Environmental Microbiology and Microbial Ecology Commons^™

The Contribution Of Foliar Fungi To Agricultural Soil Microbiomes In An Organic Cropping System., Derek R. Newberger

Creative Activity and Research Day - CARD

With finite arable land available to support a growing human population, sustainable agricultural techniques are increasingly needed to provide long-term food security. Traditionally, the focus of using cover crops as a technique in organic agriculture has been on the improved nutrient and physical properties of soil that result from their use. However, recent technological developments in sequencing have enabled a new window into the benefits of plant microbiomes in agriculture that extend beyond these traditionally touted effects. This project will investigate one relatively under-described effect of using cover cropping systems – the transfer of microbes from plants to soil. Specifically, …

Microbial Abundance And The Pattern Of Escherichia Coli Antibiotic Sensitivity And Resistance In Deer Creek And The Potential Impact Of A Veterinarian Hospital’S Input, Sarah Boxer, Tim Gsell

Research Days

The gram-negative bacteria, E. coli, is an indicator of fecal input for both point and non-point source origin. The veterinarian hospital located on Deer Creek may contribute to high antibiotic levels, which are known to select for resistant strains of bacteria living in impacted waters. The water running north of the veterinarian hospital was considered potentially antibiotic influenced as it was downstream of the site. The origin of the stream and sites upstream from the hospital were considered influent water. Sediments were also collected from these sites to determine if more long term resident E. coli were present with elevated …

Identification Of Bird-Associated Nonpoint Sources Of Microbial Contamination In Sediments, Savannah D. Mullins

Honors College Theses

Fecal indicator bacteria (FIB), such as Enterococci, are commonly used to monitor the microbial contamination of recreational beach waters based on standards set by the United States Environmental Protection Agency. Sediment and sand may also harbor FIB and reintroduce these bacteria to the water column. Enterococci may be originated from various non-point sources such as humans and wildlife. Recent literature has shown that avian feces also harbor high concentrations of Enterococci. The purpose of this study is identify the relationship between Enterococci and avian-associated markers in sediments. Sediment samples were collected monthly from four sites at Kings Ferry Beach in …

Consistency Is Futile!: Selecting Phycoremediators For Consortia, Tori Spencer

BIO 410 Spring 2019 Research Papers

Bioremediation is the process by which organisms remove and transform toxic compounds in a contaminated source. This is a waste management technique currently used to clean up man-made contamination. Many organisms act as natural remediators; in the case of algae, they are called phycoremediators who perform phycoremediaton. The term algae encompasses a variety of taxonomic groups and their diversity is still being realized; there are over 44,000 named species of the 72,000 species that we have identified. Some estimates calculate that there are over 200,000 diatom species alone. This diversity continues to be difficult to organize, which is problematic for …

Combating Drug Resistance - Comparison Of The Antibiotic Effect Of Hydrastis Canadensis Extract And Pure Berberine Via Minimum Inhibitory Concentration Assay, William Luke Scott, Timothy D. Trott

Research in Biology

Herbal medicines are a melee of complex organic chemicals, making it difficult to ascertain their direct mechanism of action. In contrast to mainstream pharmaceuticals, it is argued that herbal medicines are effective because of multiple constituents working synergistically. The complexity of herbal medicines may give them advantages over simpler pharmaceuticals in combating antibiotic resistant microbes, but these advantages can be difficult to quantitate. Popular literature frequently espouses the healing properties of herbal medicines, but many of these claims are not scientifically supported. Many gains could be realized in public health and medicine if more research was aimed at validating / …

Genetic Diversity In The Leucoagaricus Cultivar Fungus Of Trachymyrmex Septentrionalis Fungus-Growing Ants, Lee Deininger

MCB Articles

No abstract provided.

