Theses and Dissertations from UMD
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New submissions to the thesis/dissertation collections are added automatically as they are received from the Graduate School. Currently, the Graduate School deposits all theses and dissertations from a given semester after the official graduation date. This means that there may be up to a 4 month delay in the appearance of a give thesis/dissertation in DRUM
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Item Investigating the Microbial Diversity and Ecophysiology of Filamentous Cyanobacteria on the Susquehanna Flats, Chesapeake Bay(2024) Keller, Shayna Aryn; O'Neil, Judith M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The Susquehanna Flats is a biodiverse and resilient submerged aquatic vegetation (SAV) bed just below the mouth of the Susquehanna River in the Chesapeake Bay. The Susquehanna River, the largest tributary of the Chesapeake Bay, discharges more water than all other tributaries in the Bay combined. This makes the SAV bed at the Susquehanna Flats important for nutrient removal of the water discharged into the headwaters of the Bay. The Susquehanna Flats is also a unique part of the oligohaline portion of the Chesapeake Bay as it is one of the most prolific and diverse SAV beds that make up ~8% of SAV in the Chesapeake Bay. The SAV bed was devastated by Hurricane Agnes in 1972 and did not reappear until the early 2000s when an extended dry period and long-term reductions in nutrient loading facilitated its resurgence. Since then, it has recovered to be the most abundant and biodiverse SAV bed within the upper Chesapeake Bay. However, a nitrogen fixing filamentous Cyanobacteria, morphologically identified as Microseira (Lyngbya) wollei, has seasonally bloomed at the Susquehanna Flats since the early 2000s. Over the ensuing decade, anecdotal evidence suggested an overall increase of Cyanobacteria on the SAV beds on the Susquehanna Flats, which raised concerns about the impact of this growth on the resilience of the recovering SAV bed. Despite the consistent summer blooms, the filamentous Cyanobacterial mats and its microbiome at the Susquehanna Flats has not been molecularly identified and its characteristics have not been investigated to date. Additionally, new DNA sequencing technology has become more readily available, and the identification and taxonomy of the Cyanobacteria family Oscillatoriaceae, of which Microseira (Lyngbya) wollei is a part of, has become more refined and organized. Due to this, molecularly identifying the filamentous Cyanobacterial mats and investigating its microbiome has become much easier with current methods that can provide detailed taxonomic information that can help implement management strategies. Using PacBio long-read amplicon sequencing on the 16S rRNA genes and Illumina short-read amplicon sequencing on the nifH genes of the filamentous Cyanobacteria mats and a newly observed mucilaginous Cyanobacteria mat collected at the Susquehanna Flats, the host organisms and microbial compositions were revealed. The results indicate that the dominant filamentous Cyanobacterial mat host is Microseira (Lyngbya) wollei and these mats contain a complex microbial community. The host of a newly observed mucilaginous mats was revealed to be a novel strain of Phormidium sp. To understand the basic nutrient requirements and preferences of the Microseira (Lyngbya) wollei at the Susquehanna Flats, nutrient bioassay growth and nitrogen fixation experiments were initiated to assess its growth and nitrogen fixation qualities. Samples received nutrient treatments of nitrate, phosphate, nitrate + phosphate, and ammonium compared to the growth of control samples that did not receive nutrient treatments in the summers of 2022 and 2023. The results demonstrated that Microseira (Lyngbya) wollei has variable growth rates, with higher rates in the mid to late part of the summer season, with significant growth stimulations from added nitrogen and phosphorus. In terms of nitrogen fixation, rates were higher in the beginning of the season, with significant stimulation with phosphorus additions. It is likely that lower rates measured at the end of the season, were due to the increased availability of regenerated nitrogen within the system. More detailed investigation of the seasonal nutrient dynamics are warranted to fully understand the dynamics between these Cyanobacterial mats and the SAV beds.Item AUGMENTING SEQUENCING TECHNOLOGY FOR BETTER INFERENCE IN SOIL MICROBIOME ANALYSIS(2023) Epp Schmidt, Dietrich; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The advent of DNA sequencing revolutionized the field of microbiome research. Many organisms, by virtue of their codependence and/or growth rate, are either