Matching Items (112)
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Description
The ability to find evidence of life on early Earth and other planets is constrained by the current understanding of biosignatures and our ability to differentiate fossils from abiotic mimics. When organisms transition from the living realm to the fossil record, their morphological and chemical characteristics are modified, usually resulting in the loss of information. These modifications can happen during early and late diagenesis and differ depending on local geochemical properties. These post-depositional modifications need to be understood to better interpret the fossil record. Siliceous hot spring deposits (sinters) are of particular interest for biosignature research as they are early Earth analog environments and targets for investigating the presence of fossil life on Mars. As silica-supersaturated fluids flow from the vent to the distal apron, they precipitate non-crystalline opal-A that fossilizes microbial communities at a range in scales (μm-cm). Therefore, many studies have documented the ties between the active microbial communities and the morphological and chemical biosignatures in hot springs. However, far less attention has been placed on understanding preservation in systems with complex mineralogy or how post-depositional alteration affects the retention of biosignatures. Without this context, it can be challenging to recognize biosignatures in ancient rocks. This dissertation research aims to refine our current understanding of biosignature preservation and retention in sinters. Biosignatures of interest include organic matter, microfossils, and biofabrics. The complex nature of hot springs requires a comprehensive understanding of biosignature preservation that is representative of variable chemistries and post-depositional alterations. For this reason, this dissertation research chapters are field site-based. Chapter 2 investigates biosignature preservation in an unusual spring with mixed opal-A-calcite mineralogy at Lýsuhóll, Iceland. Chapter 3 tracks how silica diagenesis modifies microfossil morphology and associated organic matter at Puchuldiza, Chile. Chapter 4 studies the effects of acid fumarolic overprinting on biosignatures in Gunnuhver, Iceland. To accomplish this, traditional geologic methods (mapping, petrography, X-ray diffraction, bulk elemental analyses) were combined with high-spatial-resolution elemental mapping to better understand diagenetic effects in these systems. Preservation models were developed to predict the types and styles of biosignatures that can be present depending on the depositional and geochemical context. Recommendations are also made for the types of deposits that are most likely to preserve biosignatures.
ContributorsJuarez Rivera, Marisol (Author) / Farmer, Jack D (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Shock, Everett (Committee member) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems. The ecological consequences of their activity, unlike those of other populational loss factors like viral infection or grazing by protists, are yet to be assessed. During large-scale cultivation of biological soil crusts intended for arid soil rehabilitation, episodes of catastrophic failure were observed in cyanobacterial growth that could be ascribed to the action of an unknown predatory bacterium using bioassays. This predatory bacterium was also present in natural biocrust communities, where it formed clearings (plaques) up to 9 cm in diameter that were visible to the naked eye. Enrichment cultivation and purification by cell-sorting were used to obtain co-cultures of the predator with its cyanobacterial prey, as well as to identify and characterize it genomically, physiologically and ultrastructurally. A Bacteroidetes bacterium, unrelated to any known isolate at the family level, it is endobiotic, non-motile, obligately predatory, displays a complex life cycle and very unusual ultrastructure. Extracellular propagules are small (0.8-1.0 µm) Gram-negative cocci with internal two-membrane-bound compartmentalization. These gain entry to the prey likely using a suite of hydrolytic enzymes, localizing to the cyanobacterial cytoplasm, where growth begins into non-compartmentalized pseudofilaments that undergo secretion of vesicles and simultaneous multiple division to yield new propagules. I formally describe it as Candidatus Cyanoraptor togatus, hereafter Cyanoraptor. Its prey range is restricted to biocrust-forming, filamentous, non-heterocystous, gliding, bundle-making cyanobacteria. Molecular meta-analyses showed its worldwide distribution in biocrusts. Biogeochemical analyses of Cyanoraptor plaques revealed that it causes a complete loss of primary productivity, and significant decreases in other biocrusts properties such as water-retention and dust-trapping capacity. Extensive field surveys in the US Southwest revealed its ubiquity and its dispersal-limited, aggregated spatial distribution and incidence. Overall, its activity reduces biocrust productivity by 10% at the ecosystem scale. My research points to predatory bacteria as a significant, but overlooked, ecological force in shaping soil microbiomes.
