Environmental Microbiology and Microbial Ecology Commons^™

Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert

LSU Doctoral Dissertations

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …

Harnessing The Anopheles Microbiome To Conditionally Express Anti-Plasmodial Effectors During The Blood Meal, Jackie Shane

Electronic Theses and Dissertations

The control of vector-borne diseases such as malaria has been an extremely important research subject for hundreds of years. Because of the complex lifecycles of the pathogens that cause these diseases, finding a comprehensive treatment or preventative strategy has proven extremely difficult. Malaria alone is responsible for almost half a million deaths annually, most of them children under 5 years old. This disease is caused by parasitic protists in the genus Plasmodium that are transmitted to humans from Anopheles sp. mosquitoes. Most preventative strategies that are in use today revolve around controlling the vectors, including bed nets, insecticides, and larval …

Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern

Biological Sciences Undergraduate Honors Theses

Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial …

Novel Inactivation Of The Causative Fungus Of White Nose Syndrome With Methoxsalen And Ultraviolet A Light, Colin J. Hartman, Joseph Mester Phd, Alan Cohen Md

Posters-at-the-Capitol

White Nose Syndrome (WNS) is a newly recognized disease responsible for the rapid mass destruction of the North American bat populations. This study addressed the novel inactivation of fungal spores from Pseudogymnoascus destructans, the causative agent of WNS, using ultraviolet A (UVA) light at 365nm and methoxsalen, a photosensitizer from a family of compounds known as furanocoumarins. Penicillium crustosum, an environmental fungus, was studied as a comparator.

Spore suspensions were soaked in specific concentrations of methoxsalen and subsequently exposed to UVA light. The plates were examined for both spore inactivation and resultant inhibition of colony growth. The results demonstrated …

Triatomines: Trypanosomatids, Bacteria, And Viruses Potential Vectors?, Caroline Barreto Viera, Yanna Reis Praça, Kaio Luis Da Silva Bentes, Paula Beatriz Santiago, Sofia Marcelino Martins Silva, Gabriel Dos Santos Silva, Flávia Nader Motta, Izabela Marques Dourado Bastos, Jaime Martins De Santana, Carla Nunes De Araújo

Harold W. Manter Laboratory of Parasitology: Library Materials

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission …

High-Resolution Identification Of Multiple Salmonella Serovars In A Single Sample By Using Crispr-Seroseq, Cameron P. Thompson, Alexandra N. Doak, Naufa Amirani, Erin A. Schroeder, Justin Wright, Subhashinie Kariyawasam, Regina Lamendella, Nikki Shariat

Biology Faculty Publications

Salmonella enterica is represented by >2,600 serovars that can differ in routes of transmission, host colonization, and in resistance to antimicrobials. S. enterica is the leading bacterial cause of foodborne illness in the United States, with well-established detection methodology. Current surveillance protocols rely on the characterization of a few colonies to represent an entire sample; thus, minority serovars remain undetected. Salmonella contains two CRISPR loci, CRISPR1 and CRISPR2, and the spacer contents of these can be considered serovar specific. We exploited this property to develop an amplicon-based and multiplexed sequencing approach, CRISPR-SeroSeq (serotyping by sequencing of the CRISPR loci), to …

Theory On Thermodynamic Constraints To Biogeochemical And Metabolic Diversity, Jordan Okie, Everett Shock

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Identification Of Microbiota Associated With The Ectosymbiotic Community Structure Of The Appalachian Brook Crayfish (Cambarus Bartonii), Matthew M. Cooke 6268927, Luke T. Fischer, Taylor Griffin, Sherrie Jeffers

Montview Journal of Research & Scholarship

Microbes play a significant role in ecosystems, effecting the vital functions of other organisms, interspecies relationships, and population sizes. Based upon previous research (Skelton et al., 2016), it has been hypothesized that crayfish symbionts (branchiobdellidans) play a significant role in regulating the amount of microbiota associated with the host. A growing body of knowledge is known regarding both the condition of gill fouling and the annelid worm’s symbiotic relationship with the crayfish (Skelton et al., 2016; Skelton et al., 2016). However, there is little to no evidence available concerning the bacteria’s role in the process (Skelton et al., 2016). Microbial …

Maxent Estimation Of Aquatic Escherichia Coli Stream Impairment, Dennis Gilfillan, Timothy Andrew Joyner, Phillip R. Scheuerman

ETSU Faculty Works

Background: The leading cause of surface water impairment in United States’ rivers and streams is pathogen contamination. Although use of fecal indicators has reduced human health risk, current approaches to identify and reduce exposure can be improved. One important knowledge gap within exposure assessment is characterization of complex fate and transport processes of fecal pollution. Novel modeling processes can inform watershed decision-making to improve exposure assessment.

