, a new figure type that visualizes heat map responses through expanding and contracting sequence clustering specificities. Heat maps are useful for comparing data across a range of possible states. However, data binning is sensitive to clustering cutoffs which are often arbitrarily introduced by researchers and can substantially change the heat map response of any single data point. With an understanding of how the architectural elements of dendrograms and heat maps affect data visualization, I have integrated their salient features to create a figure type aimed at viewing multiple levels of clustering cutoffs, allowing researchers to better understand the effects of environment on metabolism or phylogenetic lineages.
ContributorsKellom, Matthew (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Elser, James (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2017
Description
In this project, I investigated the ecosystem services, or lack thereof, that landscape designs created in terms of microclimate modification at 11 residential homes throughout the Phoenix Metro Area. I also created an article for the homeowners who participated, explaining what I did and how they could apply my research. My research question was how a person can achieve a comfortable outdoor climate in their yard without over-using scarce water resources. I hypothesized that there would be a negative correlation between the maximum air temperature and the percent shade in each yard, regardless of the percent grass. I analyzed the data I collected using the program, R, and discovered that my hypothesis was supported for the month of July. These results are in line with previous studies on the subject and can help homeowners make informed decisions about the effects their landscaping choices might have.
ContributorsBarton, Erin Michaela (Author) / Hall, Sharon (Thesis director) / Ruddell, Benjamin (Committee member) / Spielmann, Katherine (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor)
Created2014-05
Description
The Prosopis genus of trees, also known as mesquites, are uniquely equipped to allow for an agroforestry regime in which crops can be grown beneath the canopy of the tree. Mesquites have the ability to redistribute water moisture in such a way that allows plants under the canopy to use water that has been brought up by the roots of mesquite trees. This means that there is a potential for food crops to be grown under the trees without using additional irrigation measures. This could be used where access to water is limited or for a sustainability-minded farmer who is trying to reduce water inputs in an arid environment. Mesquite trees produce a variety of products, including lumber and bean pods that can be ground down into an edible flour. Both products demand a high price in the marketplace and are produced in addition to the crops that can potentially be grown beneath the mesquite tree. In order to determine whether or not it is possible to grow crops under mesquite trees, I reviewed a wide range of literature regarding hydraulic redistribution, mesquite trees in general, and what plants might be best suited for growing beneath a mesquite. The list of plants was narrowed down to four crops that seemed most likely to survive in shaded, low water conditions in a hot environment. There has not been any research done on crops growing beneath mesquite trees, so the next step for research would be to experiment with each of the crops to determine how well each species can adapt to the specified conditions.
ContributorsMesser, Luke Winston (Author) / Eakin, Hallie (Thesis director) / Hall, Sharon (Committee member) / School of Sustainability (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Biological soil crusts (BSCs), topsoil microbial assemblages typical of arid land ecosystems, provide essential ecosystem services such as soil fertilization and stabilization against erosion. Cyanobacteria and lichens, sometimes mosses, drive BSC as primary producers, but metabolic activity is restricted to periods of hydration associated with precipitation. Climate models for the SW United States predict changes in precipitation frequency as a major outcome of global warming, even if models differ on the sign and magnitude of the change. BSC organisms are clearly well adapted to withstand desiccation and prolonged drought, but it is unknown if and how an alteration of the precipitation frequency may impact community composition, diversity, and ecosystem functions. To test this, we set up a BSC microcosm experiment with variable precipitation frequency treatments using a local, cyanobacteria-dominated, early-succession BSC maintained under controlled conditions in a greenhouse. Precipitation pulse size was kept constant but 11 different drought intervals were imposed, ranging between 416 to 3 days, during a period of 416 days. At the end of the experiments, bacterial community composition was analyzed by pyrosequencing of the 16s rRNA genes in the community, and a battery of functional assays were used to evaluate carbon and nitrogen cycling potentials. While changes in community composition were neither marked nor consistent at the Phylum level, there was a significant trend of decreased diversity with increasing precipitation frequency, and we detected particular bacterial phylotypes that responded to the frequency of precipitation in a consistent manner (either positively or negatively). A significant trend of increased respiration with increasingly long drought period was detected, but BSC could recover quickly from this effect. Gross photosynthesis, nitrification and denitrification remained essentially impervious to treatment. These results are consistent with the notion that BSC community structure adjustments sufficed to provide significant functional resilience, and allow us to predict that future alterations in precipitation frequency are unlikely to result in severe impacts to BSC biology or ecological relevance.
