Matching Items (86)
Description
Human activity has increased loading of reactive nitrogen (N) in the environment, with important and often deleterious impacts on biodiversity, climate, and human health. Since the fate of N in the ecosystem is mainly controlled by microorganisms, understanding the factors that shape microbial communities becomes relevant and urgent. In arid land soils, these microbial communities and factors are not well understood. I aimed to study the role of N cycling microbes, such as the ammonia-oxidizing bacteria (AOB), the recently discovered ammonia-oxidizing archaea (AOA), and various fungal groups, in soils of arid lands. I also tested if niche differentiation among microbial populations is a driver of differential biogeochemical outcomes. I found that N cycling microbial communities in arid lands are structured by environmental factors to a stronger degree than what is generally observed in mesic systems. For example, in biological soil crusts, temperature selected for AOA in warmer deserts and for AOB in colder deserts. Land-use change also affects niche differentiation, with fungi being the major agents of N2O production in natural arid lands, whereas emissions could be attributed to bacteria in mesic urban lawns. By contrast, NO3- production in the native desert and managed soils was mainly controlled by autotrophic microbes (i.e., AOB and AOA) rather than by heterotrophic fungi. I could also determine that AOA surprisingly responded positively to inorganic N availability in both short (one month) and long-term (seven years) experimental manipulations in an arid land soil, while environmental N enrichment in other ecosystem types is known to favor AOB over AOA. This work improves our predictions of ecosystem response to anthropogenic N increase and shows that paradigms derived from mesic systems are not always applicable to arid lands. My dissertation also highlights the unique ecology of ammonia oxidizers and draws attention to the importance of N cycling in desert soils.
ContributorsMarusenko, Yevgeniy (Author) / Hall, Sharon J (Thesis advisor) / Garcia-Pichel, Ferran (Thesis advisor) / Mclain, Jean E (Committee member) / Schwartz, Egbert (Committee member) / Arizona State University (Publisher)
Created2013
Description
Microbial electrochemical cells (MXCs) are promising platforms for bioenergy production from renewable resources. In these systems, specialized anode-respiring bacteria (ARB) deliver electrons from oxidation of organic substrates to the anode of an MXC. While much progress has been made in understanding the microbiology, physiology, and electrochemistry of well-studied model ARB such as Geobacter and Shewanella, tremendous potential exists for MXCs as microbiological platforms for exploring novel ARB. This dissertation introduces approaches for selective enrichment and characterization of phototrophic, halophilic, and alkaliphilic ARB. An enrichment scheme based on manipulation of poised anode potential, light, and nutrient availability led to current generation that responded negatively to light. Analysis of phototrophically enriched communities suggested essential roles for green sulfur bacteria and halophilic ARB in electricity generation. Reconstruction of light-responsive current generation could be successfully achieved using cocultures of anode-respiring Geobacter and phototrophic Chlorobium isolated from the MXC enrichments. Experiments lacking exogenously supplied organic electron donors indicated that Geobacter could produce a measurable current from stored photosynthate in the dark. Community analysis of phototrophic enrichments also identified members of the novel genus Geoalkalibacter as potential ARB. Electrochemical characterization of two haloalkaliphilic, non-phototrophic Geoalkalibacter spp. showed that these bacteria were in fact capable of producing high current densities (4-8 A/m2) and using higher organic substrates under saline or alkaline conditions. The success of these selective enrichment approaches and community analyses in identifying and understanding novel ARB capabilities invites further use of MXCs as robust platforms for fundamental microbiological investigations.
ContributorsBadalamenti, Jonathan P (Author) / Krajmalnik-Brown, Rosa (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Rittmann, Bruce E. (Committee member) / Torres, César I (Committee member) / Vermaas, Willem (Committee member) / Arizona State University (Publisher)
Created2013
Description
The Cape Floral Region (CFR) in southwestern South Africa is one of the most diverse in the world, with >9,000 plant species, 70% of which are endemic, in an area of only ~90,000 km2. Many have suggested that the CFR's heterogeneous environment, with respect to landscape gradients, vegetation, rainfall, elevation, and soil fertility, is responsible for the origin and maintenance of this biodiversity. While studies have struggled to link species diversity with these features, no study has attempted to associate patterns of gene flow with environmental data to determine how CFR biodiversity evolves on different scales. Here, a molecular population genetic data is presented for a widespread CFR plant, Leucadendron salignum, across 51 locations with 5-kb of chloroplast (cpDNA) and 6-kb of unlinked nuclear (nuDNA) DNA sequences in a dataset of 305 individuals. In the cpDNA dataset, significant genetic structure was found to vary on temporal and spatial scales, separating Western and Eastern Capes - the latter of which appears to be recently derived from the former - with the highest diversity in the heart of the CFR in a central region. A second study applied a statistical model using vegetation and soil composition and found fine-scale genetic divergence is better explained by this landscape resistance model than a geographic distance model. Finally, a third analysis contrasted cpDNA and nuDNA datasets, and revealed very little geographic structure in the latter, suggesting that seed and pollen dispersal can have different evolutionary genetic histories of gene flow on even small CFR scales. These three studies together caution that different genomic markers need to be considered when modeling the geographic and temporal origin of CFR groups. From a greater perspective, the results here are consistent with the hypothesis that landscape heterogeneity is one driving influence in limiting gene flow across the CFR that can lead to species diversity on fine-scales. Nonetheless, while this pattern may be true of the widespread L. salignum, the extension of this approach is now warranted for other CFR species with varying ranges and dispersal mechanisms to determine how universal these patterns of landscape genetic diversity are.
