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 …

Considerations For The Use Of Mycorrhizal Fungi Inoculants In Coal Mine Reclamation And Reforestation In Appalachia: A Guide Of Best Practices And Management Recommendations, Cole Hansen Reistrup

Master's Projects and Capstones

Nearly all terrestrial plants form symbiotic relationships with mycorrhizal fungi. These beneficial soil microbes support plant health by increasing plants’ access to nutrients and water, protecting them from pathogens, improving soil properties, and more. A challenge to restoring forests on coal mined land in Appalachia is that mine soils are often degraded in a number of ways, including lacking mycorrhizal fungi, which makes mine soils difficult for trees to grow upon. Substantial improvements to coal mine reforestation success have been made since the development of the Forestry Reclamation Approach in 2005 that provides guidelines for how to create a suitable …

Changes And Relationships Of Soil Aluminum, Organic Matter, And Hydrogen Ion Concentration With Rye Cover Crop, Arron Wilder

Cal Poly Humboldt theses and projects

Soil acidity is a common agricultural problem worldwide, as approximately 50% of all potentially arable soils are affected by pH limitations. At soil pH 3+) is considered to be the chemical form of aluminum in acid soil that hinders plant growth the most. Potentially, soil organic matter (SOM) can ameliorate the toxic effects of Al³⁺ on plants and microbes by binding with Al³⁺, thus preventing Al³⁺ (and other species of aluminum) from interacting in the rhizosphere. Increasing SOM also increases soil health indicators (i.e., microbial activity, soil water holding capacity, aggregate stability, porosity, etc.) while the …

Application Of A 14c-Assay To Assess Methanotrophic Biodegradation Of Tce In Low Ph Groundwater, Evan Groome

All Theses

Current biological strategies for remediating trichloroethylene (TCE) in low pH aquifers (i.e., pH14C-TCE assay was developed to determine pseudo first-order rate constants for the degradation of TCE in microcosms containing soil and groundwater from the Boeing Michigan Aeronautical Research Center (BOMARC) superfund site, where the pH ranges from 4.1 to 4.9. The ¹⁴C-TCE assay was also adapted to calculate soil-normalized rate constants for data from this site, as well as data that Szwast²¹ collected from the Beltsville Agricultural Research Center (BARC). In addition to natural attenuation, biostimulation through amendments of methane and nutrients were also assessed. This treatment …

Genomic Analysis And Characterization Of Surface Properties Of Naphthalene Degrading Acinetobacter Isolates, Gunn Emilie Berge

<strong> Theses and Dissertations </strong>

No abstract provided.

Biomass Estimation Of Marine Biofilms On Plastic Surfaces, Kian Banihashemi, Fernando Javier Gil

Biological Sciences

Plastics have become a major source of marine pollution, which threatens food safety and quality, human health, and marine ecosystems. Due to the drastic negative effects of plastics in a marine environment, alternative biodegradable plastics are being generated that are more eco-friendly and have less environmental impact. Though some of these plastics are known to biodegrade, the process of degradation for bioplastics has not been heavily studied in a marine environment. This pilot project sought to both quantify the process of biodegradation and compare across different methods for effectiveness of biomass estimation, which serves as an indicator of biodegradation. Plastics …

Evaluating Soil Health Changes Following Cover Crop And No-Till Integration Into A Soybean (Glycine Max) Cropping System In The Mississippi Alluvial Valley, Alexandra Gwin Firth

Theses and Dissertations

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, …

Comparative Transcriptomic Study Between Cyanobacteria That Contain Chlorophyll D And Those That Lack Chlorophyll D, Fernanda Montoya

Honors Capstones

All cyanobacteria, which perform oxygenic photosynthesis on Earth, contain the photosynthetic pigment chlorophyll a (Chl a) that absorbs light in the violet and red region of the visible spectrum. Cyanobacteria of the Acaryochloris species, however, contain the rare photosynthetic pigment chlorophyll d (Chl d) that absorbs light in the far-red region. Chl d’s ability to absorb light in this region allows it to avoid competing with other photosynthetic organisms for light. Creating a photosystem that uses Chl d in plants would be of great use for agricultural land optimization, but requires knowledge of the biosynthetic pathways of …

Using A Machine Learning Model To Predict Plant Inflorescences Based Upon Its Soil Microbiome, Luke Denoncourt

Undergraduate Honors Theses

The UN estimates that the global population could reach 9.7 billion by 2050 (United Nations). As a result, the amount of food required to feed humanity is thought to double by 2050 (Ray et al., 2012). Humanity must find a way to increase crop production without increasing fertilizer usage and eutrophication, which can be done using the soil microbiome. Using potted plants with soils inoculated with Pseudomonas alcaligenes, Pseudomonas denitrificans, Bacillus polymyxa, and Mycobacterium phlei, both the shoot and root growth of pea and cotton plants was significantly increased (Egamberdieva & Höflich, 2004). In this study, utilizing a random forest …

Analysis Of Edna To Assess Effects Of Water Quality On Freshwater Fungal Diversity In A Virginia Coastal Watershed, Lauren French