Methods: We used the ecological model, Maxent, and the fecal indicator bacterium Escherichia coli to identify environmental factors associated with surface water impairment. Samples were collected August, November, February, and May for 8 …

Maxent Estimation Of Aquatic Escherichia Coli Stream Impairment, Dennis Gilfillan, Timothy A. Joyner, Phillip Scheuerman

ETSU Faculty Works

Background.The leading cause of surface water impairment in United States’ rivers and streams is pathogen contamination. Although use of fecal indicators has reduced human health risk, current approaches to identify and reduce exposure can be improved. One important knowledge gap within exposure assessment is characterization of complex fate and transport processes of fecal pollution. Novel modeling processes can inform watershed decision-making to improve exposure assessment.

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr.

Georgia Journal of Science

Pueraria montana, better known as kudzu, is an invasive species rapidly spreading throughout the southeastern United States. This plant can form root nodules which house nitrogen-fixing bacteria, allowing atmospheric nitrogen to be converted into biologically available forms of nitrogen for use by the plant host. Given the centrality of these bacteria to the spread of kudzu, isolates from nodules were characterized after collection from seven different locations across the metropolitan Atlanta area. Twenty-five isolates were grown on two different variants of nitrogen free media. Four different carbon sources were evaluated as well. Finally, growth under both aerobic and anaerobic …

Investigation Of Biogeochemical Mechanisms Of Greenhouse Gas Production In The Urban Hudson River Estuary, Brian Alan Brigham

Dissertations, Theses, and Capstone Projects

Coastal megacities deposit significant amounts of carbon (C), nitrogen (N) and other pollutants into surrounding waters. These inputs, including wastewater and surface water runoff, may affect estuarine and adjacent wetland biogeochemical cycles, microbial production and ultimately greenhouse gas (GHG) efflux. In many megacities pollutant loading is typically greatest after periods of precipitation when the volume of wastewater and storm water runoff exceeds local sanitation capacity, resulting in the discharge of raw sewage into adjacent waters. These combined sewage overflow (CSO) events have received considerable attention primarily due to their potential impact on human health and eutrophication. However, whether these events …

Ecology And Prevalence Of Ticks And Tick-Borne Bacterial Pathogens In Southeast Kansas, Abrar Alzahrani

Electronic Theses & Dissertations

Ticks are small arachnids which have the ability to acquire, maintain, and transfer pathogenic bacteria to human and animals by feeding on their blood. Diseases such as Anaplasmosis, Babesiosis, Colorado tick fever, Ehrlichiosis, Lyme disease, and Rocky Mountain spotted fever (RMSF), are becoming more prevalent in populations, creating global health and economic problems.

This research aimed to determine the frequency of three species of ticks, the Lone Star tick (Amblyomma americanum), the Dog tick (Dermacentor variabilis), and Black-legged tick (Ixodes scapularis) in southeast Kansas and adjacent areas. Another objective of the study was to determine …

Next Generation Sequencing Methods For Coastal Zone Water Quality Monitoring, Catherine Iskrenko

HCNSO Student Capstones

When analyzing the water quality of the coastal zone, culture-based techniques have been utilized most often to identify Fecal Indicator Bacteria in samples. Since the advent of the Sanger Method for DNA sequencing, other techniques have arisen that provide significantly more information on the microorganisms in sample, but they are still not the mainstream for water quality analysis. This capstone reviews and compares culture-based techniques, DNA sequencing, RNA sequencing, qPCR for biomarker, and 16S rDNA sequencing to highlight their merits and shortcomings for analyzing environmental water samples. The technique presented that provides the broadest range of information (including the identification …