ContributorsTassone, Erica (Author) / Verrelli, Brian C (Thesis advisor) / Dowling, Thomas (Committee member) / Cartwright, Reed (Committee member) / Rosenberg, Michael S. (Committee member) / Wojciechowski, Martin (Committee member) / Arizona State University (Publisher)
Created2013
Description
The presence of a number of extinct radionuclides in the early Solar System (SS) is known from geochemical and isotopic studies of meteorites and their components. The half-lives of these isotopes are short relative to the age of the SS, such that they have now decayed to undetectable levels. They can be inferred to exist in the early SS from the presence of their daughter nuclides in meteoritic materials that formed while they were still extant. The extinct radionuclides are particularly useful as fine-scale chronometers for events in the early SS. They can also be used to help constrain the astrophysical setting of the formation of the SS because their short half-lives and unique formation environments yield information about the sources and timing of delivery of material to the protoplanetary disk. Some extinct radionuclides are considered evidence that the Sun interacted with a massive star (supernova) early in its history. The abundance of 60Fe in the early SS is particularly useful for constraining the astrophysical environment of the Sun's formation because, if present in sufficient abundance, its only likely source is injection from a nearby supernova. The initial SS abundance of 60Fe is poorly constrained at the present time, with estimates varying by 1-2 orders of magnitude. I have determined the 60Fe-60Ni isotope systematics of ancient, well-preserved meteorites using high-precision mass spectrometry to better constrain the initial SS abundance of 60Fe. I find identical estimates of the initial 60Fe abundance from both differentiated basaltic meteorites and from components of primitive chondrites formed in the Solar nebula, which suggest a lower 60Fe abundance than other recent estimates. With recent improved meteorite collection efforts there are more rare ungrouped meteorites being found that hold interesting clues to the origin and evolution of early SS objects. I use the 26Al-26Mg extinct radionuclide chronometer to constrain the ages of several recently recovered meteorites that sample previously unknown asteroid lithologies, including the only know felsic meteorite from an asteroid and two other ungrouped basaltic achondrites. These results help broaden our understanding of the timescales involved in igneous differentiation processes in the early SS.
ContributorsSpivak-Birndorf, Lev (Author) / Wadhwa, Meenakshi (Thesis advisor) / Hervig, Richard (Committee member) / Timmes, Francis (Committee member) / Williams, Lynda (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2012
Description
Harsh environments have conditions that make collecting scientific data difficult with existing commercial-off-the-shelf technology. Micro Electro Mechanical Systems (MEMS) technology is ideally suited for harsh environment characterization and operation due to the wide range of materials available and an incredible array of different sensing techniques while providing small device size, low power consumption, and robustness. There were two main objectives of the research conducted. The first objective was to design, fabricate, and test novel sensors that measure the amount of exposure to ionizing radiation for a wide range of applications including characterization of harsh environments. Two types of MEMS ionizing radiation dosimeters were developed. The first sensor was a passive radiation-sensitive capacitor-antenna design. The antenna's emitted frequency of peak-intensity changed as exposure time to radiation increased. The second sensor was a film bulk acoustic-wave resonator, whose resonant frequency decreased with increasing ionizing radiation exposure time. The second objective was to develop MEMS sensor systems that could be deployed to gather scientific data and to use that data to address the following research question: do temperature and/or conductivity predict the appearance of photosynthetic organisms in hot springs. To this end, temperature and electrical conductivity sensor arrays were designed and fabricated based on mature MEMS technology. Electronic circuits and the software interface to the electronics were developed for field data collection. The sensor arrays utilized in the hot springs yielded results that support the hypothesis that temperature plays a key role in determining where the photosynthetic organisms occur. Additionally, a cold-film fluidic flow sensor was developed, which is suitable for near-boiling temperature measurement. Future research should focus on (1) developing a MEMS pH sensor array with integrated temperature, conductivity, and flow sensors to provide multi-dimensional data for scientific study and (2) finding solutions to biofouling and self-calibration, which affects sensor performance over long-term deployment.
