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 Methane Biogeochemistry and Microbial Communities in Natural and Restored Freshwater Depressional Wetlands(2024) Hamovit, Nora David; Yarwood, Stephanie A; Behavior, Ecology, Evolution and Systematics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Wetlands are the largest natural source of methane (CH4), a potent greenhouse gas. Wetland CH4 emissions are dependent on rates of microbial CH4 production (methanogenesis) and consumption (methanotrophy). These processes vary spatially and temporally with environmental conditions, edaphic characteristics, and microbial community structure, making it difficult to predict wetland CH4 emissions. This high variability can be further pronounced in restored wetlands that have undergone environmental and edaphic disturbances. The following work aims to understand this variability by assessing patterns of methanogenesis and methanotrophy, and their associated microbial communities, across natural and restored freshwater depressional wetlands on the Delmarva Peninsula (USA). Sites addressed in this work were restored from agricultural land between 1986 and 2004 through multiple programs funded by the United States Department of Agriculture (USDA). In the first set of experiments, we identified a high abundance of active acetoclastic methanogens in intact core incubations from a restored wetland suggesting a higher potential for methanogenesis in situ compared to the natural wetland assessed. The co-occurrence of active methanogens and Fe-reducing bacteria in these restored wetland cores contradicted the hypothesis that loss of competition may allow methanogens to be the primary users of acetate. Following assessments across vegetative-hydrologic zones in a series of restored wetlands of varying ages, and their natural counterparts, highlighted vegetation type and extent as a driver of methanogen community abundance, composition, and activity. In turn, restored wetlands showed elevated potentials rates of methanogenesis compared to natural sites. Potential rates of methanotrophy (aerobic and anaerobic), however, were also elevated in restored wetlands, which could constrain CH4 emissions in situ. Variability of environmental conditions (ie. hydrology and vegetation) and edaphic measures (ie. soil organic matter (SOM)) across all sites sampled are reflected in distinct microbial community composition and CH4 biogeochemistry. Clear patterns of SOC accumulation and CH4 biogeochemistry with restoration age were not observed for these wetlands, and variability in environmental conditions and edaphic measures across the sites (restored and natural), emphasize the need for continued monitoring and maintenance of the wetlands. Our results suggest efforts to manage herbaceous vegetation extent and maintain regular seasonal hydrology in future restorations may help prevent high potentials for CH4 production, and thus emissions.Item How do resource availability, information flow and targeted interactions shape eco-evolutionary processes in microbial organisms across scale?(2022) Swain, Anshuman; Fagan, William; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This work explores the crucial link between biological organization and dynamics in microbes. I have developed and applied different sets of quantitative tools to investigate this theme using a multi-disciplinary approach. My first project uses flow optimization tools to explore microbial intra-cellular dynamics as a function of resources, cell structure, and trade-offs between major energy production processes. This model explains emergent cell-level properties such as the dependence of bacterial growth rates on cell shape, size patterns in long-term evolutionary experiments, and the intriguing Warburg effect – wherein cells use inefficient anaerobic energy production pathways instead of efficient aerobic processes, despite ample oxygen availability. Moving to the community-level, I explored the mechanisms by which high levels of diversity are maintained in natural systems. Via a cutting-edge agent-based model that incorporates biologically realistic higher-order interactions, a continuous species space in which microbes interact via antibiotics and defenses, and an evolution-via-mutation regime, I link the trajectory of community assembly to both spatial heterogeneity patterns and diversity dynamics, thereby providing a new perspective on the origin and maintenance of diversity in complex communities. At the ecosystem-level, I built a dynamical system model to explore how the availability of resources and oxygen—mediated by interactions among microbial functional groups—affect environmental production of major greenhouse gases, like methane, especially on early Earth. This work provides 1) the first ecosystem-based functional explanation of periodic global methane ‘hazes’ in Earth’s early atmosphere and 2) a way to predict oxygen concentrations of ancient environments in a novel way. Lastly, in research that can involve multiple scales of biological organization, I use novel network science and information theoretic metrics to understand differences in interaction patterns in networks through the lens of degeneracy, noise, and determinism. The tradeoff between degeneracy and determinism can help us define the most informative scale of a network, and this is explored in the project through the development of new openly accessible toolkits.Item Soil microbial processes and community structure in natural and restored tidal freshwater wetlands of the Chesapeake Bay, Maryland, USA(2017) Maietta, Christine E.; Yarwood, Stephane A.; Baldwin, Andrew H.; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Tidal freshwater wetlands are integral to downstream water quality because they capture, store, and