Physical Sciences and Mathematics Commons^™

Exploring Soil Microbial Dynamics In Southern Appalachian Forests: A Systems Biology Approach To Prescribed Fire Impacts, Saad Abd Ar Rafie

Doctoral Dissertations

Prescribed fires in Southern Appalachian forests are vital in ecosystem management and wildfire risk mitigation. However, understanding the intricate dynamics between these fires, soil microbial communities, and overall ecosystem health remains challenging. This dissertation addresses this knowledge gap by exploring selected aspects of this complex relationship across three interconnected chapters.

The first chapter investigates the immediate effects of prescribed fires on soil microbial communities. It reveals subtle shifts in porewater chemistry and significant increases in microbial species richness. These findings offer valuable insights into the interplay between soil properties and microbial responses during the early stages following a prescribed fire. …

Metagenomic Investigation Of Microbial Dark Carbon Fixation, Viral Interactions, And Horizonal Gene Transfer Within A Convergent Margin Subsurface Ecosystem, Timothy Joseph Rogers

Doctoral Dissertations

Convergent margins are geological regions where two or more tectonic plates collide, and the denser “subducting slab” is pushed beneath the less dense overriding plate. As the slab descends, it devolatilizes under higher temperatures and pressures, allowing dissolved inorganic carbon (DIC) and redox active volatile rich fluids to cycle between the upper crust and Earth’s mantle. These fluids migrate through cracks and fissures in the upper mantle and crust, fueling chemolithoautotrophy-based microbial ecosystems in the subsurface before they are expelled on the surface in the form of hydrothermal seeps and springs. Chemolithoautotrophic ecosystems, such as those in the Costa Rican …

Evaluating Bulk Carbon And Nitrogen Isotope Compositions Of Acidic Hydrothermal Sediments On Earth– Implications For Mars Astrobiology, Chance Sturrup

Masters Theses

Carbon isotopes have been widely used as unique biosignatures because biologic processes commonly result in distinctive negative delta ¹³C values (-35 to -10 ‰) within organic material on Earth. However, the bulk delta ¹³C analysis in Gale crater sediments on Mars revealed a wider range of values, from -25 to +56 ‰ (Franz et al., 2020), which suggests a more complex origin. To determine if bulk isotope analysis can be successfully used to detect a microbial signature in a martian analog environment, we analyzed concentrations and isotope compositions of C within hydrothermal sediments in Iceland (Námafjall, Krýsuvík, Hveragerdi) …

Manganese Geochemistry And Plant Availability In Response To Agricultural Practices, Ashleigh R. Montgomery

Masters Theses

Manganese (Mn) is an essential micronutrient for all organisms. In soils, Mn forms determine availability to plants. Most Mn research has been conducted in forest ecosystems and Mn cycling in agricultural systems is understudied. Therefore, the objective of the experiment is to understand the effect of different agricultural management strategies on Mn cycling and plant availability. First, a greenhouse experiment was conducted to determine the effect of different application rates of two Mn fertilizers (MnSO₄ and MnEDTA) on soil geochemical properties and growth of corn (Zea mays) and soybean (Glycine max). The fertilizers were applied to …

The Characterization Of Dynamic Soil Properties And Their Relation To Soil Organic Carbon In East Tennessee Soils, Shannon Marissa Newell

Masters Theses

Quantifying how dynamic soil properties (DSPs) are affected by different management regimes is essential for understanding how these vital resources can be better managed. The Dewey soil series is a critical soil series in East Tennessee. For this study, the University of Tennessee, Knoxville (UTK) worked alongside the National Cooperative Soil Survey (NCSS) in an effort to better understand the dynamics of the Dewey soil series through a wide range of DSP data. To accomplish this, Dewey soil was collected from five sites which are considered representative of five management regimes: well-managed cropland (WMC), poorly-managed cropland (PMC), well-managed pasture (WMP), …

