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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
A new analytical method is proposed for measuring the deuterium to hydrogen ratio (D/H) of non-stoichiometric water in hydrous minerals via pyrolysis facilitated gas-chromatography - isotope ratio mass spectrometry (GC-IRMS). Previously published analytical methods have reported a poorly understood nonlinear dependence of D/H on sample size, for which any accurate correction is difficult. This sample size effect been variously attributed to kinetic isotope fractionation within the mass spectrometer and peripheral instruments, ion source linearity issues, and an unstable H_3^+-factor or incorrect H_3^+-factor calculations. The cause of the sample size effect is here identified by examinations of individual chromatograms as well as bulk data from chromatographic peaks. It is here determined that it is primarily an artifact of the calculations employed by the manufacturer's computer program, used to both monitor the functions of the mass spectrometer and to collect data. Ancillary causes of the sample size effect include a combination of persistent background interferences and chromatographic separation of the isotopologues of molecular hydrogen. Previously published methods are evaluated in light of these findings. A new method of H_3^+-factor and D/H calculation is proposed which makes portions of the Isodat software as well as other published calculation methods unnecessary. Using this new method, D/H is measured in non-stoichiometric water in chert from the Cretaceous Edwards Group, Texas, as well as the Precambrian Kromberg Formation, South Africa, to assess hydrological conditions as well as to estimate the maximum average surface temperature during precipitation of the chert. Data from Cretaceous chert are consistent with previously published data and interpretations, based upon conventional analyses of large samples. Data from Precambrian chert are consistent with maximum average surface temperatures approaching 65°C during the Archean, instead of the much lower temperatures derived from erroneous methods of sample preparation and analysis. D/H is likewise measured in non-stoichiometric water in silicified basalt from the Precambrian Hooggenoeg Complex, South Africa. Data are shown to be consistent with D/H of the Archean ocean similar to present day values.
ContributorsSheehan, Michael Robert (Author) / Knauth, Leroy P (Thesis advisor) / Anbar, Ariel (Committee member) / Farmer, Jack (Committee member) / Arizona State University (Publisher)
Created2011
Description
The spectacular geological panoramas of Grand Canyon National Park (GCNP) motivate the curiosity of visitors about geology. However, there is little research on how well these visitors understand the basic geologic principles on display in the Canyon walls. The new Trail of Time (ToT) interpretative exhibit along the South Rim uses Grand Canyon vistas to teach these principles. Now being visited by thousands daily, the ToT is a uniquely valuable setting for research on informal learning of geologic time and other basic geologic concepts. At the ToT, visitors are not only asked to comprehend a linear timeline, but to associate it with the strata exposed in the walls of the Canyon. The research addressed two primary questions: (1) how do visitors of the National Park use elements of the geologic landscape of the Grand Canyon to explain fundamental principles of relative geologic time? and (2) how do visitors reconcile the relationship between the horizontal ToT timeline and the vertical encoding of time in the strata exposed in the Canyon walls? Semi-structured interviews tracked participants' understanding of the ToT exhibit and of basic principles of geologic time. Administering the verbal analysis method of Chi (1997) to the interview transcripts, the researcher identified emergent themes related to how the respondents utilized the landscape to answer interview questions. Results indicate that a majority of respondents are able to understand principles of relative geologic time by utilizing both the observed and inferred landscape of Grand Canyon. Results also show that by applying the same integrated approach to the landscape, a majority of respondents are able to reconcile stratigraphic time with the horizontal ToT timeline. To gain deeper insight into the cognitive skills activated to correctly understand geologic principles the researcher used Dodick and Orion's application of Montangero's (1996) diachronic thinking model to code responses into three schemes: (1) transformation, (2) temporal organization, and (3) interstage linkage. Results show that correct responses required activation of the temporal organization scheme or the more advanced interstage linkage scheme. Appropriate application of these results can help inform the development of future outdoor interpretive geoscience exhibits.