transform nutrients. Unfortunately, anthropogenic stressors are negatively impacting these habitats. While wetland restoration is helping to reinstate their presence in the landscape, restored wetlands frequently differ physically, chemically, and biologically from their natural counterparts. This research examined plant, soil, and microbe relationships and how their interactions affect soil carbon (C) storage and cycling in natural and restored tidal freshwater wetlands of the Chesapeake Bay, MD, USA. This research yielded important findings regarding differences between natural and restored habitats. First, we discovered soil microbial community composition of an urban tidal freshwater wetland retained similar composition as their less disturbed, suburban counterpart, and wetland sites constructed using similar restoration methodology produced similar microbial community structure and soil function. Additional research revealed that a natural and a restored wetland store soil C quite differently: A majority of soil C in the natural site was associated with large macroaggregates (> 2000 μm) whereas most soil C in the restored site was associated with smaller macroaggregates (> 250 to < 2000 μm). The distributions of six chemical compound classes (i.e., carboxylics, cyclics, aliphatics, lignin derivatives, carbohydrates derivatives, N-containing compounds) were relatively similar across the five soil fractions from both sites, however. In the final study, anaerobic laboratory mesocosms were used to evaluate the effects of clay content (%) and leaf litter quality on soil C cycling processes over time. This study found restored soils, regardless of clay content, mineralized more C as carbon dioxide (CO2) and methane (CH4) compared to natural wetland soils. Natural soils respired approximately half the volume of gas as restored soils, suggesting the addition of high- or low-quality C substrates to low C systems elicit a greater response from the heterotrophic microbial community. The results of these three studies suggest site history and edaphic features of restored wetlands are important drivers of microbial communities and their function. We propose that practitioners and researchers work together to identify practices that will enhance soil functions, particularly C storage, in tidal freshwater wetlands of the Chesapeake Bay region.Item Bacterial communities of the specialty crop phyllosphere: response to biological soil amendment use, rainfall, and insect visitation(2016) Allard, Sarah Michelle; Micallef, Shirley A; Plant Science and Landscape Architecture (PSLA); Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Microorganisms in the plant rhizosphere, the zone under the influence of roots, and phyllosphere, the aboveground plant habitat, exert a strong influence on plant growth, health, and protection. Tomatoes and cucumbers are important players in produce safety, and the microbial life on their surfaces may contribute to their fitness as hosts for foodborne pathogens such as Salmonella enterica and Listeria monocytogenes. External factors such as agricultural inputs and environmental conditions likely also play a major role. However, the relative contributions of the various factors at play concerning the plant surface microbiome remain obscure, although this knowledge could be applied to crop protection from plant and human pathogens. Recent advances in genomic technology have made investigations into the diversity and structure of microbial communities possible in many systems and at multiple scales. Using Illumina sequencing to profile particular regions of the 16S rRNA gene, this study investigates the influences of climate and crop management practices on the field-grown tomato and cucumber microbiome. The first research chapter (Chapter 3) involved application of 4 different soil amendments to a tomato field and profiling of harvest-time phyllosphere and rhizosphere microbial communities. Factors such as water activity, soil texture, and field location influenced microbial community structure more than soil amendment use, indicating that field conditions may exert more influence on the tomato microbiome than certain agricultural inputs. In Chapter 4, the impact of rain on tomato and cucumber-associated microbial community structures was evaluated. Shifts in bacterial community composition and structure were recorded immediately following rain events, an effect which was partially reversed after 4 days and was strongest on cucumber fruit surfaces. Chapter 5 focused on the contribution of insect visitors to the tomato microbiota, finding that insects introduced diverse bacterial taxa to the blossom and green tomato fruit microbiome. This study advances our understanding of the factors that influence the microbiomes of tomato and cucumber. Farms are complex environments, and untangling the interactions between farming practices, the environment, and microbial diversity will help us develop a comprehensive understanding of how microbial life, including foodborne pathogens, may be influenced by agricultural conditions.Item Alterations to headwater stream microbial communities and carbon cycling in response to environmental change.