Life Sciences 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. …

The Identification Of Small Molecule Inhibitors To Candida Albicans Phosphatidylserine Synthase, Yue Zhou

Doctoral Dissertations

Candida albicans phosphatidylserine (PS) synthase, encoded by the CHO1 gene, has been identified as a potential drug target for new antifungals against systemic candidiasis due to its importance in virulence, absence in the host and conservation among fungal pathogens. This dissertation is focused on the identification of inhibitors for this membrane enzyme. Cho1 has two substrates: cytidyldiphosphate-diacylglycerol (CDP-DAG) and serine. Previous studies identified a conserved CDP-alcohol phosphotransferase (CAPT) binding motif present within Cho1, and here we revealed that mutations in all but one conserved amino acid within the CAPT motif resulted in decreased Cho1. For serine, we have predicted a …

Impact Of Cadmium Stress On Soil Virus Reproduction And The Persistence Of Viruses Under Abiotic Conditions, Zhibo Cheng

Doctoral Dissertations

Soil viruses are ubiquitous and greatly impact the structure and function of soil microbial communities, with their effects modulated by various environmental factors. This study investigates the inactivation of naturally occurring soil viruses in sterilized soil, as well as the effects of cadmium (Cd) exposure and carbon (C) and nitrogen (N) nutrient availability on the population dynamics of virus-host communities in agricultural soil.

Lab-scale slurry and unsaturated experiments were performed to examine virus inactivation in the absence of host bacteria in sterilized soil. In slurry experiments, virus abundance declined by over 90% after 10 days of incubation. The addition of …

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 …

Exploring The Regulation Of A Bacillus Pumilus Bioplastic Degrading Protein, Elise Keara Phillips

Doctoral Dissertations

Biodegradable plastics are being adopted to reduce the environmental impacts associated with petroleum-based plastics, including long residence times, and reliance on fossil fuels as a feedstock. Microbial degradation of bioplastics is still poorly understood, which leads to inconsistent degradation outcomes and challenges for implementation. Bacillus pumilus B12 degrades the biodegradable bioplastic polylactic acid (PLA) via the protease AprE, but the regulatory mechanisms controlling aprE expression in B. pumilus B12 are largely unknown. To explore this question, we established developed a conjugation- based method to introduce DNA into B. pumilus B12 and diverse Bacillus species that is applicable to environmental and …

Novel Microbial Guilds Implicated In N2o Reduction, Guang He

Doctoral Dissertations

N₂O is a long-recognized greenhouse gas (GHG) with potential in global warming and ozone depletion. Terrestrial ecosystems are a major source of N₂O due to imbalanced N₂O production and consumption. Soil pH is a chief modulating factor controlling net N₂O emissions, and N₂O consumption has been considered negligible under acidic conditions (pH <6). In this dissertation, we obtained solids-free cultures reducing N₂O at pH 4.5. Furthermore, a co-culture (designated culture EV) comprising two interacting bacterial population was acquired via consecutive transfer in mineral salt medium. Integrated phenotypic, metagenomic and metabolomic analysis dictated that the Serratia population excreted certain …

Roles Of Soil Pores In Determining Water Retention And Microbial Dynamics, Huihui Sun

Doctoral Dissertations

Soil pore provides an essential habitat for microbial communities to participate in various biogeochemical processes. The complex pore spaces, which are defined by the arrangement of particles of varying sizes, govern the distribution of water for microbial dispersal and movement and microbial interaction with one another, such as bacterial cell-to-cell and bacterium-virus interactions. This research focused on exploring how soil pores influence soil water retention and bacterial interactions and quantify the spatial distribution of bacteria and viruses in fine-scale of soil pores. Using a mathematical model, this study simulated a soil water retention curve based on the relationship between soil …

Induction And Evasion Of Neutrophil Extracellular Traps By Campylobacter Jejuni And Its Implication In Disease, Sean M. Callahan

Doctoral Dissertations

Campylobacteriosis, the foodborne disease caused by Campylobacter spp., infects one out of 10 individuals every year. C. jejuni accounts for 90% of these infections resulting in numerous postinfectious disorders including the development of colorectal cancer, Guillain-Barré syndrome, irritable bowel syndrome, and reactive arthritis. Despite its large impact on human health, the host immune response to the bacterium is largely uncharacterized. Chapter two of this dissertation addresses the development of neutrophil extracellular traps (NETs) within human and ferret campylobacteriosis. We observed NET-associated proteins increase in the feces of C. jejuni-infected patients and that in vitro C. jejuni induces NETs, which …