ContributorsOiler, Jonathon (Author) / Yu, Hongyu (Thesis advisor) / Anbar, Ariel (Committee member) / Hartnett, Hilairy (Committee member) / Scannapieco, Evan (Committee member) / Timmes, Francis (Committee member) / Arizona State University (Publisher)
Created2013
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
A phylogenetic revision of the broad-nosed weevil genera Minyomerus Horn, 1876, and Piscatopus Sleeper, 1960 (Entiminae: Tanymecini) is presented. These genera are distributed throughout western North America, from Canada to Mexico and Baja California, primarily in arid and desert habitats, and feed on shrubs such as creosote (Larrea tridentata (DC.) Coville: Zygophyllaceae) and several Asteraceae. Piscatopus was considered monotypic, comprised solely of P. griseus Sleeper, 1960, whereas Minyomerus formerly was comprised of seven species: M. innocuus Horn, 1876 (designated as the type species for Minyomerus in Pierce, 1913), M. caseyi (Sharp, 1891), M. conicollis Green, 1920, M. constrictus (Casey, 1888), M. languidus Horn, 1876, M. laticeps (Casey, 1888), M. microps (Say, 1831). This revision includes comprehensive redescriptions of the previously described species in these genera and descriptions of ten new species: M. imberbus sp. nov., M. caponei sp. nov., M. reburrus sp. nov., M. cracens sp. nov., M. trisetosus sp. nov., M. puticulatus sp. nov., M. bulbifrons sp. nov., M. politus sp. nov., M. gravivultus sp. nov., and M. rutellirostris sp. nov. A cladistic analysis using 46 morphological characters of 22 terminal taxa (5 outgroup, 17 ingroup) was carried out in WinClada and yielded a single most-parsimonious cladogram (length = 82, consistency index = 65, retention index = 82). The monophyly of Minyomerus is supported by the preferred cladogram. The results of the cladistic analysis place Piscatopus griseus within the genus Minyomerus as sister to M. rutellirostris. Therefore, Piscatopus is demoted to a junior synonym of Minyomerus and its sole member P. griseus, is moved to Minyomerus as M. griseus (Sleeper), new combination. Additionally, the species M. innocuus Horn, 1876 is demoted to a junior synonym of M. microps (Say, 1831), based on the principle of priority, and M. microps is elevated to the rank of type for the genus. The species M. languidus, M. microps, and M. trisetosus are putatively considered parthenogenetic, and lack male specimens over a broad range of sampling events. The diversity in exterior and genitalic morphology, range of host plants, overlapping species distributions, and geographic extent suggests an origin during the Miocene (~15 mya).
ContributorsJansen, Michael Andrew (Author) / Franz, Nico M (Thesis advisor) / Wojciechowski, Martin (Committee member) / Rosenberg, Michael (Committee member) / Arizona State University (Publisher)
Created2014
Description
As the detection of planets become commonplace around our neighboring stars, scientists can now begin exploring their possible properties and habitability. Using statistical analysis I determine a true range of elemental compositions amongst local stars and how this variation could affect possible planetary systems. Through calculating and analyzing the variation in elemental abundances of nearby stars, the actual range in stellar abundances can be determined using statistical methods. This research emphasizes the diversity of stellar elemental abundances and how that could affect the environment from which planets form. An intrinsic variation has been found to exist for almost all of the elements studied by most abundance-finding groups. Specifically, this research determines abundances for a set of 458 F, G, and K stars from spectroscopic planet hunting surveys for 27 elements, including: C, O, Na, Mg, Al, Si, S, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, La, Ce, Nd, Eu, and Hf. Abundances of the elements in many known exosolar planet host stars are calculated for the purpose investigating new ways to visualize how stellar abundances could affect planetary systems, planetary formation, and mineralogy. I explore the Mg/Si and C/O ratios as well as place these abundances on ternary diagrams with Fe. Lastly, I emphasize the unusual stellar abundance of τ Ceti. τ Ceti is measured to have 5 planets of Super-Earth masses orbiting in near habitable zone distances. Spectroscopic analysis finds that the Mg/Si ratio is extremely high (~2) for this star, which could lead to alterations in planetary properties. τ Ceti's low metallicity and oxygen abundance account for a change in the location of the traditional habitable zone, which helps clarify a new definition of habitable planets.
