Environmental Microbiology and Microbial Ecology Commons^™

Breaking Virulent: The Coincidental Evolution Of Virulence Factors In Bacteria., Rhiannon Emmanuelle Cecil

Electronic Theses and Dissertations

Understanding how innocuous organisms can evolve to be pathogenic to humans is of increasing global concern. Further, understanding how existing pathogens may evolved to be more virulent is also vital to our ability to provide healthcare to people afflicted with diseases that promote chronic bacterial infections, such as cystic fibrosis. With the rise of antibiotic resistance in both bacteria and fungi it is paramount that new therapeutics are identified. Understanding what mutations occur that result in increased virulence in microbes can potentially provide new targets for antimicrobial drugs to combat antibiotic resistance. The Coincidental Evolution Hypothesis is a fundamental hypothesis …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

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, …

Evaluating Edna Metabarcoding As A Mic-Roe-Scopic Net To Catch Salmon Pathogens, Noah Burby

Honors College

Wild Atlantic salmon in the Gulf of Maine (GOM) is a Distinct Population Segment (DPS) that has been listed since 2000 as endangered by the U.S. Fish and Wildlife Service (USFWS) and the National Oceanic and Atmospheric Administration (NOAA). The current challenge is year-over-year decreases in the number of mature salmon returning to the Penobscot River for reproduction. Early detection of pathogen presence could allow for the identification of infection and the application of corrective measures. Environmental DNA (eDNA) is simply DNA that is collected from environmental samples (e.g., water, air, and soils), which consists of whole microorganisms and genetic …

Community Ecology And Disease Dynamics In Pacific Oysters: Unraveling Microbiome-Pathogen Interactions In The Wild, Victoria E. Cifelli

Cal Poly Humboldt theses and projects

In the context of multispecies microbial assemblages, disruptions can occur when there are alterations in host conditions, such as the onset of a disease. Notably, viruses have the potential to reshape a host's microbial community. However, the role of the host's habitat and environment, which could be pivotal in communities with shifting niche space and habitat filters, is often overlooked in host-microbe-pathogen interactions. Recognizing the importance of these factors, I employed a field-based approach to understand microbial community dynamics in the presence of disease. To address the influence of geographical location, I conducted an analysis involving healthy and infected oysters …

Characterizing The Cutaneous Microbiome Of Eurycea Lucifuga As A Potential Defense Against Chytridiomycosis, Madeline Key

Senior Honors Theses

Chytridiomycosis is an emerging infectious disease that is significantly reducing global amphibian populations. The disease is caused by Batrachochytrium dendrobatidis (Bd), a fungus that lethally modifies amphibian skin. Recent research has suggested that the cutaneous microbiome of individual amphibians may play a role in susceptibility to the pathogen. In this study, twelve cave salamanders (Eurycea lucifuga) were collected. Cutaneous bacteria from each salamander were isolated and identified using Sanger Sequencing. Additionally, a Bd-challenge assay was performed to determine each isolate’s antifungal activity. Results indicated many microbial isolates possessed inhibitory capabilities against Bd, which may …

Novel Signal Sequences And Fusion Partners For Paratransgenesis In Asaia, Christina Grogan

Electronic Theses and Dissertations

Mosquitoes transmit many pathogens that cause human disease. One such disease, malaria, is caused by parasites in the genus Plasmodium, infecting over 200 million people and killing over 600,000 per year. Current strategies to control vector-transmitted diseases are increasingly undermined by mosquito and pathogen resistance. Research has turned to additional and novel methods of control, such as altering the microbiota of the vectors. In this method, called paratransgenesis, symbiotic bacteria are genetically modified to affect the mosquito’s phenotype by engineering them to deliver antiplasmodial molecules into the midgut to kill parasites. These molecules must be released by the …

Genome Sequence Of Sn1, A Bacteriophage That Infects Sphaerotilus Natans And Pseudomonas Aeruginosa, K.M. Damitha Gunathilake, Denise M. Tremblay, Pier-Luc Plante, Ellen Jensen, Kenneth Nickerson, Sylvain Moineau

Kenneth Nickerson Papers

Phage SN1 infects Sphaerotilus natans and Pseudomonas aeruginosa strains. Its genome consists of 61,858 bp (64.3% GC) and 89 genes, including 32 with predicted functions. SN1 genome is very similar to Pseudomonas phage M6, which contains hypermodified thymidines. Genome analyses revealed similar base-modifying genes as those found in M6.