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

Subaerial biofilms (SABs) grow at the interface between the atmosphere and rock surfaces in terrestrial and subterranean environments around the world. Multi-colored SABs colonizing relatively dry and nutrient-limited cave surfaces are known to contain microbes putatively involved in chemolithoautotrophic processes using inorganic carbon like carbon dioxide (CO₂) or methane (CH₄). However, the importance of CO₂ and CH₄ to SAB biomass production has not been quantified, the environmental conditions influencing biomass production and diversity have not been thoroughly evaluated, and stable carbon and nitrogen isotope compositions have yet to be determined from epigenic cave SABs. …

Fire-Vegetation-Climate Interactions Across The Holocene On The U.S. Southeastern Coastal Plain, Mathew S. Boehm

Doctoral Dissertations

This dissertation research examined multiple proxy indicators in sediment cores from one lake and one wetland to reconstruct long-term relationships between fire, vegetation, and climate in the southeastern U.S.

At Lake Balboa (30.6992 N, 83.2031 W; 48 m elevation), a sinkhole pond located in southern Georgia, Bølling-Allerød conditions were sufficiently wet to maintain a shallow wetland at the site. Evidence for fire was minimal. Between 12,600 and 9200 cal yr BP, water availability declined, leading to a potential hiatus in sedimentation. During the early Holocene moisture availability increased, leading to greater primary productivity within and outside the lake, triggering an …

Biogeochemical Characteristics Of Organic Matter In A Karst Groundwater System, Teresa Lynn Brown

Doctoral Dissertations

Development of regional groundwater carbon budgets hinges on the ability to quantify and monitor biogeochemical processes controlled by microbial recycling of natural dissolved organic matter (DOM) in carbon-limited (oligotrophic) areas. DOM is the major reservoir of organic carbon in aquatic ecosystems. However, isolation and characterization of DOM in oligotrophic freshwater systems has been limited by operational protocols and instrumentation. The goals of this research were to investigate the seasonal dynamics of microbially-driven organic matter degradation in a karst groundwater system influenced by surface water, and to identify analytical tools and biomarkers to measure long-term hydro-ecological trends in the Appalachian region. …

Influence Of Environmental Conditions And Inundation History On Bacterial Diversity Of Salt Marsh Soils In Southern Louisiana, Brandon M. Bagley

Masters Theses

Diversity patterns and controls on bacterial community composition were investigated from coastal salt marsh soils in southern Louisiana (USA) from 2012 – 2014. These salt marshes are part of an extensive coastal landscape that is experiencing land loss due to subsidence, sea-level rise, and anthropogenic activities, including from the impacts of the Deepwater Horizon oil spill in 2010. Prior to the oil spill, microbiology research focused predominately on biogeochemical roles and not on taxonomic representation in the soils or on understanding the significance of taxonomic diversity at the microbial level to marsh food webs or ecosystem dynamics. The purpose of …

Influence Of Algae On Soil Saturated Hydraulic Conductivity: An In Situ Treatment Option For Reducing Infiltration Beneath Unlined Algae Cultivation Ponds, Molly Brianne Pattullo

Masters Theses

Commercial production of algal biofuels is currently limited by high capital costs, including the cost of installation and maintenance of plastic pond liners, which mitigate seepage of cultivation fluids and control the release of salts and nutrients into the subsurface beneath outdoor algae cultivation ponds. However, studies of animal waste settling lagoons show that underlying soils ranging from sands to clay loams can exhibit reduced hydraulic conductivity within days to weeks after construction, reducing the need for plastic liners. The mechanisms of the hydraulic conductivity reductions, or “soil sealing”, are physical rearrangement of soil particles, buildup of fines, and the …

Determining Sources Of Nitrate In The Semi-Arid Rio Grande Using Nitrogen And Oxygen Isotopes, Diego Alberto Sanchez Hernandez

Masters Theses

The Rio Grande, a semi-arid river in the American Southwest, is a major source of surface water for agriculture and drinking supplies in New Mexico and Texas. In addition to increasing salinity, considerable increases of NO₃^- [nitrate] have been observed in the semi-arid portion of the Rio Grande. It is possible that elevated water salinity inhibits denitrification on irrigated fields and, thus, fails to mediate excess nutrient load from anthropogenic activities. Therefore, two major goals of this project were to 1) characterize and quantify major NO₃^- sources, and 2) assess whether elevated water salinity affects microbial …