(2015) Hosen, Jacob Daniel; Palmer, Margaret A; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Organic carbon, principally as dissolved organic matter (DOM), is a fundamental energy source that powers microbial metabolism and shapes food webs in stream ecosystems. The community structure and metabolic activity of stream microbes are significantly impacted by the quantity and quality (i.e. molecular structure) of organic matter resources. Much of the organic matter in headwater streams originates on landscapes. Thus, external inputs of terrestrial organic carbon shape microbial community structure and, subsequently, food webs of headwater streams. Despite the recognized importance of DOM, there is limited understanding of how stream organic matter resources and bacterial community structure respond to watershed urbanization. I studied DOM quantity and quality, microbial heterotrophic function, and bacterial community composition along a gradient of watershed urbanization in headwater streams of the Parkers Creek watershed (Coastal Plain, Maryland, USA). In Chapter 1, I found that watershed impervious cover was significantly related to stream water DOM composition: increasing impervious cover was associated with decreased amounts of natural humic-like DOM and enriched amounts of anthropogenic fulvic acid-like and protein-like DOM. The DOM found in urbanized streams was more bioavailable, but only during spring and summer experiments. I report in Chapter 2 that microbial heterotrophic enzyme production was not strongly related to urbanization. Instead, enzyme levels were most strongly related to temperature and natural groundwater chemical gradients. I show in Chapter 3 that bacterial community composition and co-occurrence patterns also changed significantly in response to increasing urbanization, becoming more dominated by primary producers common to eutrophic waters. I conclude from my research that watershed urbanization fundamentally alters microbial communities and carbon cycling in headwater streams. This urbanized material is more readily metabolized by microbial communities, but only during warmer months. Increased biodegradation of DOM in warm seasons was related to greater microbial enzyme activity, which generally responds positively to increasing temperature. Thus, rising temperatures with climate change and urbanization combined with altered organic matter content are predicted to result in greater CO2 evasion from urbanized streams.Item Back to Earth: Molecular Approaches to Microbial Ecology Must Consider Soil Morphology and Physicochemical Properties(2015) Dlott, Glade; Yarwood, Stephanie A; Environmental Science and Technology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)This project studied the influence of different long-term agricultural management regimes on soil microbial communities, and compared survival strategies of individual prokaryotic OTUs in diverse soils subjected to long-term incubation. Together these would show whether alterations to microbial communities affect rates of soil carbon cycling. Agricultural soils were sampled at arbitrary depths above and below the plow layer, and relative abundances of microbes were measured using high-throughput sequencing. `Activity' (rRNA:rDNA) ratios were calculated for individual OTUs identified by high-throughput sequencing of tropical rainforest and temperate cornfield soils after incubation for one year with differing water and carbon availabilities. It was found that depth controls microbial communities to a greater degree than agricultural management, and that the characterization of microbial trophic strategies might be complicated by the often-ignored DNA preservation potential of soil. The study highlights the need for holistic approaches to testing hypotheses in modern microbial ecology.Item MICROBIAL ECOLOGY AND ENDOLITH COLONIZATION: SUCCESSION AT A GEOTHERMAL SPRING IN THE HIGH ARCTIC(2012) Starke, Verena; Robb, Frank T; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)A critical question in microbial ecology concerns how environmental conditions affect community makeup. Arctic thermal springs enable study of this question due to steep environmental gradients that impose strong selective pressures. I use microscopic and molecular methods to quantify community makeup at Troll Springs on Svalbard in the high arctic. Troll has two ecosystems, aquatic and terrestrial, in proximity, shaped by different environmental factors. Microorganisms exist in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Environmental conditions modulate community composition. The strongest relationships of environmental parameters to composition are pH and temperature in aquatic samples, and water content in terrestrial samples. Periphyton becomes trapped by calcite precipitation, and is a precursor for endolithic communities. Microbial succession takes place at Troll in response to incremental environmental disturbances. Photosynthetic organisms are dominantly eukaryotic algae in the wet, high-illumination environments, and Cyanobacteria in the drier, lower-illumination endolithic environments. Periphyton communities vary strongly from pool to pool, with a few dominant taxa. Endolithic communities are more even, with bacterial taxa and cyanobacterial diversity similar to alpine and other Arctic endoliths. Richness and evenness increase with successional age, except in the most mature endolith where they diminish because of sharply reduced resource and niche availability. Evenness is limited in calcite-poor environments by competition with photosynthetic eukaryotes, and in the driest endolith by competition for water. Richness is influenced by availability of physical niches, increasing as calcite grain surfaces become available for colonization, and then decreasing as pore volume decreases. In most endoliths, rock predates microbial colonization; the reverse is true at Troll. The harsh Arctic environment likely imposes a lifestyle in which microbes survive best in embedded formats, and to preserve live inocula for regrowth. ARISA is commonly used to assess variations in microbial community structure. Applying a uniform threshold across a sample set, as is normally done, treats samples non-optimally and unequally. I present an algorithm for optimal threshold selection that maximizes similarity between replicate pairs, improving results.