Properties Of A Genetically Unique Mycobacteriophage, Amanda K. Staples

Masters Theses & Specialist Projects

Bacteriophage MooMoo is a temperate phage that was isolated and propagated on Mycobacterium smegmatis (M. smeg). It typically produces turbid plaques, however spontaneous clear plaque mutants can be readily isolated. Both turbid (MooMoo-T) and clear plaque (MooMoo-C) formers can establish stable lysogens, but the parental turbid plaque forming phage has a higher lysogenic frequency. The phage repressor protein typically plays the central role in regulating the lysis/lysogeny decision. Therefore, we expected that the mutation responsible for the clear plaque phenotype would be located in the repressor gene. Remarkably, whole genome sequencing detected a single base pair mutation in the minor …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Modelling Non-Linear Functional Responses In Competitive Biological Systems., Nickolas Goncharenko

Western Research Forum

One of the most versatile and well understood models in mathematical biology is the Competitive Lotka Volterra (CLV) model, which describes the behaviour of any number of exclusively competitive species (that is each species competes directly with every other species). Despite it's success in describing many phenomenon in biology, chemistry and physics the CLV model cannot describe any non-linear environmental effects (including resource limitation and immune response of a host due to infection). The reason for this is the theory monotone dynamical systems, which was codeveloped with the CLV model, does not apply when this non-linear effect is introduced. For …

Effect Of Environmental Factors And Residual Sanitizers On Survival And Attachment Of Indicator Organism And Human Pathogens On Fresh Produce, Vijay Singh Chhetri

LSU Doctoral Dissertations

A comprehensive understanding of the behavior of microbial contaminants on produce surfaces in agricultural farms and during post-harvest activities is essential for the development of produce safety risk management strategies. Our studies investigated the survival and the attachment of E. coli on watermelon surfaces in agricultural settings with different levels of vegetation, and the effect of residual sanitizers on the survival and the attachment of E. coli O157: H7 and L. monocytogenes on spinach leaves. The attachment strength (S_R) of the E. coli cells on watermelon surfaces significantly increased (P<0.05) from 0.04 to 0.99 in the first 24 h, which was primarily due to the decrease in loosely attached population, given that the population of strongly attached cells was constant. The daily die-off rate of E. coli ranged from -0.12 …

Cyanobacterial And Algal Abundance And Biomass In Cave Biofilms And Relation To Environmental And Biofilm Parameters, Slađana Popović, Nataša Nikolić, Jelena Jovanović, Dragana Predojević, Ivana Trbojević, Ljiljana Manić, Gordana Subakov Simić

International Journal of Speleology

Due to life in extreme environments, cyanobacteria and algae from cave biofilms that form at the entrances or deep inside the cave around artificial lights are of increasing interest to many scientists. It is well-known that many phototrophic microorganisms are first to colonize exposed substrata and produce the organic matter on which other biofilm constituents relly. Many studies dealing with phototrophic microorganisms from biofilms focus on the diversity and community composition of cyanobacteria and algae, while quantitative assessments are rarely implemented. Biofilm sampling was conducted in Degurić and Vernjikica Cave located in Western and Eastern Serbia, respectively. Ecological parameters (temperature, …

Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana

Dissertations, Theses, and Capstone Projects

Medicinal plants are one of the biggest sources of natural products with therapeutic importance. There are currently over 28,000 plants with putative medicinal values. Plant-derived compounds have been explored extensively for various biological activities ranging from anti-cancer, immune-boosting to anti-inflammatory and anti-oxidant. Some of the most important therapeutic agents are of plant-origin, such as paclitaxel from Pacific yew (Taxus brevifolia) and artemisinin from qinghao su (a Chinese medicinal herb; a.k.a. Artemisia annua) to name a few.

The study presented in this thesis started out as classical pharmacognosy research, which focused on the identification of immunostimulatory factors in …

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

High-Throughput Cultivation Of Bacterioplankton From The Gulf Of Mexico And Genomics Of The First Cultured Ld12 Representative, Michael Winslow Henson

LSU Doctoral Dissertations

Cultivation of microorganisms facilitates characterization of metabolism, interspecies dependencies, virus-host interactions, and other information necessary to resolve the functions and distribution of individual taxa. However, the metabolic and physiological capacities for the majority of microbes remains unresolved because of the lack of cultivated representatives for many groups limits our ability to test cultivation-independent observations. The Northern Gulf of Mexico offers a diversity of ecosystems under the continuous threat from natural and anthropogenic disturbances, yet little is known about its native bacterioplankton community. This dissertation sought to use high-throughput cultivation over three-years at six sites to isolate important coastal bacteria to …

Assessing The Prevalence Of Multidrug Resistant Salmonella Enterica From Stream Sediment And Poultry Litter In The Shenandoah Valley Of Virginia, Noah Greenman

