Microbiology Commons^™

Evaluating The Role Of The Bovine Vaginal Microbiome In Neonatal And Maternal Health Outcomes, Riley D. Messman

Theses and Dissertations

The dam vaginal microbiota is the first major microbial inoculating community within the neonate. The composition of the dam vaginal microbiota has implications in calf commensal microbiota development. Alterations of the dam microbial community prior to parturition could alter inoculating communities and immune responses in both the dam and calf. Thus, authors aimed to elucidate the microbial community composition of the bovine dam vaginal and calf nasal microbiota post-partum after utilizing betadine lavages (BL). The dam vaginal and calf nasal microbial communities and immune responses were evaluated at 0-, 15-, 30- and 60-day post-partum. Microbiota composition of the dam haircoat, …

Effect Of Authentic Kefir And Nigella Sativa On Broilers Challenged By Coccidia And Clostridium Perfringens, Julian E. Nixon

All Dissertations

Black seed oil concentrations of 0%, 0.1%, 1% and 5% were added to milk inoculated with kefir grains and incubated at 25°C for 22 h. The pH and microbial count indicated 1% black seed oil caused low inhibition (P > 0.05) of fermentation, but 5% black seed oil caused significant inhibition of the kefir microorganisms (P < 0.05).

Cobb 500 male chicks (n = 256) were distributed in a randomized block design and received one of four treatments: CTRL1 (Non-medicated, no kefir, no Clostridium perfringens), CTRL2 (Non-medicated, no kefir, C. perfringens inoculated), CTRL3 (BMD medicated, no kefir, C. perfringens inoculated), KTRT (Non-medicated, …

Sympatric Soil Microbe Interactions Between Streptomyces And Fusarium Isolates, Lehren A. Olk-Szost

All NMU Master's Theses

Interkingdom interactions between soil bacteria and fungi may play a critical role in occurrence of disease suppressive soils, yet our understanding of these interactions remains limited. Streptomyces are well-known producers of antimicrobial compounds important to medicine and agriculture. Production of these secondary metabolites is often mediated by quorum sensing. Most Streptomyces research occurs in single species experiments, yet new metabolites have been discovered in interspecies co-culture experiments. Interspecies, intergenic, and interkingdom co-culture research will likely reveal many valuable compounds, and strengthen our understanding of complex ecological interactions in soil microbiomes. Interactions between sympatric Streptomyces and Fusarium isolates from disease suppressive …

Evaluación De Bacterias Con Potencial En La Promoción Del Crecimiento Vegetal En Agraz Silvestre Vaccinium Meridionale Swartz, Angie Sofia Barbosa Romero

Biología

El agraz (Vaccinium meridionale) es una planta promisoria con un fruto de gran aceptación en los mercados locales e internacionales por su alto valor en antioxidantes, antocianinas, vitaminas, y su amplia utilización gastronómica. Sin embargo, existen dificultades a la hora de establecer cultivos, las cuales están asociadas principalmente con la germinación de las semillas. Debido a que las bacterias promotoras de crecimiento vegetal son una alternativa sostenible para el manejo agrícola, con varios beneficios para la planta-bacteria. Como la fijación de nitrógeno y la producción de fitohormonas, el objetivo de esta investigación fue evaluar el efecto de bacterias con potencial …

Distribution Patterns Of Allorhizobium Vitis In Missouri Vineyards And Non-Vineyard Soils, Jacquelyn M. Wray

MSU Graduate Theses

Crown gall disease causes significant economic loss to the grape and wine industry. Preventive strategies are most effective for mitigating the loss of grapevines in vineyards, as there is no known cure for this disease. The bacterium Allorhizobium vitis carrying a tumor-inducing (Ti) plasmid is the causative agent. A. vitis bacteria live systemically in the grapevine before causing visible symptoms and can survive in residual plant tissues and soil for more than two years. Diagnostic methods have been developed to detect A. vitis bacteria in grapevines and soil. However, more reliable, specific, and high-throughput diagnostics are still needed for screening …

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 …

Mechanisms For High Light Tolerance In A Fast-Growing Cyanobacterium, Patricia Walker

Arts & Sciences Electronic Theses and Dissertations

Through oxygenic photosynthesis, cyanobacteria, algae, and plants convert light into chemical energy. However, highly energetic light often damages the photosynthetic apparatus, which can lead to the decline of photosynthetic activity (photoinhibition), and prolonged photoinhibition can lead to cell death. Cyanobacteria enact various protective mechanisms to mitigate photodamage, many of which have been conserved in plants. Repair of PSII reaction centers, decreased light absorption, quenching of excess absorbed energy, and biosynthesis of antioxidants all work to mitigate damage during high light. Due to the adjustments to photosynthesis, acclimation to high light requires remodeling of cellular metabolism and physiology. Therefore, phototrophs have …

