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. …

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 …

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 …

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. …

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 …

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 …

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 …

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 …

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, …

Soil Moisture Sensitivity Of Microbial Processing Of Soil Organic Carbon, Shikha Singh

Doctoral Dissertations

Soil organic carbon (SOC) is the largest terrestrial C pool and understanding SOC decomposition in response to environmental factors is critical for accurate predictions of climatic change. Soil moisture is one of the most important, yet less explored, environmental factors controlling soil microbial respiration. The relationship between soil moisture and respiration also varies with soil texture. Currently, it is difficult to predict feedbacks to climatic changes from changes in soil moisture, as most earth system models lack site-specific, experimentally-derived parameters to represent soil moisture-texture-respiration relationships. The overarching goals of this dissertation are to gain a fundamental understanding of the interactive …

More Than The Sum Of Their Parts: Building A Framework For Understanding Host-Microbe Interactions In Medicago Sativa, Katherine Mackenzie Moccia

Doctoral Dissertations

This dissertation seeks to understand plant-microbe interactions in the agriculturally relevant plant Medicago sativa from three distinct vantage points within microbiology. Within the plant microbiome, we examine how primer usage and the application of peptide nucleic acids impacts 16S and 18S rRNA gene sequencing. In doing so, we design a novel peptide nucleic acid, PNA, and test its impact using multiple primers and sequencing protocols. Once microbial sequencing methodology is established, we generate a synthetic consortium of bacterial isolates from M. sativa leaves and modulate nitrogen levels to better understand microbial structure. Drop out communities, where we remove one member …

Extracting Detailed Metabolic Information And Connections From Mammalian Gut Microbiomes Via Metaproteomics, Jose A. Blakeley-Ruiz

Doctoral Dissertations

A diverse community of bacteria populates the mammalian gastrointestinal tract. These populations exist in a balance with the host assisting with key functions, particularly metabolism of intractable fibers and immune modulation. Disruption of this balance can lead to diseases such as infection, inflammatory bowel syndrome, and obesity. Common symptoms include chronic pain, chronic inflammation, and altered metabolism. Several taxonomic classifications of bacteria have been associated with these diseases, but Recent studies have indicated that these finding are not always statistically valid. An explanation for this is that microbial communities between individuals and even across time can vary substantially even when …

Root Phosphomonoesterase As A Vital Component Of Increasing Phosphorus Availability In Tropical Forests, Kristine Grace Manno Cabugao

Doctoral Dissertations

Tropical forests, relative to other terrestrial ecosystems, exchange the largest amount of carbon with the atmosphere and also constitute a significant carbon sink. However, nutrient limitation, particularly of phosphorus (P), could limit growth of tropical forests and their function with the global carbon cycle. Thus, understanding root mechanisms to acquire P is necessary to representing the P cycle and corresponding interactions with plant growth. A large portion of total soil P in tropical forests occurs in organic forms, only accessible through root and microbial production of phosphatase enzymes. These phosphatase enzymes mineralize organic P into orthophosphate, the form of P …

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 …

Theoretical And Quantitative Methods Connecting Characterizing Micoribal Metabolism Diversity: Implciations From Phylogenetics, Community Diversity, And Organic Geochemistry, Taylor Royalty

Doctoral Dissertations

Biogeochemistry is controlled by microorganisms obtaining nutrients and energy. Thus, microbial metabolisms directly link microbial ecology and geochemistry. The extent that microbial ecology and geochemistry microbial ecology and geochemistry affects the other requires constraint on the spatiotemporal distribution and abundance of microbial metabolisms with respect to geochemistry, or the microbial niches. Elucidating microbial metabolisms was challenging prior to the advent of ‘omics sequencing technologies, as most microbial lineages lack cultured representatives. Although revolutionizing microbial ecology, challenges still exist in fully leveraging information derived from ‘omics technologies. This dissertation attempts to address a small subset of these challenges that include quantifying …

Needles In A Haystack Of Protein Diversity: Interrogation Of Complex Biological Samples Through Specialized Strategies In Bottom-Up Proteomics Uncover Peptides Of Interest For Diverse Applications, Manuel I. Villalobos Solis