Microbial Extracellular Enzymes In Marine Sediments: Methods Development And Potential Activities In The Baltic Sea Deep Biosphere, Jenna Marie Schmidt

Masters Theses

The deep biosphere is defined as the subsurface ecosystem in which little energy is available to microorganisms and microorganisms can live for thousands of years. Heterotrophic microbes survive in the deep biosphere even though organic matter is limited and highly recalcitrant in nature. Measuring microbial extracellular enzyme activity provides a potential means to evaluate the rate at which microorganisms are performing carbon remineralization in the energy limited sediment beneath the seafloor. Extracellular enzymes breakdown organic compounds so that the nutrients can move inside the cell and be used for energy. This study explored the role extracellular enzymes play in the …

Bacterial Diversity And Function Within An Epigenic Cave System And Implications For Other Limestone Cave Systems, Kathleen Merritt Brannen-Donnelly

Doctoral Dissertations

There are approximately 48,000 known cave systems in the United States of America, with caves formed in carbonate karst terrains being the most common. Epigenic systems develop from the downward flow of meteoric water through carbonate bedrock and the solutional enlargement of interconnected subsurface conduits. Despite carbonate karst aquifers being globally extensive and important drinking water sources, microbial diversity and function are poorly understood compared to other Earth environments. After several decades of research, studies have shown that microorganisms in caves affect water quality, rates of carbonate dissolution and precipitation, and ecosystem nutrition through organic matter cycling. However, limited prior …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Long-Term Impacts Of Conservation Management Practices On Soil Carbon Storage, Stability, And Utilization Under Cotton Production In West Tennessee, Candace Brooke Wilson

Masters Theses

Biogeochemical cycling of soil carbon (C) is heavily influenced by conservation agricultural (CA) practices. This study examined SOC stability under three CA practices: reduced nitrogen (N) fertilizer application rate, cover cropping, and zero-tillage implemented for 31 years. Respiration rates measured from a 602-day incubation period were fitted to a double-pool first order exponential model of SOC decomposition. The active [respired] SOC pool showed distinct differences between applications of reduced (34N kg ha^-1 [-1]) and high fertilization rates (101N kg ha^-1) combined with tillage, and suggest that high fertilizer applications with conventional tillage allocated more C into a …

Environmental Controls On The Diversity And Distribution Of Endosymbionts Associated With Phacoides Pectinatus (Bivalvia: Lucinidae) From Shallow Mangrove And Seagrass Sediments, St. Lucie County, Florida, Thomas Walters Doty

Masters Theses

Lucinid bivalves are capable of colonizing traditionally inhospitable shallow marine sediments due to metabolic functions of bacterial endosymbionts located within their gills. Because lucinids can often be the dominant sediment infauna, defining their roles in sediment and pore fluid geochemical cycling is necessary to address concerns related to changes in coastal biological diversity and to understanding the sensitivity of threatened coastal ecosystems over time. However, there has been limited research done to understand the diversity and distribution of many lucinid chemosymbiotic systems. Therefore, the goals of this thesis were to evaluate the distribution of Phacoides pectinatus and its endosymbiont communities …

Evidence Of Late Quaternary Fires From Charcoal And Siliceous Aggregates In Lake Sediments In The Eastern U.S.A., Joanne P. Ballard

Doctoral Dissertations

The late-glacial transition to the Holocene, 15,000–11,600 cal yr BP, is an enigmatic period of dynamic global changes and a major extinction event in North America. Fire is an agent of disturbance that transforms the environment physically and chemically, and affects plant community composition. To improve understanding of the linkages between fire, vegetation, and climate over the late glacial and Holocene in the eastern U.S., I analyzed lake-sediment cores for charcoal and indicators of wood ash, and compared results to existing pollen records. A new microscopic charcoal record from Anderson Pond, Tennessee revealed high fire activity from 23,000–15,000 cal yr …

Characterizing Groundwater Ch4 And 222rn In Relation To Hydraulic Fracturing And Other Environmental Processes In Letcher County, Ky, St. Thomas Majeau Ledoux