ContributorsBethany Rakes, Julie Ann (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Gile, Gillian (Committee member) / Cao, Huansheng (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2022
Description
High throughput transcriptome data analysis like Single-cell Ribonucleic Acid sequencing (scRNA-seq) and Circular Ribonucleic Acid (circRNA) data have made significant breakthroughs, especially in cancer genomics. Analysis of transcriptome time series data is core in identifying time point(s) where drastic changes in gene transcription are associated with homeostatic to non-homeostatic cellular transition (tipping points). In Chapter 2 of this dissertation, I present a novel cell-type specific and co-expression-based tipping point detection method to identify target gene (TG) versus transcription factor (TF) pairs whose differential co-expression across time points drive biological changes in different cell types and the time point when these changes are observed. This method was applied to scRNA-seq data sets from a SARS-CoV-2 study (18 time points), a human cerebellum development study (9 time points), and a lung injury study (18 time points). Similarly, leveraging transcriptome data across treatment time points, I developed methodologies to identify treatment-induced and cell-type specific differentially co-expressed pairs (DCEPs). In part one of Chapter 3, I presented a pipeline that used a series of statistical tests to detect DCEPs. This method was applied to scRNA-seq data of patients with non-small cell lung cancer (NSCLC) sequenced across cancer treatment times. However, this pipeline does not account for correlations among multiple single cells from the same sample and correlations among multiple samples from the same patient. In Part 2 of Chapter 3, I presented a solution to this problem using a mixed-effect model. In Chapter 4, I present a summary of my work that focused on the cross-species analysis of circRNA transcriptome time series data. I compared circRNA profiles in neonatal pig and mouse hearts, identified orthologous circRNAs, and discussed regulation mechanisms of cardiomyocyte proliferation and myocardial regeneration conserved between mouse and pig at different time points.
ContributorsNyarige, Verah Mocheche (Author) / Liu, Li (Thesis advisor) / Wang, Junwen (Thesis advisor) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2022
Description
ABSTRACT Over the past several decades, the dilemma of free-roaming horses in the U.S. has proven to be one of the most divisive issues in management of public lands. According to federal land management agencies, without population regulation, horses can increase at the rate of 15-20% a year on arid rangelands with inadequate numbers of natural, large predators. Horses compete for valuable forage and water resources alongside cattle and native wildlife in delicate riparian areas highly susceptible to the negative ecological effects of soil compaction and overgrazing. Most U.S. management policies, therefore, call for increased removal of free-roaming horses as they are categorized as “un-authorized livestock” or "non-native" species. Wild horse advocates, however, continue to petition for improvement in animal welfare and expansion of the horses’ territory. With heightened social conflict spurred by animal rights and ecological concerns, not to mention the often-stark differences over what really “belongs” on the landscape, the success of appropriate management strategies hinges on managing agencies’ preparedness and ability to respond in a timely and inclusive manner. A critical element of the management context is the public’s views toward the wild horse and the science used to manage them. Synthesizing the vast literature in the history and philosophy of wildlife management in the American West, and utilizing an ethnographic and case study approach, my research examines the range of stakeholder concerns and analyzes the factors that have led to the disconnect between public values of wild horses and public policy for the management of the federally protected free-roaming horses in Arizona’s Apache-Sitgreaves National Forests.
ContributorsMurphree, Julie Joan (Author) / Minteer, Ben A. (Thesis advisor) / Schoon, Michael (Thesis advisor) / Bradshaw, Karen (Committee member) / Chew, Matthew (Committee member) / Arizona State University (Publisher)
Created2022
Description
Beta-Amyloid(Aβ) plaques and tau protein tangles in the brain are now widely recognized as the defining hallmarks of Alzheimer’s disease (AD), followed by structural atrophy detectable on brain magnetic resonance imaging (MRI) scans. However, current methods to detect Aβ/tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (positron emission tomography (PET)). And one of the particular neurodegenerative regions is the hippocampus to which the influence of Aβ/tau on has been one of the research projects focuses in the AD pathophysiological progress.