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, …

Green Tea Polyphenol Epigallocatechin-3-Gallate-Stearate Inhibits The Growth Of Streptococcus Mutans: A Promising New Approach In Caries Prevention, Amy Lynn Melok, Lee Lee, Siti Ayuni Mohamed Yussof, Tinchun Chu

Department of Biology Faculty Scholarship and Creative Works

Streptococcus mutans (S. mutans) is the main etiological bacteria present in the oral cavity that leads to dental caries. All of the S. mutans in the oral cavity form biofilms that adhere to the surfaces of teeth. Dental caries are infections facilitated by the development of biofilm. An esterified derivative of epigallocatechin-3-gallate (EGCG), epigallocatechin-3-gallate-stearate (EGCG-S), was used in this study to assess its ability to inhibit the growth and biofilm formation of S. mutans. The effect of EGCG-S on bacterial growth was evaluated with colony forming units (CFU) and log reduction; biofilm formation was qualitatively determined by Congo red assay, …

Influence Of A Guanidine Riboswitch In Bacterial Cells, Erik S. Timsak, Jefferey A. Kimbrel, Chris S. Ward, Rhona K. Stuart, Michael P. Thelen

STAR Program Research Presentations

Bacteria live in environments containing complex ecologies of other microbes that communicate and survive through the action of a variety of small metabolic compounds. One common yet relatively unstudied metabolite is guanidine. Although it can be toxic to cells, recent studies have revealed that guanidine may function as a cellular metabolite through a specialized RNA sequence known as a riboswitch. Within our overall project on improving algal productivity, the focus of this study is to: (a) describe various guanidine riboswitch sequences in bacteria that interact with biofuel producing algae; and (b) determine if guanidine has a positive or negative influence …

Detecting A Probiotic Product Within The Gut Of Broiler Chickens, Anneka Pisula

Master's Theses

As of January 2017, the U.S. poultry industry banned the use of antibiotics and now relies on alternatives such as probiotics to help protect animal health. Although probiotic use is not a new concept in the poultry industry, identifying the best combination of bacterial strains to generate an effective probiotic formula requires further investigation. This study aimed to detect a probiotic product of four bacterial strains (Pedioccoccus acidilactici, Pediococcus pentosaceus, Lactobacillus plantarum, and Bacillus subtilis) in a feeding trial with broiler chickens. Birds given the probiotic were predicted to show an improved growth performance with …

Effects Of Toxic Fescue Exposure On Vaginal Microbial Communities Of Crossbred Beef Cows, Abby Ratton

Animal Science Undergraduate Honors Theses

The consumption of toxic fescue by beef cattle results in several adverse physiological effects such as reduced reproductive success, severe vasoconstriction resulting in hoof sloughing, low body condition scores, hyperthermia, decreased prolactin levels, and reduced hair shedding. The purpose of this study is to characterize bacterial community of the reproductive tract as a potential predictor for toxin exposure. One-hundred fall-calving crossbred cows were allocated to graze Toxic (Toxic: n=50) or Novel (Novel: n= 50) fescue pastures for five months (March-August). Treatments were blocked by sire breed (Charolais or Hereford) and by parity (first, second, third). Animals rotated pastures biweekly and …

Dietary Inclusion Of Enriched Chicken Bone Broth Prevents Trigeminal Sensitization Meditated By Early Life Stress, Orion Peterson

Graduate Theses/Dissertations

Early life stress is considered a risk factor for development of migraine, which is a prevalent painful neurological disorder involving sensitization and activation of trigeminal neurons, and irritable bowel syndrome, a condition often comorbid with chronic migraine. The focus of my study was to determine the effects of early life stress and dietary inclusion of enriched chicken bone broth on trigeminal nociceptor sensitization and the gut microbiota. Adult Sprague-Dawley male “sender” rats subjected to primary traumatic stress were placed next to breeding or pregnant female rats that served as “receiver” rats (secondary traumatic stress) and in proximity to the offspring …