Phage SN1 was isolated in 1979 from activated sludge samples obtained from a wastewater treatment plant (Lincoln, Nebraska, USA) using S. natans ATCC 13338 as the host (1, 2). An early study showed that the siphophage SN1 has unusual bases in its genome as confirmed by cellulose thin-layer chromatography (1). Its …

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 …

Analysis Of Soxs In S. Typhimurium By Transposon Mutagenesis, Joel Hanns, Brenda Pratte, Lon Chubiz Phd, Lauren Daugherty

Undergraduate Research Symposium

The mar-sox-rob regulon has been implicated in transcriptional regulation of several stress responses, such efflux of antibiotics, enzymes that break down reactive oxygen species, repression of biofilm formation, or repression of motility through downregulation of flagellar expression. This system is conserved among enteric bacteria and has been studied in species, such as E. coli and S. typhimurium. Some of these mechanisms can be costly and slow cell growth while increasing the probability of survival through tolerance of toxic environments. SoxS works in coordination with SoxR to respond to redox stress encountered by the cell. Interestingly, the overexpression of SoxS …

The Microbiome Characterization And Comparison Of Loggerhead (Caretta Caretta) And Green (Chelonia Mydas) Sea Turtle Eggs In Broward County, Florida, Colleen Mcmaken

All HCAS Student Capstones, Theses, and Dissertations

All seven extant species of sea turtles are classified as threatened or endangered due to natural and anthropogenic impacts. Sea turtle conservation efforts are largely dedicated to ensuring healthy nesting activity. Hatching success of sea turtle eggs can be affected by several factors including the proliferation of pathogenic microbes. However, it is unclear as to which microbes have the most impact on hatching success and how they are transmitted into the eggs. The primary aims of this study characterized and compared the bacterial communities (microbiomes) from the i) cloaca of nesting sea turtles; ii) sand within and surrounding the nests …

Diversity Of Bacteriophage In Burkholderia Species, Abigail Price

Honors Projects

Bacteriophages are viruses that infect and replicate within bacteria and offer the potential of a therapeutic alternative to chronic infections that do not respond to antibiotic-based therapies. B. vietnamiensis is one of a number of Burkholderia species involved with chronic drug resistant infections in the lungs of individuals with compromised respiratory systems, as found in those with chronic obstructive pulmonary disease and, most especially, are of particular significance in patients with cystic fibrosis. The diversity of the Burkholderia species is explored by using online databases and looking at bacteriophage or phage-encoding viruses found in B. vietnamiensis. The open reading frames …

Microbial Contamination On Ambulance Surfaces: A Systematic Literature Review, Adam Obenza, Patricia Cruz, Mark Buttner, D. Woodard

Environmental & Occupational Health Faculty Publications

Healthcare-associated infections (HAIs) are infections that patients acquire while receiving medical treatment in a healthcare facility. During ambulatory transport, the patient may be exposed to pathogens transmitted from emergency medical service (EMS) personnel or EMS surfaces. The aim of this study was to determine whether organisms commonly associated with HAIs have been detected on surfaces in the patient-care compartment of ambulances. Five electronic databases – PubMed, Scopus, Web of Science, Embase and Google Scholar were used to search for articles using inclusion and exclusion criteria following the PRISMA checklist. Inclusion criteria consisted of articles published in English, between 2009 and …