Masters Theses

Hydraulic fracturing of shale deposits has greatly increased the productivity of the natural gas industry by allowing it to exploit previously inaccessible reservoirs. However, previous research has demonstrated that this practice can contaminate shallow aquifers with CH₄ [methane] from deeper formations. This study compares concentrations and isotope compositions of CH₄ sampled from domestic groundwater wells in Letcher County, Kentucky in order to characterize its occurrence and origins in relation to neighboring hydraulically fractured natural gas wells. Additionally, this study tests the reliability of ²²²Rn [radon] as an alternative tracer to CH₄ in identifying processes of gas …

Reaping The Benefits Of Conservation Tillage: Implications Of Increased Soil Organic Matter And Aggregation In Surface Soils, Kenna Elizabeth Rewcastle

Chancellor’s Honors Program Projects

No abstract provided.

Investigating The Effects Of Urbanization On Residual Forest Soils In Knox Co., Tennessee, Benjamin Lee Reichert

Masters Theses

As the process of urbanization advances across the country, so does the importance of urban forests, which include both trees and the soils in which they grow. Soil microbial biomass, which plays a critical role in nutrient transformation in urban ecosystems, is affected by factors such as soil type and the availability of water, carbon, and nitrogen. However, the microbial dynamics of urban forest soils remain largely unknown. A key mechanistic link between plant species diversity and ecosystem function is heterotrophic microbial communities that inhabit the soil and mediate principal processes that control ecosystem carbon (C) and nitrogen (N) cycling. …

Mineralized Microbialites As Archives Of Environmental Evolution Of A Hypersaline Lake Basin: Laguna Negra, Catamarca Province, Argentina, Joy Buongiorno

Masters Theses

Environmental fluctuations related to climate, biological productivity, and evaporation can be recorded by sedimentary archives within lacustrine depositional systems. Sediments within terminal, closed-basin lakes are amongst the most sensitive paleoenvironmental indicators, and have great potential for permitting detailed reconstruction of environmental conditions via a variety of geochemical and isotopic proxies. Microbialites, however, have been largely overlooked as repositories of paleoenvironmental data. Here, we investigate mineralized microbialites within Laguna Negra, a high-altitude (4100 meters above sea level) hypersaline, closed-basin lake in the Argentinian Puna region and explore the potential recovery of environmental signals from these unique sedimentary archives. Mineralized microbialites within …

Genetic Analysis Of Bacterial Gene Variations In Sulfidic Springs And The Influence On Geochemistry, Brendan Joseph Headd

Doctoral Dissertations

Culture-independent methods have revolutionized environmental microbiology and geomicrobiology studies and next-generation sequencing and metagenomics techniques continue to reveal the vast genetic diversity of microorganisms. But, these approaches provide comparatively little quantitative information about the roles that naturally occurring microbial gene variations play in local biogeochemical cycling. The goal of this study was to identify how the physical distribution and genetic diversity of microbial genes within a habitat impact environmental geochemistry by examining the biogeography of 16S rRNA genes and bacterial sulfur oxidation (Sox) genes in terrestrial sulfidic springs. 16S rRNA gene pyrosequences were obtained from microbial mats inhabiting eight sulfidic …

A Morphological And Geochemical Investigation Of Grypania Spiralis: Implications For Early Earth Evolution, Miles Anthony Henderson

Masters Theses

Macroscopic “carbonaceous” fossils such as Grypania, Katnia, Chuaria, and Tawuia play a critical role in our understanding of biological evolution in the Precambrian and their environmental implications. Unfortunately, understanding of these fossils remains limited by their relative simplicity of form, mode of preservation, and broad taphonomic variability. As a result, debate continues as to even the fundamental taxonomic affinity of the organisms. Megascopic coiled forms (i.e. Grypania and Katnia), for instance, have been interpreted as trace fossils, multicellular algae, prokaryotic filaments, macroscopic bacteria, cyanobacteria, or a transitional form from macroscopic to megascopic bacterial life. Similarly, Chuaria …