Investigating Drivers Of Algal Bloom Succession In Lake Erie, Brittany Zepernick

Doctoral Dissertations

Harmful Algal Blooms (HABs) are algae undergoing prolific, unregulated growth. A well-documented HAB taxa is the cyanobacterium Microcystis spp., which induces anthropogenic, ecological, and economic consequences due to the production of toxins and biomass which results in lake hypoxia. Microcystis spp. blooms are globally distributed in freshwater systems, with climate change and the aquatic continuum serving to further exacerbate bloom distribution, duration, and frequency. Thus, there is a need to elucidate the factors driving the ecological success of Microcystis spp., and the ecological “failures” of their competitors, such as diatoms. In Lake Erie, a seasonal pattern of algal bloom succession …

Unraveling Plant-Microbe-Microbe Interactions: Host And Microbial Colonization Determinants Across Experimental Scales, Bridget O'Banion

Doctoral Dissertations

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host and microbial mechanisms are likely important mediators of interactions. We combine information from large-scale datasets across diverse plant hosts with experimental genetic manipulation assays in model Arabidopsis seedlings to converge on a conserved role for metabolite production and transport in mediating host-microbe interactions. Applying a diverse set of analytical tools to microbial communities at various complexity levels will advance our knowledge of the scalability of observed phenotypes and, ultimately, help to decipher the mechanisms dictating plant–microbe interactions …

Identification Of The Type Eleven Secretion System (T11ss) And Characterization Of T11ss-Dependent Effector Proteins, Alex S. Grossman

Doctoral Dissertations

Host-associated microbes live in dangerous environments as a result of host immune killing, nutrient provisioning, and physiological conditions. Bacteria have evolved a host of surface and secreted proteins to help interact with this host environment and overcome nutrient limitation. The studies included within this dissertation describe the identification of a novel bacterial secretion system which has evolved to transport these symbiosis mediating proteins. This system, termed the type eleven secretion system (T11SS), is present throughout the Gram negative phylum Proteobacteria, including many human pathogens such as Neisseria meningitidis, Acinetobacter baumanii, Haemophilus haemolyticus, and Proteus vulgaris. Furthermore, …

An Investigation Of Intrinsic And Extrinsic Factors That Influence Soil Microbial Succession During Human Decomposition, Allison R. Mason

Doctoral Dissertations

Decomposer organisms play a vital role in terrestrial nutrient cycling, breaking down complex organic compounds and providing nutrients for primary producers. Microbial communities and other decomposers associated with a vertebrate carcass, or the “necrobiome”, are critical for degradation and recycling of soft tissues following vertebrate mortality. The impact of microbial decomposers in vertebrate decomposition has been shown with regard to soil microbial communities, where the presence of soil microbes impact decomposition rate and undergo succession. However, current assessments of microbial ecology within decomposition-impacted soils have primarily focused on one aspect of microbial succession: succession of bacterial taxa for forensic applications. …

Enterobactin-Based Immune Interventions Against Gram-Negative Bacterial Infections, Huiwen Wang

Doctoral Dissertations

Enterobactin (Ent)-mediated iron acquisition is critical for many Gram-negative bacteria to survive in the host. Given the bacteriostatic effect of lipocalin-2 resulting from its potent Ent-binding ability, immune interventions directly targeting Ent is a promising antimicrobial strategy against Gram-negative bacterial infections. Moreover, hyperimmune egg yolk antibody is an emerging passive immune agent for the control of bacterial infections. Oral administration of anti-Ent egg yolk antibody may confer passive immune protection against Ent-dependent enteric pathogens. In this dissertation study, multidisciplinary approaches in conjunction with different model systems (in vitro, in vivo, and ex vivo) were used to …

Metabolism In The Colonocyte: Where Bacteria And Diet Meet, Bohye Park

Doctoral Dissertations

The host-microbiome interaction and the functions of microbial-derived metabolites, including butyrate, are important in colon health. Butyrate is the preferred energy source in colonocytes and has multiple physiological functions in the colon. A metabolic shift in colonocytes toward increased glucose utilization from butyrate oxidation is followed by several critical genetic modifications in cancerous colonocytes. Moreover, it has been suggested that the gut-microbiota composition is influenced by environmental factors, such as diets and the host's physiological status. Therefore, an understanding of the role of colonocyte metabolism toward impacting the host-microbiota commensal relationship would be an important step in understanding the functional …