Doctoral Dissertations

Peptide identification is at the core of bottom-up proteomics measurements. However, even with state-of the-art mass spectrometric instrumentation, peptide level information is still lost or missing in these types of experiments. Reasons behind missing peptide identifications in bottom-up proteomics include variable peptide ionization efficiencies, ion suppression effects, as well as the occurrence of chimeric spectra that can lower the efficacy of database search strategies. Peptides derived from naturally abundant proteins in a biological system also have better chances of being identified in comparison to the ones produced from less abundant proteins, at least in regular discovery-based proteomics experiments. This dissertation …

From Genes To Ecosystems: Resource Availability And Dna Methylation Drive The Diversity And Abundance Of Restriction Modification Systems In Prokaryotes, Spiridon E. Papoulis

Doctoral Dissertations

Together, prokaryotic hosts and their viruses numerically dominate the planet and are engaged in an eternal struggle of hosts evading viral predation and viruses overcoming defensive mechanisms employed by their hosts. Prokaryotic hosts have been found to carry several viral defense systems in recent years with Restriction Modification systems (RMs) were the first discovered in the 1950s. While we have biochemically elucidated many of these systems in the last 70 years, we still struggle to understand what drives their gain and loss in prokaryotic genomes. In this work, we take a computational approach to understand the underlying evolutionary drivers of …

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …

Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins

Doctoral Dissertations

Nitrous oxide (N₂O) is a gas responsible for significant ozone layer depletion and contributes to greenhouse effects in Earth’s atmosphere. N₂O is primarily generated by denitrification, whereby nitrate (NO_3-) or nitrite (NO_2-) is converted to gaseous N₂O or N2. Teragram quantities of N₂O are emitted annually from agricultural soils treated with nitrogenous fertilizers due to the activity of soil microbiota. Although bacteria and fungi harbor genes permitting denitrification, fungi lack NosZ, an enzyme responsible for reducing N₂O into inert N2 gas. Historically, scientists have linked fungi …

Managing Exoelectrogenic Microbial Community Development Through Bioprocess Control For Conversion Of Biomass-Derived Streams, Alex James Lewis

Doctoral Dissertations

Bioelectrochemical systems are an emerging technology capable of utilizing aqueous waste streams generated during biomass conversion of lignocellulosic feedstocks to produce valuable co-products and thus, have potential to be integrated into biorefineries. In a microbial electrolysis cell, organic compounds are converted to electrons, protons, and CO₂ by fermentative and exoelectrogenic bacteria in the anode compartment. By having the ability to extract electrons from waste streams, these systems can treat water while also producing hydrogen, and thus can improve the efficiency of biomass to fuel production by minimizing external hydrogen requirement and enabling water recycle. The overall goal of this …

Ecological And Evolutionary Dynamics Of Plant-Soil Feedbacks: Influences On Evolution And Range Dynamics, Michael E. Van Nuland

Doctoral Dissertations

Plants interact with, modify, and are affected by their soil environments. Though plant-soil interactions are well known to be important and active regulators of ecosystem function and community structure, much less is known about how these interactions affect plant evolution. The primary goal of my dissertation was to examine plant-soil interactions under a range of ecological and evolutionary contexts to better understand patterns of biodiversity, ecosystem function, and whole system responses to environmental change. Taking such an eco-evolutionary perspective allows for a holistic understanding of the causes and consequences of complex abiotic and biotic interactions that link ecosystem ecology and …

The Microbial Ecology Of Bacterial Lignocellulosic Degradation In The Ocean, Hannah Laing Yee Woo

Doctoral Dissertations

The overarching theme of my dissertation is to study the role of bacteria in lignocellulose degradation. In recent years, more research has investigated the biodegradability of lignocellulose for biofuel production. The components of the lignocellulosic plant cell wall are considered intrinsically recalcitrant due to their structure. However, we hypothesize that these components are not intrinsically recalcitrant but their biodegradation is contingent on the environmental conditions, particularly the bacterial diversity. We believe bacteria will become especially important in lignocellulose degradation in conditions that are unfavorable for white-rot fungi. Therefore, we investigated the potential for lignin degradation by bacteria in the ocean …