Undergraduate Honors Theses

Freshwater fungi comprise a phylogenetically and functionally diverse group which contributes to wide-ranging ecosystem processes in aquatic systems. Saprotrophic fungi convert detritus into nutrient-rich food sources for fish and invertebrates, whereas pathogenic and parasitic fungi can cause disease and population declines of other aquatic organisms. With their diverse and important roles, changes in freshwater fungal community structure may have far-reaching impacts on ecosystems. To understand how natural and anthropogenic stressors to freshwater systems impact fungal-mediated ecosystem processes, a greater understanding of the taxonomic and functional composition of freshwater fungal communities is needed. We assessed relationships among freshwater habitat types, water …

Development Of A Methodology For The Quantification Of Reaerosolization Of A Biological Contaminant Surrogate Particle From Military Uniform Fabric, George D. Cooksey

Theses and Dissertations

During a mass casualty medical evacuation after a bioaerosol attack, a decontamination method is needed that is effective at both decontamination and preventing the secondary hazard of biological particles reaerosolizing from contaminated clothing. However, neither the efficacy of current decontamination methods nor the risk of biological particle reaerosolization is significantly explored in existing literature. The goals of this thesis were to develop a repeatable methodology to quantify the reaerosolization of a biological contaminate off Airman Battle Uniform (ABU) fabric swatches, and to test the efficacy of one decontamination method (high-volume, low-pressure water) using 1 mpolystyrene latex (PSL) spheres as a …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

The Influence Of Hydrogen Peroxide On The Enrichment Of Fe(Iii) Reducing Bacteria From Acid Mine Drainage, Susami Seth

Williams Honors College, Honors Research Projects

It is hypothesized that the ocean of Europa, a Jupiter moon, hosts bacteria on its oceanic floor. Understanding how Fe(III) reducing bacteria (FeRB) from AMD utilize organic materials within its surrounding environment outlines how FeRB could thrive and tolerate extreme conditions. FeRB are known to tolerate metals and highly reactive oxidants species (ROS), but in this experiment, H₂O₂ was the experimental factor to further test FeRB tolerance. H₂O₂ is a common ROS and is damaging to living material such as proteins, DNA, and RNA. A range of H₂O₂ concentrations were fed …

The Effects Of Hydrologic Heterogeneity On Harmful Algal Blooms In Freshwater Reservoir, Lake Sinclair, Georgia, Margaret Blackledge

Biology Theses

Aquatic habitats are frequently studied after a major water quality problem like the occurrence of an algal bloom. In this study, A proactive rather than a reactive response was considered, where the complexity of conditions conducive to uncontrolled cell growth were studied before a bloom took place by sampling regularly. This study aimed to monitor water quality by monthly sampling of algal communities for approximately one year. As the base of the aquatic food web, algae are a highly diverse group of organisms with varying sensitivity to physical and chemical changes in the environment. Four shallow sites were monitored at …

Investigation Into Bacterial Impairment Of Greene And Polk County Water Systems, John C. Kincaid

MSU Graduate Theses

Bacterial impairment of water systems is a major issue facing mankind. Bacteria that are introduced into a system have the potential to cause harmful diseases to wildlife and humans. In Greene and Polk counties, many water systems have become bacterially impaired over the years. Despite this, little is known about the contamination of known harmful bacteria in this region. To address this issue, I investigated the presence of known human pathogens across water systems in these two counties, many of which have displayed high levels of E. coli and fecal indicator microorganisms over many years. I used a high-throughput sequencing …

Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells

Master's Theses

The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …

Investigation Of Shocked Basalts From Vargeão Dome And Vista Alegre: Implications For The Search For Life On Mars, Nikol Posnov

Electronic Thesis and Dissertation Repository

Impact craters represent excellent astrobiological targets for planetary exploration missions to Mars. The impact of an asteroid or comet into a crystalline, H₂O-bearing target may result in development of a hydrothermal system and increase the habitability of the substrate for the colonization of endolithic microorganisms. Given that Mars’ surface is covered by cratered basaltic rock, this study investigated target rocks and impact breccias from Vargeão Dome and Vista Alegre impact structures that formed in basalt in the Paraná Basin of Brazil.

Utilizing petrography and micro-X-ray diffraction (μXRD), the degree of shock metamorphism in plagioclase was quantitively determined. Measuring …

Fungi Associated With Herbaceous Plants In Coastal Northern California, Greg Huffman

Natural Sciences and Mathematics | Biological Sciences Master's Theses

The presence of fungal species associated with herbaceous plants was monitored in coastal Marin County, California, USA. The research involved a combination of field sampling surveys and data collection using a stratified random design, pathogen identification through microbiological and molecular analysis, and descriptive analysis and ordination of results. A total of two years of repeated sampling (four times a year) was organized to allow for the detection of seasonal differences in pathogen presence on aerial plant parts. The objective of this study was to identify microbial species present on herbaceous plants using ITS1 sequence analysis. Throughout March of 2018 to …

Physiological Constraints, Mechanisms, And Mineral Transformations Of Iron Reduction In Hyperthermophilic Crenarchaea, Srishti Kashyap