African Trypanosomes Evade Immune Clearance By Oglycosylation Of The Vsg Surface Coat, Jason Pinger, Dragana Nešić, Liaqat Ali, Francisco Aresta-Branco, Mirjana Lilic, Shanin Chowdhury, Hee-Sook Kim, Joseph Verdi, Jayne Raper, Michael A. J. Ferguson, F. Nina Papavasiliou, C. Erec Stebbins

Publications and Research

The African trypanosome, Trypanosoma brucei spp., is a paradigm for antigenic variation, the orchestrated alteration of cell surface molecules to evade host immunity. The parasite elicits robust antibody-mediated immune responses to its Variant Surface Glycoprotein (VSG) coat, but evades immune clearance by repeatedly accessing a large genetic VSG repertoire and “switching” to antigenically distinct VSGs. This persistent immune evasion has been ascribed exclusively to amino acid variance on the VSG surface presented by a conserved underlying protein architecture. We establish here that this model does not account for the scope of VSG structural and biochemical diversity. The 1.4Å resolution crystal …

Plant And Microbial Responses To Repeated Cu(Oh)2 Nanopesticide Exposures Under Different Fertilization Levels In An Agro-Ecosystem, Marie Simonin, Benjamin P. Colman, Weiyi Tang, Jonathan D. Judy, Steven M. Anderson, Christina M. Bergemann, Jennifer D. Rocca, Jason M. Unrine, Nicolas Cassar, Emily S. Bernhardt

Plant and Soil Sciences Faculty Publications

The environmental fate and potential impacts of nanopesticides on agroecosystems under realistic agricultural conditions are poorly understood. As a result, the benefits and risks of these novel formulations compared to the conventional products are currently unclear. Here, we examined the effects of repeated realistic exposures of the Cu(OH)₂ nanopesticide, Kocide 3000, on simulated agricultural pastureland in an outdoor mesocosm experiment over 1 year. The Kocide applications were performed alongside three different mineral fertilization levels (Ambient, Low, and High) to assess the environmental impacts of this nanopesticide under low-input or conventional farming scenarios. The effects of Kocide over time were …

Utilizing Molecular And Statistical Modeling Methods To Enhance White Nose Syndrome Detection In Bat Hibernacula, Samuel Miller

Electronic Theses & Dissertations

White Nose Syndrome (WNS) is a fungal infection in bats caused by Pseudogymnoascus destructans (Pd). Successfully identifying hibernacula infected with WNS is essential to help control and regulate the spread of WNS. Assessing the presence of WNS in bat hibernacula is usually done by visually confirming Pd on hibernating bats within infected hibernacula. This can be problematic because most visual confirmation occurs during the winter when bat populations are at their peak within hibernacula. When surveys are conducted in the winter, there is an increased chance of disturbing bats. One alternative method to visually confirming WNS on bats …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

Isolating And Identifying Fungal Endophytes From Roots Of Rare Orchid Cypripedium Arietinum In Grand Sable Dunes, Michigan, Kari Farkas-Lasich

All NMU Master's Theses

Recently the population of Cypripedium arietinum in Grand Sable Dunes, Michigan was estimated at more than 3.5 million plants, greater than 90% of the world’s known population. There is little research on this species’ root associated fungal endophytes. This new population estimate allows the ethical, destructive sampling required to shed light on root associated symbionts and further successful preservation and restoration of the species. Samples were collected of current year’s roots from 75 C. arietinum orchids at 75 locations within 4 jack pine forests in the Grand Sable Dunes, Pictured Rocks National Lakeshore, Michigan. Fungal endophyte cultures were obtained from …

Functions Of Ecosystems: Stream Metabolism As An Efficient And Effective Means To Gage The Health And Understand The Interworking Of Urban Streams In A Watershed Of Rock Island, Il, Ryan Johnson, Dr. Kevin Geedey

Celebration of Learning

Stream metabolism is a critical functional measure of stream health that integrates physical parameters like slope and discharge, with ecosystem functions like photosynthesis and respiration. Stream metabolism is widely studied; however, urban stream metabolism remains poorly understood. Stream metabolism was measured for five streams ranging from 1^st to 5^th orders from October 11^th to October 18^th 2017 and four streams ranging from 1^st to 4^th order from October 22^nd to 25^th 2017 located within an approximately 9.3 square kilometer watershed of Rock Island, IL that has an urban to suburban type of …