ContributorsMyers, Natalie Kristine (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Hall, Sharon (Committee member) / Turner, Benjamin (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2013
Description
Evaluations of chemical energy supplies for redox reactions used by chemotrophs in water-rock hosted ecosystems are often done separately from evaluations of chemotroph diversity. However, given that energy is a fundamental and unifying parameter for life, much can be gained by evaluating chemical energy as an ecological parameter of water-rock hosted ecosystems. Therefore, I developed an approach that combines evaluation of chemical energy supplies with 16S and 18S rRNA gene amplicon sequencing. I used this approach to assess drivers of microbial distribution, diversity and activity in serpentinized fluids of the Samail Ophiolite of Oman and in hot springs in Yellowstone National Park.
Through the application of the approach, microbiological interactions in serpentinized fluids were found to be more complex than anticipated. Serpentinized fluids are hyperalkaline and pH is often considered the driving parameter of microbial diversity, however hydrogenotrophic community composition varies in hyperalkaline fluids with similar pH. The composition of hydrogenotrophic communities in serpentinized fluids were found to correspond to the availability of the electron acceptor for hydrogenotrophic redox reactions. Specifically, hydrogenotrophic community composition transitions from being dominated by the hydrogenotrophic methanogen genus, Methanobacterium, when the concentration of sulfate is less than ~10 μm. Above ~10 μm, sulfate reducers are most abundant. Additionally, Methanobacterium was found to co-occur with the protist genus, Cyclidium, in serpentinized fluids. Species of Cyclidium are anaerobic and known to have methanogen endosymbionts. Therefore, Cyclidium may supply inorganic carbon evolved from fermentation to Methanobacterium, thereby mitigating pH dependent inorganic carbon limitation.
This approach also revealed possible biological mechanisms for methane oxidation in Yellowstone hot springs. Measurable rates of biological methane oxidation in hot spring sediments are likely associated with methanotrophs of the phylum, Verrucomicrobia, and the class, Alphaproteobacteria. Additionally, rates were measurable where known methanotrophs were not detected. At some of these sites, archaeal ammonia oxidizer taxa were detected. Ammonia oxidizers have been shown to be capable of methane oxidation in other systems and may be an alternative mechanism for methanotrophy in Yellowstone hot springs. At the remaining sites, uncharacterized microbial lineages may be capable of carrying out methane oxidation in Yellowstone hot springs.
Through the application of the approach, microbiological interactions in serpentinized fluids were found to be more complex than anticipated. Serpentinized fluids are hyperalkaline and pH is often considered the driving parameter of microbial diversity, however hydrogenotrophic community composition varies in hyperalkaline fluids with similar pH. The composition of hydrogenotrophic communities in serpentinized fluids were found to correspond to the availability of the electron acceptor for hydrogenotrophic redox reactions. Specifically, hydrogenotrophic community composition transitions from being dominated by the hydrogenotrophic methanogen genus, Methanobacterium, when the concentration of sulfate is less than ~10 μm. Above ~10 μm, sulfate reducers are most abundant. Additionally, Methanobacterium was found to co-occur with the protist genus, Cyclidium, in serpentinized fluids. Species of Cyclidium are anaerobic and known to have methanogen endosymbionts. Therefore, Cyclidium may supply inorganic carbon evolved from fermentation to Methanobacterium, thereby mitigating pH dependent inorganic carbon limitation.
This approach also revealed possible biological mechanisms for methane oxidation in Yellowstone hot springs. Measurable rates of biological methane oxidation in hot spring sediments are likely associated with methanotrophs of the phylum, Verrucomicrobia, and the class, Alphaproteobacteria. Additionally, rates were measurable where known methanotrophs were not detected. At some of these sites, archaeal ammonia oxidizer taxa were detected. Ammonia oxidizers have been shown to be capable of methane oxidation in other systems and may be an alternative mechanism for methanotrophy in Yellowstone hot springs. At the remaining sites, uncharacterized microbial lineages may be capable of carrying out methane oxidation in Yellowstone hot springs.
ContributorsHowells, Alta Emily Gessner (Author) / Shock, Everett (Thesis advisor) / Collins, James (Committee member) / Anbar, Ariel (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2020
Description
Due to analytical limitations, thermodynamic modeling is a lucrative alternative for obtaining metal speciation in chemically complex systems like life. However, such modeling is limited by the lack of equilibrium constant data for metal-complexation reactions, particularly for metal-organic species. These problems were ameliorated estimating these properties from 0-125°C for ~18,000 metal complexes of small molecules, proteins and peptides.
The estimates of metal-ligand equilibrium constants at 25°C and 1 bar were made using multiple linear free energy relationships in accordance with the metal-coordinating properties of ligands such as denticity, identity of electron donor group, inductive effects and steric hindrance. Analogous relationships were made to estimated metal-ligand complexation entropy that facilitated calculation of equilibrium constants up to 125°C using the van’t Hoff equation. These estimates were made for over 250 ligands that include carboxylic acids, phenols, inorganic acids, amino acids, peptides and proteins.
