Environmental Microbiology and Microbial Ecology Commons^™

Hawk On Wire: Ecopoems By Scott T. Starbuck, Vivian M. Hansen

The Goose

Review of Scott T. Starbuck’s Hawk on Wire: Ecopoems

Culture-Based Analysis Of ‘Cave Silver’ Biofilms On Rocks In The Former Homestake Mine In South Dakota, Usa, Amanpreet K. Brar, David Bergmann

International Journal of Speleology

Tunnels in a warm, humid area of the 1478 m level of the Sanford Underground Research Facility (SURF), located in a former gold mine in South Dakota, USA, host irregular, thin whitish, iridescent biofilms, which appear superficially similar to ‘cave silver’ biofilms described from limestone and lava tube caves, despite the higher rock temperature (32°C) and differing rock surface (phyllite) present at SURF. In this study, we investigated the diversity of cultivable bacteria constituting the cave silver by using several media: CN agar, CN gellan gum and 0.1X R2A agar. The highest colony count (CFU/g of sample) was observed on …

Investigation Of Origin And Growth Of Fungi In Coastal Beach Sand, Ruth L. Wright

Honors Theses

In a previous study from this lab (Stevens, Evans, & Aguirre, 2012) yeast colonies were isolated and grown grown from sand collection at pristine, medium use and high use beaches along the grand strand. In that study greater yeast abundance and greater diversity both correlated with higher census of human use, suggesting that some yeast growth of sites was anthropogenic. However the sand matrix itself also varied from very fine, uniform, dark sand at the pristine beach to coarser, color varying, less tightly packed sand at residential and commercial beaches. This suggested an alternative hypothesis to differential colonization and growth …

See The Forest For The Leaves: Foliar Fungal Community Composition And Volatile Organic Compound Production, Joshua Copeland

Master's Theses

Endophytes are microbes that live within plants without causing detectable illness. These microorganisms can emit volatile organic compounds (VOCs), airborne signaling molecules that can significantly affect plant growth. Despite the prevalence of endophytes and their VOCs, little is known about these factors important to plant health. With this in mind I isolated fungal endophytes from leaves of Populus trichocarpa and Populus fremontii, tree species with economic and environmental uses, to determine if endophyte communities are reserved between the closely related tree species and over seasons. Surface sterilized leaf fragments were plated onto malt extract agar and the resulting fungi were …

The Effects Of Constructed Wetlands On Metal Solubilization And Bioavailability In Passive Mine Remediation, Elizabeth Cochran

Electronic Theses and Dissertations

The legacy of coal mining in Appalachia has left many watersheds impacted by abandoned mine drainage. The drainage degrades streams, groundwater and habitats with acidity and toxic heavy metals. The Lowber Passive Remediation System has been in operation since 2004 to remediate high amounts of dissolved Fe, SO₄, Al, and Mn. The site consists of six settling ponds and an extensive wetlands at the finish. This study investigated the resolubilization of Fe and Mn in the wetlands and the role of bacteria in resolubilization. During three seasons, field measurements of water quality and lab analysis of Fe, Mn, …

Fungi In A Hot, Dry, Changing World, Miriam I. Hutchinson

Biology ETDs

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient …

Warming Up: Climate Change Related Shifts Of Mycorrhizal Fungal Communities In High Latitude Ecosystems, Megan Rae Devan

Biology ETDs

This dissertation examines how climate change affects mycorrhizal fungal communities in boreal and arctic ecosystems. In chapter one, I revealed that increases in fire severity and related increases in deciduous tree dominance result in greater Ascomycota relative abundance (RA) and subsequent declines in Basidiomycota RA. In chapter two I analyzed the effects of post-fire mycorrhizal fungal communites on host growth. There were trends at the fungal genus level that were largely reflected at the guild level across all hosts; however, there were some fungal genera that had the opposite effect on different host species. In chapter three, I found host …

Developing A Modern Microbiology Laboratory Manual To Enhance Student Learning, Alexander Yonchak

Senior Honors Projects

My project has been addressing the issue of incorporating recent developments in biosafety and pedagogical approaches for lab-courses into our existing educational curriculum by developing a new, modern lab manual aimed at improving experiential learning for introductory microbiology teaching labs. Through researching the most recent safety regulations, industry standards, & guidelines for such teaching labs, my manual clearly delineates learning outcomes to match the skills expected of undergraduates completing degrees within the life sciences. In addition, the lab manual that I have designed has been modernized to incorporate the most recent recommended safety precautions and is written in a user-friendly …

The Effect Of Stenotrophomonas Maltophilia On Gram-Negative Cystic Fibrosis Pathogens., Joshua D Stewart

College of Arts & Sciences Senior Theses

Cystic Fibrosis (CF) is the most common lethal genetic disorder in the Caucasian population with an incidence of 1 per 3,000 live births and a median predicted survival of only 47 years. Respiratory failure due to repeated pathological insults to lung tissue by infection is the ultimate cause of mortality in the majority of patients. The lung microenvironment created by CF highly favors colonization by opportunistic pathogens such as Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Burkholderia cenocepacia, and Achromobacter xylosoxidans. Biofilm formation by multiple bacterial species contributes to the chronic, persistent, and difficult to treat nature of CF infections. This study seeks …

Detection, Identification, And Metagenomic Characterization Of Cyanobacteria In Barnegat Bay, New Jersey, Roksana M. Rahman

Seton Hall University Dissertations and Theses (ETDs)

Cyanobacterial harmful algal blooms (CHAB), caused by eutrophication, is known to threaten both wildlife and human health. Barnegat Bay, also home to Oyster Creek nuclear power plant, has experienced an elevated levels of nitrogen due to human activity such as recreational activity and urbanization. This has caused an increase of CHAB’s at a more frequent rate within Barnegat Bay. In order to detect possible CHAB causing cyanobacteria, water samples were collected from 12 different locations within Barnegat Bay. Each sample was filtered through a 30- and 0.4-mm polycarbonate filter sequentially. Chelex DNA extraction, polymerase chain reaction (PCR), and gel electrophoresis …

The Chelation Of Metal Ions By Vicibactin, A Siderophore Produced By Rhizobium Leguminosarum Atcc 14479, Joshua Stinnett

Undergraduate Honors Theses

Vicibactin is a small, high-affinity iron chelator produced by Rhizobium leguminosarum ATCC 14479. Previous work has shown that vicibactin is produced and secreted from the cell to sequester ferric iron from the environment during iron-deplete conditions. This ferric iron is then transported into the cell to be converted into ferrous iron. This study uses UV-Vis spectroscopy as well as ion trap-time of flight mass spectroscopy to determine that vicibactin does form a complex with copper(II) ions, however, at a much lower affinity than for iron(III). Stability tests have shown that the copper(II)-vicibactin complex is stable over time. The results of …

Characterization Of Microtubule Organizing Centers In The Genus Protostelium, Including Evolutionary Implications, Ethan Taylor Ozment

Graduate Theses and Dissertations

Microtubule organizing centers (MTOCs) are cellular regions of microtubule nucleation. The best known MTOCs are those associated with the centrosome, but several non-centrosomal MTOCs are known in eukaryotes, especially in land plants. MTOCs are poorly characterized across the breadth of amoebozoan diversity, but are well-known in certain amoebozoan lineages, including the genus of protosteloid slime molds Protostelium. The structure of the MTOC is known for two non-ciliated species, P. nocturnum and P. mycophaga, as well as P. aurantium, which can reversibly become ciliated under appropriate conditions. P. nocturnum and P. mycophaga have acentriolar centrosomal MTOCs while P. aurantium has a …

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, …

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 …

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 …

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 …

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 …

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 …