Cloning And Characterization Of A Pyrethroid Pesticide Decomposing Esterase Gene, Est3385, From Rhodopseudomonas Palustris Psb-S, Xiangwen Luo, Deyong Zhang, Xuguo Zhou, Jiao Du, Songbai Zhang, Yong Liu

Entomology Faculty Publications

Full length open reading frame of pyrethroid detoxification gene, Est3385, contains 963 nucleotides. This gene was identified and cloned based on the genome sequence of Rhodopseudomonas palustris PSB-S available at the GneBank. The predicted amino acid sequence of Est3385 shared moderate identities (30–46%) with the known homologous esterases. Phylogenetic analysis revealed that Est3385 was a member in the esterase family I. Recombinant Est3385 was heterologous expressed in E. coli, purified and characterized for its substrate specificity, kinetics and stability under various conditions. The optimal temperature and pH for Est3385 were 35 °C and 6.0, respectively. This enzyme could …

Examining Manganese Oxidation In Bacteria Through Bioinformatics And Environmental Sampling, T'Onna Collins

Undergraduate Theses and Capstone Projects

Manganese is an essential element for all living things. Manganese plays a role in geochemical cycles, like the nitrogen fixation cycle and the oxygen-evolving complex. The focus of this study is the manganese oxidation mechanism. Manganese oxidation plays a role in metabolic and antioxidant processes. Pseudomonas putida GB-1 is commonly used to study the process of manganese oxidation in bacteria. We used the previously identified Mn-oxidase genes, mopA, mnxG and mcoA, from P. putida GB-1 to look for conservation of manganese oxidation in other organisms. Basic Local Alignment Search Tool (BLAST) was used to find homologs of these three genes …

Sulfur Cave (Romania), An Extreme Environment With Microbial Mats In A Co2-H2S/O2 Gas Chemocline Dominated By Mycobacteria, Serban M. Sarbu, Joost W. Aerts, Jean-François Flot, Rob J.M. Van Spanning, Calin Baciu, Artur Ionescu, Boglárka M. Kis, Reka Incze, Sándor Sikó-Barabási, Zoltan Para, Botond Hegyeli, Nicu-Viorel Atudorei, Casey Barr, Kenneth Nealson, Ferenc L. Forray, Cristian Lascu, Emily J. Fleming, Wilbert Bitter, Radu Popa

International Journal of Speleology

Sulfur Cave (Puturosu Mountain, Romania) is an extreme environment, unique for displaying life in a gas chemocline. The lower part of the cave is filled with CO₂, CH₄, and H₂S of mofettic origin, while the upper part contains air that floats above the heavier volcanic gasses. S° and H₂SO₄ (from sulfur-oxidation) cover the cave wall at and below the CO₂-H₂S:O₂ gas/gas interface. On the cave wall, near the interface the pH is < 1 and unusual microbial biofilms occur on the rock’s surface. We provide context information on the geology, mineralogy, chemistry and biology to better understand this unique environment. We have used X-ray diffraction, optical microscopy, scanning electron microscopy with EDAX capabilities, stable isotope analysis and 16S and 18S rDNA amplicon sequencing. The most common taxa in the microbial biofilms are Mycobacteria, Acidithiobacillus and Ferroplasmaceae. Liquid water in this system originates solely from condensation of water …

Exploring The Microbiome: Diversity Of The Microbial Community Of Three Foam Nesting Frogs, Genus: Polypedates, Across A Developmental Gradient, Sarah Mcgrath

Masters Theses, 2010-2019

Characterization of microbial biodiversity, including that of the amphibian skin-associated microbiome, is a frontier of research recently made accessible through advances in sequencing technology. Microbial interaction with a host has been determined to have profound influences on host health across a wide range of macroscopic organisms. For amphibians, the influence of the skin-associated microbiome has been found to have particular importance, as amphibians are currently one of the fastest disappearing vertebrate groups on the planet, largely in part to skin-associated diseases caused by pathogenic microbes. Therefore, it is important to characterize the amphibian skin-associated microbiome, particularly for species with no …