The stability constants mentioned above were used to obtain metal speciation in several microbial growth media including past bioavailability studies and compositions listed on the DSMZ website. Speciation calculations were also carried out for several metals in blood plasma and cerebrospinal fluid that include metals present at over micromolar abundance (sodium, potassium, calcium, magnesium, iron, copper and zinc) and metals of therapeutic or toxic potential (like gallium, rhodium and bismuth). Metal speciation was found to be considerably dependent on pH and chelator concentration that can help in the selection of appropriate ligands for gallium & rhodium based anticancer drugs and zinc-based antidiabetics. It was found that methanobactin can considerably alter copper speciation and is therefore a suitable agent for the treatment of Wilson Disease. Additionally, bismuth neurotoxicity was attributed to the low transferrin concentration in cerebrospinal fluid and the predominance of aqueous bismuth trihydroxide. These results demonstrate that metal speciation calculations using thermodynamic modeling can be extremely useful for understanding metal bioavailability in microbes and human bodily fluids.
The estimates of metal-ligand equilibrium constants at 25°C and 1 bar were made using multiple linear free energy relationships in accordance with the metal-coordinating properties of ligands such as denticity, identity of electron donor group, inductive effects and steric hindrance. Analogous relationships were made to estimated metal-ligand complexation entropy that facilitated calculation of equilibrium constants up to 125°C using the van’t Hoff equation. These estimates were made for over 250 ligands that include carboxylic acids, phenols, inorganic acids, amino acids, peptides and proteins.
The stability constants mentioned above were used to obtain metal speciation in several microbial growth media including past bioavailability studies and compositions listed on the DSMZ website. Speciation calculations were also carried out for several metals in blood plasma and cerebrospinal fluid that include metals present at over micromolar abundance (sodium, potassium, calcium, magnesium, iron, copper and zinc) and metals of therapeutic or toxic potential (like gallium, rhodium and bismuth). Metal speciation was found to be considerably dependent on pH and chelator concentration that can help in the selection of appropriate ligands for gallium & rhodium based anticancer drugs and zinc-based antidiabetics. It was found that methanobactin can considerably alter copper speciation and is therefore a suitable agent for the treatment of Wilson Disease. Additionally, bismuth neurotoxicity was attributed to the low transferrin concentration in cerebrospinal fluid and the predominance of aqueous bismuth trihydroxide. These results demonstrate that metal speciation calculations using thermodynamic modeling can be extremely useful for understanding metal bioavailability in microbes and human bodily fluids.
ContributorsPrasad, Apar (Author) / Shock, Everett (Thesis advisor) / Trovitch, Ryan (Committee member) / Redding, Kevin (Committee member) / Arizona State University (Publisher)
Created2019
Description
Modern agriculture faces multiple challenges: it must produce more food for a growing global population, adopt more efficient and sustainable management strategies, and adapt to climate change. One potential component of a sustainable management strategy is the application of biochar to agricultural soils. Biochar is the carbon-rich product of biomass pyrolysis, which contains large proportions of aromatic compounds that influence its stability in soil. Concomitant with carbon sequestration, biochar has the potential to increase soil fertility through increasing soil pH, moisture and nutrient retention. Changes in the soil physical and chemical properties can result in shifts in the soil microbiome, which are the proximate drivers of soil processes. This dissertation aims to determine the compositional and functional changes in the soil microbial community in response to the addition of a low-volatile matter biochar. First, the impact of biochar on the bacterial community was investigated in two important agricultural soils (Oxisol and Mollisol) with contrasting fertility under two different cropping systems (conventional sweet corn and zero-tillage napiergrass) one month and one year after the initial addition. This study revealed that the effects of biochar on the bacterial community were most pronounced in the Oxisol under napiergrass cultivation, however soil type was the strongest determinant of the bacterial community. A follow-up study was conducted using shotgun metagenomics to probe the functional community of soil microcosms, which contained Oxisol soil under napiergrass two years after the initial addition of biochar. Biochar significantly increased total carbon in the soils but had little impact on other soil properties. Theses analyses showed that biochar-amended soil microcosms exhibited significant shifts in the functional community and key metabolic pathways related to carbon turnover and denitrification. Given the distinct alterations to the biochar-amended community, deoxyribose nucleic acid (DNA) stable isotope probing was used to target the active populations. These analyses revealed that biochar did not significantly shift the active community in soil microcosms. Overall, these results indicate that the impact of biochar on the active soil community is transient in nature. Yet, biochar may still be a promising strategy for long-term carbon sequestration in agricultural soils.
ContributorsYu, Julian (Author) / Penton, C. Ryan (Thesis advisor) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Hall, Sharon (Committee member) / Arizona State University (Publisher)
Created2020