impossible or extremely challenging to get into pure culture. Sequencing allows important taxonomic and phylogenetic information to be obtained independent of culturing. Development of the sequencing technology itself has allowed for high throughput workflow that has allowed low cost and extensive sampling of microbiomes across environments. The co-development of reference datasets for taxonomy and functional assignments, along with open-source bioinformatics pipelines has further empowered scientists to explore microbiomes in many environments. However, there are limitations to sequence data that have constrained the ecological inferences in microbiome research. One such limitation, the compositional nature of sequence data, has impeded our ability to make accurate inferences about the environmental drivers of taxon abundance and covariance across conditions. In this dissertation I explore the use of quantitative PCR in combination with sequencing techniques to generate “Quantitative Sequencing” data (QSeq) that mitigates the limitations of compositionality on inferences relating to taxon abundance and covariance across environmental gradients. In chapter 1, I reviewed key characteristics of the soil environment and sequencing as a mechanism for sampling. In chapter 2, I leveraged modeling, synthesis, and literature review methods to establish the questions and data characteristics that demand QSeq methodology. I show that even small amounts of variation in total abundance make determining the effects of environment (biotic and abiotic factors) on any given taxon unreliable without QSeq. In Chapter 3, I extend the logic of quantitative sequencing to improve metagenome prediction from PICRUSt2. Using data synthesis methods, accounting for 16S gene abundance consistently improved the accuracy of predicted functional genes. This was confirmed by high correlations between predicted and measured gene abundance (QPCR). There was however a large variation in prediction accuracy, likely due in part to database biases and in part to decoupling of bacterial function from taxonomy. In Chapter 4, I applied QSeq in the context of an experimental, long-term farming system that has large gradients in total abundance with depth, and I used QSeq to identify taxa that changed in abundance due to different farming system management and soil depth. Finally in Chapter 5, I used QSeq to identify putative N-fixing taxa that responded to glyphosate in four experimental farming systems. I show that the abundance of these taxa were decoupled from other effects of glyphosate on N-fixation in soybean across farming systems.Item Small Molecule Activation and Atom and Group Transfer Reactions Mediated by Mid Valent Group 6 'CPAM' Complexes(2015) Farrell, Wesley Scott; Sita, Lawrence R; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The use of organometallic compounds to activate small molecules (e.g. CO2, N2, N2O, O2, etc.) has long been of significant scientific interest. Described here is the synthesis and characterization of mid valent group 6 compounds supported by the pentamethylcyclopentadienyl, amidinate (CpAm) ligand framework, along with their ability to not only activate small molecules that are inexpensive, abundant, and/or hazardous, but use them to generate many value added products under mild conditions. Sulfur atom transfer (SAT) was employed to catalytically prepare carbonyl sulfide and isothiocyanates from elemental sulfur. In the case of carbonyl sulfide, this process was able to be performed in the presence of primary amines, allowing for the isolation of symmetric ureas, and in the case of isothiocyanates, the reaction was successful in the presence of benzhydrazide to allow for the isolation of aroylthiosemicarbazides in good yields. Molecular oxygen was found to afford high valent dioxo species which were inactive towards oxygen atom transfer (OAT). However, OAT was achieved for the catalytic deoxygenation of sulfoxides. Dinitrogen fixation has previously been discovered by our group to afford -ER3 (E = C, Si, Ge) derivatized isocyanates through [2+1] cycloaddition of CO. Reported here is an extension of this work to include N2 fixation with concomitant reduction of the greenhouse gas CO2 to prepare the same isocyanates via [2+2] cycloaddition of CO2. Furthermore, the completion of several efficient N2 fixation synthetic cycles through two distinct pathways is discussed. Additionally, given the tremendous impact of high valent group 6 alkylidene compounds to catalyze olefin metathesis reactions, the synthesis of mid valent CpAm group 6 alkylidenes was a challenging, yet attractive target. Attempts to isolate such compounds are presented, along with descriptions of the products obtained and their reactivity towards small molecules.