ContributorsFrus, Rebecca (Author) / Semken, Steven (Thesis advisor) / Baker, Dale (Committee member) / Farmer, Jack (Committee member) / Arizona State University (Publisher)
Created2011
Description
Finding life beyond Earth could change our understanding of life and habitability. The best place to look for life beyond Earth is Jupiter's moon, Europa. It has been estimated Europa may have a liquid, salt-water subsurface with 2 to 3 times the volume of all Earth's oceans. Knowing that all life requires water, it is in our best interest to explore Europa. This thesis explored the plausibility of life on Europa in four of its environments: on the surface, under the ice shell, in the liquid subsurface, and at the bottom of the liquid subsurface. Each of these environments were defined from science literature and compared to known Earth analogs. Europa's surface is not likely to support life, as there is not liquid water present. There is also extremely high radiation bombardment and extremely low surface temperatures that are estimated to be well out of the range for supporting life. It is more plausible that life could be under Europa's ice shell than on the surface. Under the surface, radiation exposure dramatically reduces. Researchers have found organisms on Earth that can live in similar environments as Europa's ice as well. These organisms require some interaction with liquid water though. Uncertainties about Europa's ice shell thickness and radiation load per depth it experiences, as well as there being limited research on organisms in ice environments, hinder us from definitively assessing the plausibility of life under the surface. The best environment on Europa to look for life on Europa is the subsurface. There remain a lot of uncertainties about the subsurface, however, that make it difficult to assess the plausibility of finding life. These uncertainties include its depth, water activity, salinity, temperature, pressure, and structure. This subsurface may be suitable for life, but until we can further understand the environment of the subsurface, we cannot make definite conclusions. As for assessing the plausibility of life at the bottom of Europa's subsurface, there is not much we know about this environment either. It has been suggested there may be hydrothermal vents, but no evidence has either supported or rejected this idea. Without a clear understanding of the environment at the bottom of the subsurface, the plausibility of life here cannot be definitively answered. It is apparent we need to further study Europa. In particular, we need to focus on understanding the subsurface. When the subsurface is better defined, we can better assess the plausibility of life being present. Fortunately, both NASA and the ESA are currently planning missions to Europa that are scheduled to launch in the 2020s.
ContributorsHoward, Cheyenne Whiffen (Author) / Farmer, Jack (Thesis director) / Shock, Everett (Committee member) / School of Earth and Space Exploration (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Understanding the structural evolution of planetary surfaces provides key insights to their physical properties and processes. On the Moon, large-scale tectonism was thought to have ended over a billion years ago. However, new Lunar Reconnaissance Orbiter Camera (LROC) Narrow Angle Camera (NAC) high resolution images show the Moon’s surface in unprecedented detail and show many previously unidentified tectonic landforms, forcing a re-assessment of our views of lunar tectonism. I mapped lobate scarps, wrinkle ridges, and graben across Mare Frigoris – selected as a type area due to its excellent imaging conditions, abundance of tectonic landforms, and range of inferred structural controls. The distribution, morphology, and crosscutting relationships of these newly identified populations of tectonic landforms imply a more complex and longer-lasting history of deformation that continues to today. I also performed additional numerical modeling of lobate scarp structures that indicates the upper kilometer of the lunar surface has experienced 3.5-18.6 MPa of differential stress in the recent past, likely due to global compression from radial thermal contraction.
Central pit craters on Mars are another instance of intriguing structures that probe subsurface physical properties. These kilometer-scale pits are nested in the centers of many impact craters on Mars as well as on icy satellites. They are inferred to form in the presence of a water-ice rich substrate; however, the process(es) responsible for their formation is still debated. Previous models invoke origins by either explosive excavation of potentially water-bearing crustal material, or by subsurface drainage of meltwater and/or collapse. I assessed radial trends in grain size around central pits using thermal inertias calculated from Thermal Emission Imaging System (THEMIS) thermal infrared images. Average grain size decreases with radial distance from pit rims – consistent with pit-derived ejecta but not expected for collapse models. I present a melt-contact model that might enable a delayed explosion, in which a central uplift brings ice-bearing substrate into contact with impact melt to generate steam explosions and excavate central pits during the impact modification stage.