Doctoral Dissertations

Dissimilatory iron reduction by hyperthermophilic archaea occurs in many geothermal environments and typically relies on microbe-mineral interactions that transform various iron oxide minerals. However, the kinds of iron oxides that can be used, growth rates, extent of iron reduction, and the mineral transformations that occur due to this metabolism are poorly understood. This dissertation improves our fundamental understanding of the physiological mechanisms and mineral transformations of hyperthermophilic iron reduction using two model crenarchaea, Pyrodictium delaneyi and Pyrobaculum islandicum. Using growth yields and metabolite production rates, we demonstrated that a broad range of Fe(III) (oxyhydr)oxides of variable thermodynamic stability was …

Possibilities & Potential Of Perennial Wheat: A Comparison Of Arbuscular Mycorrhizal Fungi Diversity And Abundance Between Winter Wheat And Kernza, Tess Noble Strohm

Senior Projects Spring 2021

In an effort to harness the benefits of perenniality on soil health, a perennial wheatgrass called Kernza (Thinopyrum intermedium) has been developed for commercial use at the Land Institute in Salina, Kansas. The effects of a cultivar of Kernza intended for the Hudson Valley, NY were examined in this study using Arbuscular Mycorrhizal fungi (AMF) as an indicator of soil health. AMF are an obligate symbiotic fungi known to provide physical and biological benefits to soil and plant systems. Fields containing one and four year old Kernza, as well as a field of an annual winter wheat were sampled to …

Comparing Capabilities Of Shewanella Oneidensis Mr-1 And The Microbial Community Of Iron Caves To Reduce Fe(Iii), Aaron Douglas Pham

Williams Honors College, Honors Research Projects

Caves are generally formed by the erosion and/or dissolution of rock and its subsequent removal by water. Iron ore caves (IOCs) form despite being hosted by relatively insoluble and weathering-resistant rock. Due to the discovery of a microbial community behind the walls of these caves, it was hypothesized that these bacteria could be responsible for speleogenesis. Iron ore exists in an oxidized (Fe(III)) state, but reduced (Fe(II)) form is soluble. It was further reasoned that the bacteria might be able to reduce Fe(III) through direct metabolic activity, which uses iron as an electron acceptor. Here we show that cave microorganisms …

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. …

Using Soil Geospatial Properties And Environments To Explore Microbial Diversity, Sharon Faye Smith

Graduate Theses and Dissertations

Soil microorganisms help maintain nutrient cycling, control carbon sequestration, impact plant productivity, and influence several soil chemical and physical properties; yet, the processes that control the microbial composition of soil and how environmental changes may affect the composition and activity of these organisms at different scales remains a difficult and intriguing puzzle for soil scientists, ecologists, and modelers. Wetlands are endangered and important ecosystems that provide several services, which are directly linked to soil function. However, few wetland assessments consider the soil environment and microbial ecology. Linking soil microbial community composition and distribution patterns to soil physio-chemical properties would provide …

Analysis Of Biofilm Remediation Capacity For Octenyl Succinic Anhydride (Osa), A Bioactive Food Starch Modifier Compound, Matthew R. Borglin

Master's Theses

Matthew R. Borglin

This thesis demonstrates efficacy of Octenyl Succinic Anhydride (OSA), as a biofilm sanitizer. Biofilms allow bacteria to adhere to solid surfaces with the use of excreted polymeric compounds. For example, surfaces found in food production or processing facilities such as the interior of a raw milk holding tank, are some of the most susceptible to biofilm contamination. When present, biofilms can cause a variety of negative effects, which include; reduction of product shelf life, corrosion, and outbreaks of foodborne illnesses. The close association of biofilms with the majority of foodborne illness cases led the US Environmental Protection …

Effects Of Warming On Decomposition Of Submerged Plant Litter And Associated Microorganisms In Streamside Channels, Kaity Ackerman

Electronic Theses and Dissertations

Surface air temperatures are predicted to increase in the near future, which will likely affect microbial activity and carbon flow in stream ecosystems. I performed an experiment in streamside channels at Coweeta Hydrological Laboratory, NC to assess responses of litter-associated microorganisms to moderate increases in water temperature (5 levels, ambient to +4°C). The objectives of the experiment were to determine: (1) if there are differences in the magnitude of responses to temperature among various microbial parameters and (2) whether microbial responses to temperature vary among plant litter of different carbon quality. Thus, I measured litter decomposition rate, fungal biomass (ergosterol), …

Effects Of Light, Nutrients, And Salts On Microbial Biofilm Productivity And Detrital Processing In Aquatic Mesocosms, Bethanie Brooke Howard-Parker

Graduate Theses and Dissertations

Anthropogenic activities associated with urbanization, agriculture, and resource extraction continue to increase to support increasing needs of the growing population. These activities increase the amounts of pollutants entering freshwater streams and put aquatic ecosystems at structural and functional risk. Aquatic microbes play an important role in detrital processing in streams as a key linkage in moving carbon from detrital stocks into aquatic food webs. My research investigates the effects of light, nutrients, and salts on detrital microbes and decomposition in freshwaters using a mesocosm approach. In chapter one, I modified a current priming effect (PE) hypothesis model to include light …