Metagenomic Analysis Of Root-Associated Microbiome Of Healthy And Taproot Decline-Affected Soybeans And Identification Of Healthy Soybean Root Endophytes With Protective Activity Against The Causal Agent, Xylaria Necrophora, Uyen Wesser

Theses and Dissertations

Plant roots are associated with a diverse microbial community of bacteria and fungi. The root microbiome communities associate with the root surface or penetrate the superficial layers of root tissues. It is of high agronomic interest to characterize root microbiomes and identify microbes with beneficial effects on plant defense against pathogens. Soybean taproot decline (TRD) is an emerging soil-borne disease caused by a fungus classified as Xylaria necrophora, challenging to control and with devastating effects on yield. Our group has initiated a study of the soybean root microbiome with three primary experiments: (I) perform a comparative study of root …

Evaluation Of Novel Litter Amendments For Use In The Commercial Broiler Industry, Jorge A. Urrutia

Theses and Dissertations

Poultry litter amendments (LA) are commonly used to maintain good litter quality; the most common ones; are acidifiers. However, concern over the lifespan of LA acidifiers (d) and corrosive nature revealed a need for alternative LA. Products of interest include biochar (BC), superabsorbent polymers (SAPs), and alum mud (AM). Experiment 1 was a screening study (n=17 treatments, no birds) conducted to determine the optimal application rate/method of BC, SAPs, and AM vs.commercial LA and a control. Most SAPs treatments measured metrics may be similar (i.e., bacteria, water activity) or better (pH) vs. commercial LA (PLT). High inclusions of novel LA …

Weaving An Interdisciplinary Microbiome Career Using Threads From Different Ecosystems, Sarah Hosler

Electronic Theses and Dissertations

Animals have trillions of microorganisms living in or on many body sites, these communities of microorganisms are called microbiomes. Microbiomes are typically host-specific, and a lot of information about the host can be determined from investigating them. Microbiome research has many real-world applications, and this thesis utilizes the One Health perspective, which acknowledges the connection of humans, animals, and environments, and emphasizes the need for collaborative, interdisciplinary research. The first interdisciplinary project is an investigation into the bacteria in wild and cultured Atlantic deep-sea scallop, Placopecten magellanicus larvae. Adults in hatcheries can be induced to spawn, but the last two …

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, …

Effect Of Mycorrhizae Inoculation On The Growth And Success Of Three Taxodium Distichum Hybrids In Saline - Impacted Coastal Soils, Elif Ilhan

Electronic Theses and Dissertations

In 2008, Galveston Island was severely impacted by Hurricane Ike, resulting in high salt deposition in the soil and groundwater. This caused a loss of many native plant species. A study was initiated to determine effective ways to promote the growth conditions of three bald cypress genotypes (Taxodium distichum var distichum and Taxodium distichum var mexicanum crosses) in salt-affected soils. The treatments applied were mycorrhizae inoculation, fertilizer application, and a combination of mycorrhizae inoculation and fertilizer application. A total of sixty (60) trees planted in plots of three rows and divided into five randomized replication blocks of four treatments …

Screening For Binding Partners And Protein-Protein Interactions Of A Fungal Transcription Factor- Xdr1, Nishadi Punsara Gallala Gamage

Masters Theses

Clarireedia spp. (formerly Sclerotinia homoeocarpaF.T. Bennett) is the causal agent dollar spot, the most economically important turfgrass disease impacting golf courses in North America. The most effective strategy for dollar spot control is repeated application of multiple classes of fungicides. However, reliance on chemical application has led to resistance to four classes of fungicides as well as multidrug resistance (MDR). Fungi are known to detoxify xenobiotics, like fungicides, through transcriptional regulation of three detoxification phases: modification, conjugation and secretion. Little is known, however, of the protein-protein interactions that facilitate these pathways. Following next-generation RNA sequencing of Clarireedia spp., a …

Community Assembly And Stress Response Of Grassland Phyllosphere Bacteria, Emily Bechtold