Central pit craters on Mars are another instance of intriguing structures that probe subsurface physical properties. These kilometer-scale pits are nested in the centers of many impact craters on Mars as well as on icy satellites. They are inferred to form in the presence of a water-ice rich substrate; however, the process(es) responsible for their formation is still debated. Previous models invoke origins by either explosive excavation of potentially water-bearing crustal material, or by subsurface drainage of meltwater and/or collapse. I assessed radial trends in grain size around central pits using thermal inertias calculated from Thermal Emission Imaging System (THEMIS) thermal infrared images. Average grain size decreases with radial distance from pit rims – consistent with pit-derived ejecta but not expected for collapse models. I present a melt-contact model that might enable a delayed explosion, in which a central uplift brings ice-bearing substrate into contact with impact melt to generate steam explosions and excavate central pits during the impact modification stage.
ContributorsWilliams, Nathan Robert (Author) / Bell, James (Thesis advisor) / Robinson, Mark (Committee member) / Christenen, Philip (Committee member) / Farmer, Jack (Committee member) / Shirzaei, Manoochehr (Committee member) / Arizona State University (Publisher)
Created2016
Description
The search for life on Mars is a major NASA priority. A Mars Sample Return
(MSR) mission, Mars 2020, will be NASA's next step towards this goal, carrying an instrument suite that can identify samples containing potential biosignatures. Those samples will be later returned to Earth for detailed analysis. This dissertation is intended to inform strategies for fossil biosignature detection in Mars analog samples targeted for their high biosignature preservation potential (BPP) using in situ rover-based instruments. In chapter 2, I assessed the diagenesis and BPP of one relevant analog habitable Martian environment: a playa evaporite sequence within the Verde Formation, Arizona. Coupling outcrop-scale observations with laboratory analyses, results revealed four diagenetic pathways, each with distinct impacts on BPP. When MSR occurs, the sample mass returned will be restricted, highlighting the importance of developing instruments that can select the most promising samples for MSR. Raman spectroscopy is one favored technique for this purpose. Three Raman instruments will be sent onboard two upcoming Mars rover missions for the first time. In chapters 3-4, I investigated the challenges of Raman to identify samples for MSR. I examined two Raman systems, each optimized in a different way to mitigate a major problem commonly suffered by Raman instruments: background fluorescence. In Chapter 3, I focused on visible laser excitation wavelength (532 nm) gated (or time-resolved Raman, TRR) spectroscopy. Results showed occasional improvement over conventional Raman for mitigating fluorescence in samples. It was hypothesized that results were wavelength-dependent and that greater fluorescence reduction was possible with UV laser excitation. In Chapter 4, I tested this hypothesis with a time-resolved UV (266 nm) gated Raman and UV fluorescence spectroscopy capability. I acquired Raman and fluorescence data sets on samples and showed that the UV system enabled identifications of minerals and biosignatures in samples with high confidence. The results obtained in this dissertation may inform approaches for MSR by: (1) refining models for biosignature preservation in habitable Mars environments; (2) improving sample selection and caching strategies, which may increase the success of Earth-based biogenicity studies; and (3) informing the development of Raman instruments for upcoming rover-based missions.