Cat Covid, Cmv And Chemokines, Oh My!, Trevor Hancock

Doctoral Dissertations

Cytomegalovirus (CMV) is an important pathogen infecting most humans worldwide. CMV infection within immunocompromised individuals can cause severe morbidity and potential mortality. Disease during CMV infection is due to virus dissemination and subsequent inflammation. Host immune cells lie at the intersection potentially mediating both. The CMV-encoded viral chemokine vCXCL-1 is a proposed virulence factor in mouse models increasing immune cell recruitment and disease. However, the primary immune cell mediator is undetermined. To identify targets, Chapter 2 examines CXCR2 expression (receptor for vCXCL-1) among various mouse tissues and human peripheral blood under steady-state conditions. In vitro, isoforms of HCMV’s vCXCL-1 …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

The Spatial, Temporal, And Ecological Constraints Of Plant-Host Associated Microbial Communities, Jonathan Dickey

Doctoral Dissertations

With the development of next generation sequencing technology, ecologists have recently been able to describe microbial communities across a wide array of niches at an accelerated pace. De-novo-based patterns in richness and relative abundance have been described for bacterial and fungal communities in terrestrial, aquatic, and host-associated microhabitats. A recent synthesis has shown that these communities exhibit similar geographical patterns that have been traditionally described for plant and animals. Yet, there is a lack of hypothesis-based research for host-associated microbial communities. Throughout this dissertation, I will address how spatial scale, sequencing resolution, and manipulative rainfall exclusion govern host-associated microbial communities …

Making Sense Of Soil Microbiome Complexity For Plant And Ecosystem Function In A Changing World, Kendall K. Beals

Doctoral Dissertations

Soils contain the highest biodiversity on Earth. While the importance of the soil microbiome for larger-scale ecological phenomena such as nutrient and carbon cycling, plant growth and plant community dynamics is well-established, the fundamental question of the ecological and evolutionary function of this immense belowground microbial diversity for plant and ecosystem function still remains a great challenge in microbial ecology research. The objective of this dissertation is to understand how the importance of soil microbial community composition for plant and ecosystem function and how changes to soil microbial community composition from climate change-induced disturbance events, specifically fire, influence plant and …

Multi-Omic Systems Biological Analysis Of Host-Microbe Interactions, Piet Jones

Doctoral Dissertations

Systems biology offers the opportunity to understand the complex mechanisms of various biological phenomena. The wealth of data that is produced, at an increasing rate, provides the potential to meet this opportunity. Here we take an applied approach to integrate multiple omic level data sources in order to generate biologically relevant hypotheses. We apply a novel analysis pipeline to model both, in concert, the microbial and transcriptomic signature from COVID-19 positive patients. We show patients may suffer from an increased microbial burden, with an increased pathogen potential. Gene expression evidence further shows patients may exhibit a compromised barrier immunity, owing …

Response Of Soil Viral And Microbial Functional Diversity To Long-Term Agricultural Management In Jackson, West Tennessee, Ning Duan

Doctoral Dissertations

Soil microbial communities are a critical component for ecosystem stability and function. Viruses, as an important biotic controller, have the potential to regulate the abundance and diversity of bacterial communities through infection. Soil is known to harbor abundant and diverse viral assemblages but their ecological role and influence on microbial processes has not been fully elucidated. Microbes can be influenced by viruses not only from infection but though biogeochemical feedbacks of the “microbial (bacterium–phage–DOC) loop” or “viral shunt”. However, we know relatively little about the microbial community and function under the regulation of viruses in soil and how they respond …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

Determining The Ecological And Physiological Factors Contributing To The Competitive Success Of Prochlorococcus In The Oligotrophic Ocean, Benjamin C. Calfee

Doctoral Dissertations

Prochlorococcus is a genus of extremely successful marine cyanobacteria. This success is realized through its pervasive biogeographical range and presence in almost all open ocean environments where it usually it the dominant phytoplankton. Limited capabilities of culturing and genetic manipulation of this organism have resulted in assumptions about this success overwhelmingly based on field observations. These studies have assumed adaptations for resource uptake and utilization in nutrient limited environments to cause dominance of Prochlorococcus over other photosynthetic microbes. In an attempt to definitively explain this through laboratory culture, we developed a culturing system to assay questions of nutrient limitation effects …

Perturbing Fatty Acid Metabolism In Enterococcus Faecalis Disrupts Responses To Exogenous Fatty Acids And The Antibiotic Daptomycin, Rachel D. Johnston

Doctoral Dissertations

Enterococcus faecalis is an opportunistic pathogen. In the host, it is exposed to fatty acids which impact cellular physiology and induce tolerance to the antibiotic daptomycin. To determine the requirements for induction of daptomycin tolerance, I examined the impacts of blocking de novo fatty acid synthesis or protein synthesis and removing cell wall. I observed that removal of the cell wall induced daptomycin tolerance, indicating that peptidoglycan is necessary for daptomycin to function. As specific exogenous fatty acids induce protection against daptomycin in E. faecalis, I also opted to examine whether incorporation of these free fatty acids was necessary …