The Coxsackievirus And Adenovirus Receptor Has A Short Half-Life In Epithelial Cells, Poornima Kotha Lakshmi Narayan, James M. Readler, Mahmoud S. Alghamri, Trisha L. Brockman, Ray Yan, Priyanka Sharma, Vladislav Snitsarev, Katherine J.D.A Excoffon, Abimbola O. Kolawole

Department of Biology Faculty Scholarship and Creative Works

The coxsackievirus and adenovirus receptor (CAR) is an essential cellular protein that is involved in cell adhesion, cell signaling, and viral infection. The 8-exon encoded isoform (CAREx8) resides at the apical surface of polarized epithelia, where it is accessible as a receptor for adenovirus entering the airway lumen. Given its pivotal role in viral infection, it is a target for antiviral strategies. To understand the regulation of CAREx8 and determine the feasibility of receptor down regulation, the half-life of total and apical localized CAREx8 was determined and correlated with adenovirus transduction. Total and apical CAREx8 has a relatively short half-life …

Determining Effects Of Management Practices On Potato Early Dying And Soil Microbiome And Assessing Risk Of Fungicide Resistance In Verticillium Dahliae, Kedi Li

Electronic Theses and Dissertations

Potato early dying (PED) is a yield-constraining soilborne disease of potato, caused by Verticillium spp. with V. dahliae being the predominant causal agent. Since the pathogen inhabits soil for long periods, PED management aims to reduce the population of V. dahliae in soil. Benzovindiflupyr and azoxystrobin are effective chemicals and frequently used in the control of V. dahliae. In this study, field trials were conducted at Aroostook Farm, Presque Isle, ME in 2019 and 2020. Chemical and biological products have been studied for PED control, and fungicide resistance was also examined. To evaluate fungicide resistance, benzovindiflupyr was characterized on …

Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid, Kenneth Nickerson, Cory Boone, Kory Parker

Kenneth Nickerson Papers

Candida albicans is a pathogenic dimorphic fungus which is invariably found as a diploid in patients. C. albicans secretes the sesquiterpene farnesol both as a quorum sensing molecule which blocks the yeast to hypha conversion and as a virulence factor for pathogenicity. 20-25 μM farnesol kills other competing yeasts and fungi, often by triggering apoptosis, and yet wild type diploid C. albicans tolerates 300-500 μM farnesol. The recent availability of 10 haploid strains of C. albicans (5 mating type aand 5 mating type α) allowed us to compare their production of and sensitivity to farnesol. On average, the heterozygous diploid …

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and β-sitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis of the …

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 …

Investigating Distribution Of Legionella Pneumophila In Urban And Suburban Watersheds, Azlan Maqbool

Student Theses

The presence of Legionella pneumophila was assessed using a cultivation-based approach in New York City waterways, a freshwater portion of the lower Hudson River Estuary near Kingston NY, and in urban and suburban street water. Legionella pneumophila was detected in 51% of brackish New York City Estuary samples, most with concentrations near minimum detection (=>1 organism/ mL). In contrast, it was detected in 22% of suburban freshwater Hudson River Estuary samples. Levels of the bacterium were found to be higher during wet weather compared to dry weather in the highly dense urban setting, but not in the less dense …

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …

Isolation, Enumeration And Antibiotic Profiling Of Vibrio Vulnificus And V. Parahaemolyticus From Coastal Virginia, Stanley E. Peyton Jr.