Doctoral Dissertations

Grasslands are an important ecosystem with potential to help stabilize food security and reduce greenhouse gas levels. As global temperatures rise, weather patterns are predicted to drastically change. The resulting increase in intensity, duration, and frequency of drought in important grassland areas will not only affect agricultural production, but also increase grassland susceptibility to fire, disease, and soil erosion. Thus, developing ways to sustainably promote grassland health and production is essential to increase food security and reduce environmental strain. Microbes in the phyllosphere, or aerial surface of plants, promote host fitness through phytohormone and nutrient production, increased stress tolerance, and …

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 …

Evaluating The Effects Of Pine And Miscanthus Biochar On Water Activity And Escherichia Coli Populations In Commercial Broiler Litter, Christopher Austin Marty

Theses and Dissertations

The decrease in subtherapeutic antibiotic administration in poultry has increased the need to address production challenges caused by pathogens, such as E. coli. One potential way to improve bird health and reduce bacterial infection is through the addition of litter amendments that absorb moisture. Biochar (BC) has previously been shown to increase water holding capacity in poultry litter, but its effects on E. coli mitigation are unknown. The objectives of this research were to 1) evaluate water activity of poultry litter amended with pine and miscanthus BC, and 2) determine the effects of different BC inclusion rates on litter …

Developing A Toolbox To Engineer Quantitative Trait Variation In Legume Species Using Crispr/Cas Technologies., Petar Miletic

Electronic Thesis and Dissertation Repository

The impact of intensive agriculture on the environment is immense. This is especially dire with regard to the natural nitrogen (N) cycle, where the human driven interference, primarily associated with industrial fertilization, has reached unsustainable levels. Unlike cereals, legumes, such as soybean, alfalfa and common bean, have the ability to use atmospheric nitrogen, which limits the need for industrial fertilization. A more wide-spread use of legumes could alleviate some of the negative impacts on the biogeochemical cycle while also providing a useful alternative to meat consumption, an important factor in sustainability. To reach this goal, further improvements of legume crops …

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 …

Effectiveness Of Pathogen-Specific Passive Antibodies To Mitigate Infectious Diseases In Apis Mellifera, Tanner Nordseth

Honors Thesis

Honeybees (Apis mellifera) are widely recognized as a vital part of the global ecosystem and the world's food supply due to their pivotal role in the pollination of both natural and agricultural flora. Colony Collapse Disorder (CCD) is an emerging phenomenon characterized by a colony's worker bees deserting the hive and leaving the queen behind. This usually results in colony failure. CCD is a multifactorial issue, with many environmental stressors and pathogens playing a role. Deformed Wing Virus (DWV) has been identified as a leading cause in this phenomenon. Paenibacillus larvae (P. larvae) is another lethal pathogen that is …

Characterization Of The Rumen Bacterial Communities Of Bison Heifers Fed A Grass-Based Diet Vs A Grain-Based Free-Choice Diet, Anlly Miley Fresno Rueda

Electronic Theses and Dissertations

A century ago, the North American grasslands and prairie ecosystems were dominated by bison. At least 30 million bison roamed the Great Plains when the first explorers arrived. By 1900, there were little over a thousand bison remained in the United States and Canada. Recovery efforts has been made since the 20th century to reestablish the herds and increase the bison population. Today, over 500,000 bison are distributed across North America, with more than 90% of the existing bison population under commercial production. Modern conservation strategies are made via the collaborative efforts of conservationist, producers, and researchers, resulting in increased …

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 …

Roles Of Non-Frankia Bacteria In Root Nodule Formation And Function In Alnus Sp., Kelsey Christine Mercurio

Honors Theses and Capstones

Plant roots are home to a wide variety of beneficial microbes; understanding and optimizing plant-microbe interactions may be critical to enhance global food security in a sustainable, equitable way. With the help of their nitrogen-fixing bacterial partner, Frankia, actinorhizal plants form symbiotic root nodules and play important roles in agroforestry and land reclamation. However, Frankia does not live alone in nodules, and the other microbial residents may contribute to nodule formation and function. We collected root nodules from alder trees (Alnus sp.) in 2018 and 2019, then isolated DNA and individual bacterial strains to characterize the nodule microbial …

Phytophthora Capsici In Tennessee: Fungicide Resistance, Population Genetics And Cultural Control, Timothy Brent Siegenthaler

Masters Theses

Phytophthora capsici, a plant pathogenic oomycete, is the causal agent of the vegetable disease Phytophthora blight of pepper and cucurbits. Since the identification of P. capsici in 1922, a significant amount of research has been conducted to understand its biology and disease management. Despite this, little research had been conducted on this species in the state of Tennessee. Three studies were done from 2018 to 2020, focusing on fungicide resistance, population genetics, and testing management strategies in the field. In 2018 and 2019 a total of 248 isolate of P. capsici were collected from five counties in Tennessee. These isolates …