High Arctic Permafrost Microbial Characterizations: Siberian And Svalbard Microbiology Of Ancient And Active Layer Permafrost, Katie Sipes

Doctoral Dissertations

Permafrost is soil that has remained frozen for at least two years. The active layer is a surface portion above the permafrost that experiences seasonal thaw and refreezing. The environmental characteristics of permafrost and active layer are different but are directly related to each other. As the climate continues to warm, the active layer will expand into the permafrost and the continuously frozen soil will be subjected to seasonal thawing. The organisms that inhabit both the active layer and the permafrost soil will respond differently to the climate based on where in the soil they are present and the soil …

Regulation, Mechanism Of Action, And Function Of A Small Toxin Protein In Ehec, Bikash Bogati

Doctoral Dissertations

The zor-orz locus identified in the chromosome of Escherichia coli O157:H7 EDL933 is a type I toxin-antitoxin system that consists of two homologous gene pairs zorO-orzO and zorP-orzP. The zor genes encode for small toxin proteins and the orz genes encode for small RNAs. Previously it was shown that overproduction of ZorO results in cell growth stasis whereas co-expression of orzO rescues cellular growth. Within, I demonstrate that in addition to growth inhibition, ZorO overproduction results in membrane depolarization and ATP depletion but does not impact the gross morphology of E. coli. In vivo translation and subsequent impacts …

Insights Into Steinernema Carpocapsae-Xenorhabdus Nematophila Specificity And The Role Of Adult Nematode Colonization, Erin Mans

Doctoral Dissertations

The gut microbiota can provide the host with several benefits such as the production of secondary metabolites, essential amino acids, as well as the breakdown of food or protection from pathogens. The host in turn provides the microbiota with shelter and nutrients. Given the benefits that the host and microbiota receive from their association, humans and the microbiota have evolved mechanisms of selection and specificity to assure the proper symbionts colonize a host with high fidelity. Chapter two will explore mechanisms by which Xenorhabdus nematophila nematode intestinal localization (nil) genes interact with and adhere to the nematode intestinal …

Impacts Of Soil Management On Microbial Assemblages Involved In Nitrogen Transformations In Agroecosystems In Tennessee, Usa, Jialin Hu

Doctoral Dissertations

Nutrient reduction, particularly with respect to nitrogen (N) losses, is an important goal for sustainably managed agroecosystems. Soil N-cycling microbial populations that modulate these processes are affected by agricultural management regimes. This research focused on the controls and dynamics of the major N-cycling microbial populations in high-input cotton field under agricultural management regimes and low-input native C₄ forage grass systems under pasture management practices to determine the effects of management regimes on in situ seasonal dynamics of the functional microbes responsible for N fixation, nitrification, and denitrification processes. Molecular microbial ecology methods were combined with soil physicochemical properties and …

Applications Of Comparative Genomics And Data Science To Agricultural And Clinical Research, Katrina A. Schlum

Doctoral Dissertations

The advent of inexpensive, high-throughput whole genome sequencing (WGS) technologies has led to the generation of thousands of related genomes, even from a single study. Large-scale genome analysis has resulted in hypothesis-generating approaches in the fields of clinical, human and agriculture genomics. Additionally, population-level genomic sampling has resulted in a decrease in false positives in genotype-phenotype associations and an increase in understanding of the basis of disease, antibiotic and pesticide resistance. Deeper understanding of migration, genetic divergence and evolution has also been made possible due to WGS. This research applies comparative genomics, population genomics and data science approaches to whole …

Biotic And Abiotic Dehalogenation Of Halogenated Methanes: Trichlorofluoromethane, Dichlorodifluoromethane, And Tetrachloromethane, Briana M. Mcdowell

Doctoral Dissertations

Trichlorofluoromethane (CFC-11), dichlorofluoromethane (CFC-12), and tetrachloromethane (CT) are fully halogenated methanes that were produced as refrigerants in the early part of the 1900s and later used in many industrial processes. They are ozone-depleting agents and common groundwater contaminants. They are volatile chemicals that are moderately soluble in water. Due to their volatility when released to the environment, they are predominantly found in the atmosphere, though they also dissolve into the groundwater. In anaerobic environments, they can undergo dehalogenation reactions with several redox-active compounds. This dissertation presents results from two treatability studies from sites contaminated with CFC-11, CFC-12, and CT. Additionally, …

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 …