Masters Theses, 2010-2019

Multidrug resistant Salmonella enterica present in stream sediment and poultry litter represent a critical health concern. A small number of S. enterica serotypes are responsible for most lab-confirmed infections in the US each year. To assess the prevalence of these significant strains, we isolated 88 S. enterica from stream sediment and poultry litter. Sequence data for all isolates were generated using an Illumina® sequencing platform, with long-reads for some isolates from the Oxford Nanopore MinION™ used in a hybrid genome assembly approach. Isolates were typed according to their serotype and multi-locus sequence type using SeqSero/SISTR and Enterobase respectively. Antibiotic resistance …

Shrimp Production Environment And The Gut Microbiome: Effects Of Aquaculture Practices And Selective Breeding On The Gut Microbiome Of Pacific Whiteleg Shrimp, Litopenaeus Vannamei, Angela Landsman

Electronic Theses and Dissertations

Knowledge of the functional role of the gut microbiome in animal health and nutrition may provide solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth particularly with low cost feeds. Successful manipulation of bacteria found in the gut requires a deeper understanding of shrimp microbial communities and how their compositional structure is influenced by environmental conditions, and inherent host factors such as genetics. The initial research investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei) reared in pond systems compared to indoor aquaculture facilities as an exploration of the effects of aquaculture practices …

Comparing Gut Microbiome And Virome In The Breast Milk- And Formula-Fed Late Preterm Infants, Zyi Wang

Electronic Theses and Dissertations

The neonatal intestinal microbiome consists of all microorganisms in the gut. Although the microbiome is critical to human health and disease, its colonization remains incompletely understood, particularly in the preterm infant. We aimed to characterize the intestinal bacteria microbiome and virome in moderate-to-late preterm infants. We hypothesized that the bacteria microbiome and virome differs between breast milk and formula-fed infants. We collected stool samples from twenty infants born between 32 0/7 and 36 6/7 weeks gestation. Samples were collected after infants reached full volume enteral feedings. Ten infants were breast milk fed and ten received infant formula. DNA and RNA …

Linking Microbial Community Structure And Ecosystem Functions In Acidic Soil From Pennsylvania, Usa, Madison T. James, Sophia T. Farrisi, Shreya Shah, Vishal Shah

Sustainability Research & Creative Activities Grants Reports

Microorganisms play a critical role in the structure and functioning of soil ecosystems. Within acidic soil across the northeastern United States and Canada, we have little understanding of the microbial diversity present and its relationship to the biochemical cycles. The current study is aimed at understanding the taxonomical and functional diversities in the acidic soil obtained from near various types of trees, how the diversities change as a function of depth, and the linkage between taxonomical and functional diversities. From eight sampling locations, soil samples were collected from three horizons (depths). The three depths were 0-10 cm (A), 11-25 cm …

Improved Methods For The Quantification Of Viable Ascaris Suum And Application To Biosolids, Tanner Keyzers

Dissertations, Master's Theses and Master's Reports

The current method for detection of Ascaris ova in biosolids and wastewater has several drawbacks including being labor and time intensive as well as being difficult to quantify viable ova that have larvated during treatment. The goal of this thesis was to improve several methods for the detection and quantification of Ascaris ova during long term-storage of biosolids including improvement of quantifying viable ova using a heat and bleach treatment to promote movement of larvae inside of ova, and comparison of the traditional microscopic method with qPCR and PMA-qPCR to prevent the false-positive results. Improved methods to promote movement of …

Long-Term Land Management Practices And Their Effect On Soil Health And Crop Productivity, Thomas Joseph Muratore Jr.

Theses and Dissertations--Plant and Soil Sciences

Agricultural intensification reliant on monocrops could change soil health in a way that does not support maximum crop productivity. Twenty-nine-year-old no-till field plots at the University of Kentucky Spindletop research farm showed a significant reduction in corn yields from continuous corn plots compared to those from plots in various types of rotation. The objective of this study was to determine what role soil microbes might play in yield reduction and how management and time effects microbial community structure. Samples were collected from the following treatments: continuous corn (CC), continuous soybean (SS), a 2-year corn/soybean rotation (CCSS), Corn in rotation with …