Investigating The Potential Of Microbial Metabolites And Mtor Signaling On Chicken Necrotic Enteritis, Mohit Bansal

Graduate Theses and Dissertations

Necrotic enteritis (NE), caused by C. perfringens and coccidiosis, is responsible for substantial economic loss annually. In the first chapter, we investigated the effect of secondary bile acid on necrotic enteritis. Day-old broiler chicks were randomly assigned to 5 groups of diets supplemented with 0 (basal diet), 0.8, 1.0, and 1.5 g/kg (on top of basal diet) deoxycholic acid (DCA). The birds were challenged with Eimeria maxima (20,000 oocysts/bird) at d 18 and C. perfringens (109CFU/bird/day) at d 23 and d 24 to induce NE. Birds were sacrificed at d 26, and ileal tissue and digesta samples were collected. DCA …

Optimization Of In-Vessel Food Waste Composting: Enzyme Activity And Microbial Dynamics, Ayawovi Selom Ametepe

Graduate Theses and Dissertations

A series of greenhouse-based, rotary-drum bioreactor experiments was designed to study microbial dynamics and enzyme activity during optimization of food waste composting. This work aims to optimize food waste composting by defining the best food waste-to-bulking agent proportion controlling conditions and by evaluating the food waste composting process when inoculated by a bacterial inoculant product compared to uninoculated compost. Three experiments were run in total. The two first experiments were conducted for 48 days with sampling at each step of composting, while the third experiment last 50 days and included one extra sampling date. In the first experiment, 50:50, 65:35 …

Molecular Identification And Characterization Of Viral Pathogens Infecting Sweet Cherry, Aaron J. Simkovich

Electronic Thesis and Dissertation Repository

Stone fruits are a valuable crop grown worldwide, however pathogens such as viruses threaten fruit production by reducing tree health and fruit yield. In an orchard within the Niagara region of Ontario, symptoms typical of viral infection such as chlorosis and leaf deformation were seen on sweet cherry (Prunus avium L.) trees. Next generation sequencing was performed on symptomatic and asymptomatic leaves and four viruses were identified. On the tree displaying the most severe symptoms, Prune dwarf virus (PDV), was the only virus detected. A survey conducted during this work showed 42% of cherry trees on a single …

Does Circularizing Source-Separated Food Waste Present A Risk To Our Food?, Astha Thakali

Electronic Theses and Dissertations

About a third of the food produced annually is wasted. Food waste recycling can be a way to close the loop and attain a more sustainable food system, however, the system must be carefully monitored and managed to avoid the introduction and build-up of contaminants. To study the potential presence of contaminants in food waste, source-separated food waste was collected and screened for five classes of contaminants (physical contaminants, heavy metals, halogenated organic contaminants, pathogens, and antibiotic resistance genes) from two separate regulatory environments (voluntary vs mandated food separation). The regulatory environment did not affect the level of contamination, except …

The Effects Of An Applied Phyllosphere-Microbiome On Gas Exchange And Growth Of Soybean Infected With Pseudomonas Syringae: Harnessing The Power Of The Microbiome, Charles Agbavor

MSU Graduate Theses

The microbiome is an important determinant of plant health, growth and resistance to stress. This study was conducted to determine the efficacy of the phyllosphere-microbiome on managing Pseudomonas syringae pv. Glycinea (Psg), gas exchange and growth of Glycine max L. Merrill. A greenhouse study was conducted in the summer of 2019. A field isolated and cultured soybean phyllosphere-microbiome was applied to purposely infected and uninfected soybean. Gas exchange, Psg density, chlorophyll concentrations, and percent nitrogen and carbon in the leaves were measured during the V3-V6 stages of soybean. Not surprisingly, there was a two-fold reduction in copies of Pseudomonas …

Extracting Secondary Metabolites From Bacterial Endophytes To Suppress Or Promote Sweet Sorghum And Weeds, Mohammad R. Alsabri

Theses and Dissertations--Plant and Soil Sciences

Endophytic bacteria are ubiquitous in agricultural settings and have the potential to drastically affect plant growth both positively and negatively. These complex relationships play a key role in plant nutrition and are therefore of great interest to the agricultural community and beyond. With my dissertation work, I have had the opportunity to examine the relationship between endophytic bacteria and plants in various ways. The first part of my dissertation investigated how the microbial diversity found in soil affects the below- and above-ground traits of Sorghum bicolor. In the second section, I focused on a particular strain of bacteria that …