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. …

Integration Of Raman Spectroscopy And Python-Based Data Analysis For Advancing Neurobiological Research, Natalie E. Dunn

Doctoral Dissertations

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated …

The Impacts Of Tilled-In Biodegradable Plastic Mulch On Soil Microbial Communities, Corissa L. Martin

Masters Theses

Plastics mulch films are used in agriculture to help increase crop production by regulating soil water retention and soil temperature while also preventing weed growth. Despite these benefits, plastic mulches have led to higher levels of microplastic pollution as weathering occurs. In response to this issue, biodegradable plastic mulches (BDMs) have been introduced to help reduce plastic pollution as they are designed to be tilled into soil after each growing season to continue degradation. Degradation of these mulch films is dependent on climate and, in some areas, complete degradation can take years. Since some biodegradable plastic mulches are made of …

Mathematical Modeling Suggests Cooperation Of Plant-Infecting Viruses, Joshua Miller, Vitaly V. Ganusov, Tessa Burch-Smith

Chancellor’s Honors Program Projects

No abstract provided.

Probing Structure, Function And Dynamics In Bacterial Primary And Secondary Transporter-Associated Binding Proteins, Shantanu Shukla

Doctoral Dissertations

Substrate binding proteins (SBPs) are ubiquitous in all life forms and have evolved to perform diverse physiological functions, such as in membrane transport, gene regulation, neurotransmission, and quorum sensing. It is quite astounding to observe such functional diversity among the SBPs even when they are restricted by their fold space. Therefore, the SBPs are an excellent set of proteins that can reveal how proteins evolution novel function in a structurally conserved/constrained fold. This study attempts to understand the phenomenon of affinity and specificity evolution in SBPs by combining a set of biochemical, biophysical, and structural studies on the SBPs involved …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

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. …

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIP_ns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in …

Metabolomics Approaches To Decipher The Antibacterial Mechanisms Of Yerba Mate (Ilex Paraguariensis) Against Staphylococcus Aureus And Salmonella Enterica Serovar Typhimurium, Caroline Sue Rempe

Doctoral Dissertations

The increasing prevalence of drug-resistant pathogens is an urgent problem that requires novel methods of bacterial control. Plant extracts inhibit bacterial pathogens and could contain antibacterial compounds with novel mechanisms of action. Yerba mate, a common South American beverage made from Ilex paraguariensis, has antibiotic activity against a broad range of bacterial pathogens. In this work, an attempt was first made to characterize the antibacterial source of an aqueous yerba mate extract by generating a series of extract fractions, collecting GC-MS and antibacterial activity profiles, and then ranking the hundreds of compounds by their presence in fractions with high antibacterial …

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 …

Biophysical Studies Of Cell Division Protein Localization Mechanisms In Escherichia Coli, Matthew Wayne Bailey

Doctoral Dissertations

How nanometer-scale proteins position accurately within micron-scale bacteria has intrigued both biologists and physicists alike. A critical process requiring precise protein localization is cell division. In most bacteria, cell division starts with the self-assembly of the FtsZ proteins into filaments that form a ring-like structure encircling the cell at its middle, the Z-ring. The Z-ring is a scaffold for additional proteins that synthesize the lateral cell wall which separates the two daughter cells. If division planes are misplaced relative to bacterial chromosomes, also called nucleoids, daughter cells with incomplete genetic material can be produced. In Escherichia coli, research carried out …

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; …

Elucidating The Impact Of Roseophage On Roseobacter Metabolism And Marine Nutrient Cycles, Nana Yaw Darko Ankrah

Doctoral Dissertations

As the most abundant biological entities in marine environments, viruses are an important component of marine food webs. The activity of viruses contributes significantly to the mortality of marine microorganisms, ultimately influencing biological function and chemical composition of aquatic systems by impacting species composition and flow of carbon, nitrogen and other nutrients. Despite the growing recognition that viral activity contributes to marine biogeochemical cycles, the extent to which virus infection reshapes host metabolism and the effect of this alteration on the composition of host lysate remains poorly understood. Additionally, the degree to which natural bacterioplankton communities metabolise the released lysate …

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 …

Quorum Sensing And Metabolism In Marine Environments, Amanda May

Doctoral Dissertations

Quorum sensing (QS) is a phenomenon that allows bacteria to communicate with each other. Small molecules known as autoinducers are synthesized and released by bacteria, and once enough members of the community are around to ensure survival, i.e. quorum, a phenotype, e.g. bioluminescence, is expressed. There are two types of QS molecules, intra- and inter-species.

S-4,5-Dihydroxy-2,3-pentanedione (DPD) is a byproduct of the activated methyl cycle which recycles methionine. This has led to the discussion as to whether DPD is a metabolic byproduct or is the interspecies signal as proposed previously. The detection and quantitation of DPD however, has not …

Development And Application Of Liquid Chromatography-Tandem Mass Spectrometry Methods To The Understanding Of Metabolism And Cell-Cell Signaling In Several Biological Systems, Jessica Renee Gooding

Doctoral Dissertations

Liquid chromatography tandem mass spectrometry has become a powerful tool for investigating biological systems. Herein we describe the development of both isotope dilution mass spectrometry methods and targeted metabolomics methods for the study of metabolic and cell-cell signaling applications.

A putative yeast enzyme was characterized by discovery metabolite profiling, kinetic flux profiling, transcriptomics and structural biology. These experiments demonstrated that the enzyme shb17 was a sedoheptulose bisphosphatase that provides a thermodynamically dedicated step towards riboneogenesis, leading to the redefinition of the canonical pentose phosphate pathway.

An extension of metabolic profiling and kinetic flux profiling methods was developed for a set …

Non-Thermal Plasma Inactivation Of Bacillus Amyloliquefaciens Spores, Yaohua Huang

Masters Theses

Bacterial spores have remarkable resistance to a variety of harsh conditions, causing spoilage in food industry and becoming the primary bacterial agent in biowarfare and bioterrorism. In this study, inactivation mechanisms of Bacillus amyloliquefaciens (BA) spores by non-thermal plasma (NTP) were investigated by using Fourier-transform infrared spectroscopy (FTIR) as a major tool to exam spores after NTP treatment. Chemometric techniques, such as multivariate classification models based on soft independent modeling of Class Analogy (SIMCA) and Principal Component Analysis (PCA), were employed to identify functional group changes in FTIR spectra. The IR absorbance bands correlated to dipicolinic acid (DPA) decreased after …

The ‘Helper’ Phenotype: A Symbiotic Interaction Between Prochlorococcus And Hydrogen Peroxide Scavenging Microorganisms, James Jeffrey Morris

Doctoral Dissertations

The unicellular cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism throughout the temperate and tropical open oceans, but it is difficult to grow in pure cultures. We developed a system for rendering spontaneous streptomycin-resistant mutants of Prochlorococcus axenic by diluting them to extinction in the presence of “helper” heterotrophic bacteria, allowing them to grow to high cell concentrations, and then killing the helpers with streptomycin. Using axenic strains obtained in this fashion, we demonstrated that Prochlorococcus experiences a number of growth defects in dilute axenic culture, including reduced growth rate, inability to form colonies on solid media, and higher incidence …