In this dissertation, I proposed three novel machine learning and statistical models to examine subtle aspects of the hippocampal morphometry from MRI that are associated with Aβ /tau burden in the brain, measured using PET images. The first model is a novel unsupervised feature reduction model to generate a low-dimensional representation of hippocampal morphometry for each individual subject, which has superior performance in predicting Aβ/tau burden in the brain. The second one is an efficient federated group lasso model to identify the hippocampal subregions where atrophy is strongly associated with abnormal Aβ/Tau. The last one is a federated model for imaging genetics, which can identify genetic and transcriptomic influences on hippocampal morphometry. Finally, I stated the results of these three models that have been published or submitted to peer-reviewed conferences and journals.
ContributorsWu, Jianfeng (Author) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Liang, Jianming (Committee member) / Wang, Junwen (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2022
Description
Communications around sustainability have been found to be incongruent with eliciting the transformative change required to address global climate change and its' repercussions. Recent research has been exploring storytelling in sustainability, specifically with an emphasis on reflexive and emancipatory methods. These methods encourage embracing and contextualizing complexity and intend to target entire cognitive hierarchies. This study explores the possibility of using emancipatory and reflexive storytelling as a tool to change attitudes pertaining to the Valley Metro Light Rail, an example of a complex sustainability mitigation effort. I explore this in four steps: 1) Conducted a pre-survey to gauge preexisting attitudes and predispositions; 2) Provided a narrative that uses storytelling methodologies of reflexivity and emancipation through a story about the light rail; 3) Conducted a post-survey to gauge attitude shift resulting from the narrative intervention; 4) Facilitated a focus group discussion to examine impact qualitatively. These steps intended to provide an answer to the question: How does emancipatory and reflexive storytelling impact affective, cognitive and conative attitudes regarding local alternative transportation? By using tripartite attitude model, qualitative and quantitative analysis this paper determines that reflexive and emancipatory storytelling impacts attitudinal structures. The impact is marginal in the survey response, though the shift indicated a narrowing of participant responses towards one another, indicative of participants subscribing to emancipation and reflexivity of their held attitudes. From the group discussion, it was evident from qualitative responses that participants engaged in emancipating themselves from their held attitudes and reflected upon them. In doing so they engaged in collaboration to make suggestions and suggest actions to help those with experiences that differed from their own. Though this research doesn’t provide conclusive evidence, it opens the door for future research to assess these methodologies as a tool to elicit shared values, beliefs and norms, which are necessary for collective action leading to transformative change in response to global climate change.
ContributorsSwanson, Jake Ryan (Author) / Roseland, Mark (Thesis advisor) / Larson, Kelli (Committee member) / Calhoun, Craig (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2023
Description
Understanding the dynamic interactions between humans and wildlife is essential to establishing sustainable wildlife-based ecotourism (WBE). Animal behavior exists within a complex feedback loop that affects overall ecosystem function, tourist satisfaction, and socioeconomics of local communities. However, the specific value that animal behavior plays in provisioning ecosystem services has not been thoroughly evaluated. People enjoy activities that facilitate intimate contact with animals, and there are many perceived benefits associated with these experiences, such as encouraging pro-environmental attitudes that can lead to greater motivation for conservation. There is extensive research on the effects that unregulated tourism activity can have on wildlife behavior, which include implications for population health and survival. Prior to COVID-19, WBE was developing rapidly on a global scale, and the pause in activity caused by the pandemic gave natural systems the chance to recover from environmental damage from over-tourism and provided insights into how tourism could be less impactful in the future. Until now it has been undetermined how changes in animal behavior can alter the relationships and socioeconomics of this multidimensional system. This dissertation provides a thorough exploration of the behavioral, ecological, and economic parameters required to model biosocial interactions and feedbacks within the whale watching system in Las Perlas Archipelago, Panama. Through observational data collected in the field, this project assessed how unmanaged whale watching activity is affecting the behavior of Humpback whales in the area as well as the socioeconomic and conservation contributions of the industry. Additionally, it is necessary to consider what a sustainable form of wildlife tourism might be, and whether the incorporation of technology will help enhance visitor experience while reducing negative impacts on wildlife. To better ascertain whether this concept of this integration would be favorably viewed, a sample of individuals was surveyed about their experiences about using technology to enhance their interactions with nature. This research highlights the need for more deliberate identification and incorporation of the perceptions of all stakeholders (wildlife included) to develop a less-impactful WBE industry that provides people with opportunities to establish meaningful relationships with nature that motivate them to help meet the conservation challenges of today.