(MSR) mission, Mars 2020, will be NASA's next step towards this goal, carrying an instrument suite that can identify samples containing potential biosignatures. Those samples will be later returned to Earth for detailed analysis. This dissertation is intended to inform strategies for fossil biosignature detection in Mars analog samples targeted for their high biosignature preservation potential (BPP) using in situ rover-based instruments. In chapter 2, I assessed the diagenesis and BPP of one relevant analog habitable Martian environment: a playa evaporite sequence within the Verde Formation, Arizona. Coupling outcrop-scale observations with laboratory analyses, results revealed four diagenetic pathways, each with distinct impacts on BPP. When MSR occurs, the sample mass returned will be restricted, highlighting the importance of developing instruments that can select the most promising samples for MSR. Raman spectroscopy is one favored technique for this purpose. Three Raman instruments will be sent onboard two upcoming Mars rover missions for the first time. In chapters 3-4, I investigated the challenges of Raman to identify samples for MSR. I examined two Raman systems, each optimized in a different way to mitigate a major problem commonly suffered by Raman instruments: background fluorescence. In Chapter 3, I focused on visible laser excitation wavelength (532 nm) gated (or time-resolved Raman, TRR) spectroscopy. Results showed occasional improvement over conventional Raman for mitigating fluorescence in samples. It was hypothesized that results were wavelength-dependent and that greater fluorescence reduction was possible with UV laser excitation. In Chapter 4, I tested this hypothesis with a time-resolved UV (266 nm) gated Raman and UV fluorescence spectroscopy capability. I acquired Raman and fluorescence data sets on samples and showed that the UV system enabled identifications of minerals and biosignatures in samples with high confidence. The results obtained in this dissertation may inform approaches for MSR by: (1) refining models for biosignature preservation in habitable Mars environments; (2) improving sample selection and caching strategies, which may increase the success of Earth-based biogenicity studies; and (3) informing the development of Raman instruments for upcoming rover-based missions.
ContributorsShkolyar, Svetlana (Author) / Farmer, Jack (Thesis advisor) / Semken, Steven (Committee member) / Sharp, Thomas (Committee member) / Shim, Sang-Heon Dan (Committee member) / Youngbull, Aaron Cody (Committee member) / Arizona State University (Publisher)
Created2016
Description
The Juglandaceae (walnuts, hickories, pecans) has one of the best-documented fossil records in the Northern Hemisphere. The oldest modern genus, Cyclocarya, today restricted to China, first appears in the late Paleocene (57 ma) of North Dakota, USA. Unlike walnuts and pecans that produce edible fruits dispersed by mammals, Cyclocarya fruits are small nutlets surrounded by a prominent circular wing, and are thought to be wind- or water-dispersed. The current study provides the first evidence that fossil fruits were different from modern forms in the number and organization of their attachment to reproductive branches, and in their anatomical structure. Unlike the modern genus that bears separate pistillate and staminate flowers the fossil fruits had attached pollen-bearing structures. Unisexual pollen catkins are also present, suggesting the fossil Cyclocarya may have differed from its modern relative in this feature. Like several other plants from the late Paleocene Almont/Beicegel Creek floras, Cyclocarya shows a mosaic combination of characters not seen in their modern counterparts. Fossils were collected from the field, and examined for specimens exposed on the weathered rock surface. Specimens from Almont were photographed with reflected light, while those from Beicegel Creek cut into slabs and prepared by etching the rock matrix in 49% hydrofluoric and re-embedding the exposed plant material in cellulose acetate and acetone to make "peels". Selected specimens are cut out, mounted on microscope slides, and studied with light microscopy. These fossil fruits were studied because they are the earliest fossil evidence of Cyclocarya. They are exceptionally preserved and thus provide critical structural evidence for changes in that occurred during the evolution of plants within this lineage. Because Cyclocarya fruits are winged, they might be assumed to be wind-dispersed. Their radial symmetry does not have the aerodynamic qualities typical of wind-dispersed fruits, and may have been dispersed by water.