ContributorsPagano, Michael (Author) / Young, Patrick (Thesis advisor) / Shim, Sang-Heon (Committee member) / Patience, Jennifer (Committee member) / Desch, Steven (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2014
Description
The taxonomic and metabolic profile of the microbial community inhabiting a natural system is largely determined by the physical and geochemical properties of the system. However, the influences of parameters beyond temperature, pH and salinity have been poorly analyzed with few studies incorporating the comprehensive suite of physical and geochemical measurements required to fully investigate the complex interactions known to exist between biology and the environment. Further, the techniques used to classify the taxonomic and functional composition of a microbial community are fragmented and unwieldy, resulting in unnecessarily complex and often non-consilient results.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
ContributorsAlsop, Eric Bennie (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Farmer, Jack (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2014
Description
The atmosphere contains a substantial amount of water soluble organic material, yet despite years of efforts, little is known on the structure, composition and properties of this organic matter. Aqueous phase processing by fogs and clouds of the gas and particulate organic material is poorly understood despite the importance for air pollution and climate. On one hand, gas phase species can be processed by fog/cloud droplets to form lower volatility species, which upon droplet evaporation lead to new aerosol mass, while on the other hand larger nonvolatile material can be degraded by in cloud oxidation to smaller molecular weight compounds and eventually CO2.
In this work High Performance Size Exclusion Chromatography coupled with inline organic carbon detection (SEC-DOC), Diffusion-Ordered Nuclear Magnetic Resonance spectroscopy (DOSY-NMR) and Fluorescence Excitation-Emission Matrices (EEM) were used to characterize molecular weight distribution, functionality and optical properties of atmospheric organic matter. Fogs, aerosols and clouds were studied in a variety of environments including Central Valley of California (Fresno, Davis), Pennsylvania (Selinsgrove), British Columbia (Whistler) and three locations in Norway. The molecular weight distributions using SEC-DOC showed smaller molecular sizes for atmospheric organic matter compared to surface waters and a smaller material in fogs and clouds compared to aerosol particles, which is consistent with a substantial fraction of small volatile gases that partition into the aqueous phase. Both, cloud and aerosol samples presented a significant fraction (up to 21% of DOC) of biogenic nanoscale material. The results obtained by SEC-DOC were consistent with DOSY-NMR observations.
Cloud processing of organic matter has also been investigated by combining field observations (sample time series) with laboratory experiments under controlled conditions. Observations revealed no significant effect of aqueous phase chemistry on molecular weight distributions overall although during cloud events, substantial differences were apparent between organic material activated into clouds compared to interstitial material. Optical properties on the other hand showed significant changes including photobleaching and an increased humidification of atmospheric material by photochemical aging. Overall any changes to atmospheric organic matter during cloud processing were small in terms of bulk carbon properties, consistent with recent reports suggesting fogs and clouds are too dilute to substantially impact composition.
In this work High Performance Size Exclusion Chromatography coupled with inline organic carbon detection (SEC-DOC), Diffusion-Ordered Nuclear Magnetic Resonance spectroscopy (DOSY-NMR) and Fluorescence Excitation-Emission Matrices (EEM) were used to characterize molecular weight distribution, functionality and optical properties of atmospheric organic matter. Fogs, aerosols and clouds were studied in a variety of environments including Central Valley of California (Fresno, Davis), Pennsylvania (Selinsgrove), British Columbia (Whistler) and three locations in Norway. The molecular weight distributions using SEC-DOC showed smaller molecular sizes for atmospheric organic matter compared to surface waters and a smaller material in fogs and clouds compared to aerosol particles, which is consistent with a substantial fraction of small volatile gases that partition into the aqueous phase. Both, cloud and aerosol samples presented a significant fraction (up to 21% of DOC) of biogenic nanoscale material. The results obtained by SEC-DOC were consistent with DOSY-NMR observations.
Cloud processing of organic matter has also been investigated by combining field observations (sample time series) with laboratory experiments under controlled conditions. Observations revealed no significant effect of aqueous phase chemistry on molecular weight distributions overall although during cloud events, substantial differences were apparent between organic material activated into clouds compared to interstitial material. Optical properties on the other hand showed significant changes including photobleaching and an increased humidification of atmospheric material by photochemical aging. Overall any changes to atmospheric organic matter during cloud processing were small in terms of bulk carbon properties, consistent with recent reports suggesting fogs and clouds are too dilute to substantially impact composition.
ContributorsWang, Youliang (Author) / Herckes, Pierre (Thesis advisor) / Fraser, Matthew (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2014