ContributorsSurrey, Katie (Author) / Gerber, Leah (Thesis advisor) / Guzman, Hector (Committee member) / Minteer, Ben (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2023
Description
University-level sustainability education in Western academia attempts to focus on eliminating future harm to people and the planet. However, Western academia as an institution upholds systems of oppression and reproduces settler colonialism. This reproduction is antithetical to sustainability goals as it continues patterns of Indigenous erasure and extractive relationships to the Land that perpetuate violence towards people and the planet. Sustainability programs, however, offer several frameworks, including resilience, that facilitate critical interrogations of social-ecological systems. In this thesis, I apply the notion of resilience to the perpetuation of settler colonialism within university-level sustainability education. Specifically, I ask: How is settler colonialism resilient in university-level sustainability education? How are, or could, sustainability programs in Western academic settings address settler colonialism? Through a series of conversational interviews with faculty and leadership from Arizona State University School of Sustainability, I analyzed how university-level sustainability education is both challenging and shaped by settler colonialism. These interviews focused on faculty perspectives on the topic and related issues; the interviews were analyzed using thematic coding in NVivo software. The results of this project highlight that many faculty members are already concerned with and focused on challenging settler colonialism, but that settler colonialism remains resilient in this system due to feedback loops at the personal level and reinforcing mechanisms at the institutional level. This research analyzes these feedback loops and reinforcing mechanisms, among others, and supports the call for anti-colonial and decolonial reconstruction of curriculum, as well as a focus on relationship building, shifting of mindset, and school-wide education on topics of white supremacy, settler colonialism, and systems of oppression in general.
ContributorsBills, Haven (Author) / Klinsky, Sonja (Thesis advisor) / Goebel, Janna (Committee member) / Schoon, Michael (Committee member) / Arizona State University (Publisher)
Created2022
Description
There is an estimated five trillion pieces of plastic in the global ocean, with 4.8 to 12.7 million metric tons entering the ocean annually. Much of the plastic in the ocean is in the form of microplastics, or plastic particles <5mm in size. Microplastics enter the marine environment as primary or secondary microplastics; primary microplastics are pre-manufactured micro-sized particles, such as microbeads used in cosmetics, while secondary microplastics form from the degradation of larger plastic objects, such water bottles. Once in the ocean, plastics are readily colonized by a consortium of prokaryotic and eukaryotic organisms, which form dense biofilms on the plastic; this biofilm is termed the “plastisphere”. Despite growing concerns about the ecological impact of microplastics and their respective plastispheres on the marine environment, there is little consensus about the factors that shape the plastisphere on environmentally relevant secondary microplastics. The goal of my dissertation is to comprehensively analyze the role of plastic polymer type, incubation time, and geographic location on shaping plastisphere communities attached to secondary microplastics. I investigated the plastisphere of six chemically distinct plastic polymer types obtained from common household consumer products that were incubated in the coastal Caribbean (Bocas del Toro, Panama) and coastal Pacific (San Diego, CA) oceans. Genotyping using 16S and 18S rRNA gene amplification and next-generation Illumina sequencing was employed to identify bacterial and eukaryotic communities on the polymer surfaces. Statistical analyses show that there were no polymer-specific assemblages for prokaryotes or eukaryotes, but rather a microbial core community that was shared among plastic types. I also found that rare hydrocarbon degrading bacteria may be specific to certain chemical properties of the microplastics. Statistical comparisons of the communities across both sites showed that prokaryotic plastispheres were shaped primarily by incubation time and geographic location. Finally, I assessed the impact of biofilms on microplastic degradation and deposition and conclude that biofilms enhance microplastic sinking of negatively buoyant particles and reduce microplastic degradation. The results of my dissertation increases understanding of the factors that shape the plastisphere and how these communities ultimately determine the fate of microplastics in the marine environment.
ContributorsDudek, Kassandra Lynn (Author) / Neuer, Susanne (Thesis advisor) / Polidoro, Beth (Committee member) / Garcia-Pichel, Ferran (Committee member) / Cao, Huansheng (Committee member) / Arizona State University (Publisher)
Created2021