ContributorsTaylor, Malcom DeWitt (Author) / Pigg, Kathleen B (Thesis advisor) / Wojciechowski, Martin F (Committee member) / Devore, Melanie L (Committee member) / Farmer, Jack (Committee member) / Gill, Anthony (Committee member) / Arizona State University (Publisher)
Created2010
Description
This study was conducted in order to determine whether the lagomorphs of 111 Ranch- Aztlanolagus agilis, Hypolagus arizonensis, and Sylvilagus cunicularius- could be distinguished based on femora. This is because while there is a large quantity of disarticulated lagomorph postcranial fossils from 111 Ranch, the chief diagnostic traits of A. agilis and H. arizonensis are the enamel patterns on their third premolars, leaving a large swath of specimens unidentifiable by diagnostic traits alone. Specimens from the Arizona Museum of Natural History were measured and compared to specimens known to be from these genera. Additionally, morphological traits in mandibles were used to identify mandible specimens, which in turn were used to identify fossils with the same specimen label. Statistical tests such as t-tests and principal components analyses were used to examine the distributions of sizes and locate clusters of datapoints likely corresponding to each genus. Some of these could be linked to a genus based on one particular specimen, P15156, which had been identified as Hypolagus based on its mandible morphology and size. The majority of the Museum'a specimens were thus associated with one of the three species, save for those which were too damaged and intermediate in size to confidently categorize.
ContributorsTkacik, Stephanie Marie (Author) / Farmer, Jack (Thesis director) / Reed, Kaye (Committee member) / McCord, Robert (Committee member) / School of Earth and Space Exploration (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
The Mars Science Laboratory landed in Gale crater on Mars in August 2012, and the Curiosity rover then began field studies on its drive toward Mount Sharp, a central peak made of ancient sediments. CheMin is one of ten instruments on or inside the rover, all designed to provide detailed information on the rocks, soils and atmosphere in this region. CheMin is a miniaturized X-ray diffraction/X-ray fluorescence (XRD/XRF) instrument that uses transmission geometry with an energy-discriminating CCD detector. CheMin uses onboard standards for XRD and XRF calibration, and beryl:quartz mixtures constitute the primary XRD standards. Four samples have been analysed by CheMin, namely a soil sample, two samples drilled from mudstones and a sample drilled from a sandstone. Rietveld and full-pattern analysis of the XRD data reveal a complex mineralogy, with contributions from parent igneous rocks, amorphous components and several minerals relating to aqueous alteration. In particular, the mudstone samples all contain one or more phyllosilicates consistent with alteration in liquid water. In addition to quantitative mineralogy, Rietveld refinements also provide unit-cell parameters for the major phases, which can be used to infer the chemical compositions of individual minerals and, by difference, the composition of the amorphous component.
ContributorsBish, David (Author) / Blake, David (Author) / Vaniman, David (Author) / Sarrazin, Philippe (Author) / Bristow, Thomas (Author) / Achilles, Cherie (Author) / Dera, Przemyslaw (Author) / Chipera, Steve (Author) / Crisp, Joy (Author) / Downs, R. T. (Author) / Farmer, Jack (Author) / Gailhanou, Marc (Author) / Ming, Doug (Author) / Morookian, John Michael (Author) / Morris, Richard (Author) / Morrison, Shaunna (Author) / Rampe, Elizabeth (Author) / Treiman, Allan (Author) / Yen, Albert (Author) / College of Liberal Arts and Sciences (Contributor)
Created2014-10-21
Description
The Mars rover Spirit encountered outcrops and regolith composed of opaline silica (amorphous SiO2·nH2O) in an ancient volcanic hydrothermal setting in Gusev crater. An origin via either fumarole-related acid-sulfate leaching or precipitation from hot spring fluids was suggested previously. However, the potential significance of the characteristic nodular and mm-scale digitate opaline silica structures was not recognized. Here we report remarkably similar features within active hot spring/geyser discharge channels at El Tatio in northern Chile, where halite-encrusted silica yields infrared spectra that are the best match yet to spectra from Spirit. Furthermore, we show that the nodular and digitate silica structures at El Tatio that most closely resemble those on Mars include complex sedimentary structures produced by a combination of biotic and abiotic processes. Although fully abiotic processes are not ruled out for the Martian silica structures, they satisfy an a priori definition of potential biosignatures.
ContributorsRuff, Steven (Author) / Farmer, Jack (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-11-17