Masters Theses, 2020-current

Vibrio vulnificus and V. parahaemolyticus are gram-negative, halophilic bacteria that reside in estuarine waters and are associated with infections in humans. These bacteria can cause gastroenteritis through their presence in raw fish and shellfish consumed by humans. V. vulnificus can also produce wound infections leading to severe septicemia, and in some cases, death if not treated promptly. With increasing incidence of infections due to these two organisms, research efforts have focused on potential reservoirs and environmental conditions that can increase human exposure to, and infection, with these species of bacteria. This study was conducted in order to examine the role …

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 …

Microbiota Accessible Carbohydrates And Susceptibility To Clostridioides Difficile Infection, Keegan Schuchart, Jennifer Auchtung, Thomas Auchtung

UCARE Research Products

This experiment looked into the effects of dietary microbiota accessible carbohydrates (MACs)on the composition of human GI microbe colonies and their susceptibility to pathogen infection. Three different concentrations of MAC ingrained media were tested in mini bioreactor arrays, treated with antibiotics, infected with Clostridioides difficile, then allowed to recover. Microbe community was examined for strain composition and diversity before and after the antibiotic treatment and Clostridioides difficile infection. After the initial mini bioreactor run, individual isolates were investigated in their ability to respond to specific MACs Arabinoglactina, Inulin, and Soluble starch at experimental concentrations.

The Potential For Dickeya Dianthicola To Be Vectored By Two Common Insect Pests Of Potatoes, Jonas K. Insinga

Electronic Theses and Dissertations

Dickeya dianthicola (Samson) causing blackleg and soft rot was first detected in potatoes grown in Maine in 2014. Previous work has suggested that insects, particularly aphids, may be able to vector bacteria in this genus between plants, but no conclusive work has been done to confirm this theory. In order to determine whether insect-mediated transmission is likely to occur in potato fields, two model potato pests common in Maine were used: the Colorado potato beetle (Leptinotarsa decimlineata Say) and the green peach aphids (Myzus persicae Sulzer). Olfactometry and recruitment experiments evaluated if either insect discriminates between infected and …

Interaction Between Fusarium Head Blight And Crown Rot Disease Incidence And Environmental Factors And Soil Physiochemical Analysis On Wheat In The South Of Iraq, Basra Province, Mohammed Hussein Minati Dr., Mohanad Khalaf Mohammed-Ameen Dr.

Karbala International Journal of Modern Science

This study was conducted to evaluate the interaction between disease incidence of both Fusarium head blight (FHB) and crown rot (FCR) and physiochemical parameters for soil samples and environmental factors in 14 selected wheat fields in the North of Basra province. The results showed that both diseases were occurred in all surveyed fields. The level of FCR incidence was higher than FHB. The incidence of both diseases was increased with favourable weather conditions (high humidity and temperature ˃15 °C), reaching the highest levels in crucial periods before and during the ripening stage. The percentage of disease incidence ranged between 6 …

Molecular Detection Of Pathogenic Leptospira Throughout The Caribbean, Zamara R. Garcia Truitt

Biology Theses

Leptospirosis is a common widespread zoonotic disease found throughout the Caribbean. The infection is produced by a pathogenic Leptospira species found in tropical and subtropical regions. The severity of the disease ranges from a mild asymptomatic infection to death. Leptospirosis is a neglected tropical disease due to the lack of public awareness and health approaches. Therefore, misdiagnosis is common because the symptoms are similar to that of other tropical endemic diseases. The aim of the study was to determine the presence of pathogenic Leptospira in water samples collected from Puerto Rico and Trinidad. Sixty-four environmental water samples were collected throughout …

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

College of Arts & Sciences Senior Honors 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 …

Does Quorum Sensing Regulate The Conjugation Of The Two Co-Resident Megaplasmids Of Agrobacterium Tumefaciens 15955, Christopher Carter

Kansas State University Undergraduate Research Conference

While the effects of Agrobacterium tumefaciens can be easily observed and have been studied closely, the mechanisms for their virulence habits have not. Several studies have suggested the mechanisms for plasmid transfer and conjugation, particularly concerning plasmid Ti (pTi), the TraR (TraR1) regulator, and the quorum sensing (QS) system associated with it. Very little is known, however, about the second plasmid (pAt) present within the bacteria nor its regulatory QS systems. To further understand these mechanics of plasmid conjugation, we have devised a series of experiments in order to find connections between the conjugation of both pTi and pAt and …

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 / …

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 …