Biology Commons^™

Novel Microbiological Medium Developed For The Isolation Of Bacteria Associated With Estuarine Anemones, Parker K. Lund, Catalina Cuellar-Gempeler

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Out of the nearly one trillion species of microbiota estimated to inhabit Earth only ten thousand have been cultured in the laboratory. Culturing continues to play a vital role in determining the physiology and ecologic function of individual bacteria in microbial communities and for microbes associated with host organisms one of the major challenges is developing microbiological media that mimics the bacteria’s natural environment enough to promote growth. Here, we target bacteria associated with the estuary anemones Diadumene lineata and Metridium senile by developing a novel medium that uses anemone tissue as the sole source of nutrients. We further measured …

Persistence Of Wastewater-Associated Antibiotic Resistant Bacteria In River Microcosms, Aoife P. Mahaney

Theses and Dissertations

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 hours.

Both types of wastewater amendments increased the initial abundance of ARB compared to microcosms containing only river water. The increase was greatest with untreated wastewater, but that effect decreased …

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …

The Use Of Aloe-Based Silver Nanoparticles As A Possible Treatment For Contaminated Water, Lozetta Davis

Scholar Week 2016 - present

Water contamination is a world-wide issue that causes the death of millions yearly. This comes from regularly tainted water with water borne pathogens, which is typically seen in undeveloped areas. As antibiotics are used more, more resistance is being seen, and thus newer methods of microbial contamination need to be developed. Silver nanoparticles have shown success in microbial contamination on petri dishes, but not in a water system. It was hypothesized that if silver nanoparticles were added to bacteria contaminated water they would be able to reduce the amount of bacteria present. Silver nanoparticles that are synthesized from plants such …

Characterization Of The Clostridioides Difficile Glycosyl Hydrolase Ccsz, Brian Lowrance

Theses and Dissertations (Comprehensive)

Bacteria inhabit many of the harshest environments on Earth; persisting and thriving in conditions thought to be unsuitable for life. One common strategy to withstand these environments is the formation of a biofilm. Biofilm composition varies greatly, depending on the underlying community that produces it. Cellulose, a polymer consistently prevalent in biofilms, has been identified as a virulence factor in many pathogens and is suspected to be involved in pathogenesis by Clostridioides difficile. C. difficile is the #1 cause of hospital acquired diarrhea, which can range from mild to life-threatening infections. Biofilm formation is hypothesized to be involved in …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Mara Repression Of Virulence Gene Hila In Salmonella, Alexandra King, Lauren Daugherty, Lon Chubiz Phd

Undergraduate Research Symposium

Salmonella is a bacteria most commonly known for causing the eponymous food-related illness. Due to their rapid reproduction rate and their ability to be propogated and maintained in a lab setting, they are commonly used in lab studies so that we can better understand how Salmonella causes disease in organisms that are more difficult to study. One area of interest is analyzing how Salmonella controls expression of the mechanisms that actually cause disease, called virulence traits, in response to the environment. In this study, antibiotic stress was used to analyze virulence gene expression. MarA is a gene that regulates ampicillin …

Isolating Oral Bacterial Species From A Single Donor Through A Multi-Step Detection Method, Khalid Al-Lakhen

Legacy Theses & Dissertations (2009 - 2024)

The human oral microbiome is one of the most complex microbiome communities in the human body and its role in maintaining health is not fully understood. Previous research shows that the transition from health to disease is accompanied by changes in community abundance and structure. To fully understand the symbiotic relationship formed between bacterial species that leads to the formation of a functional healthy biofilm structure, we must study the various structural relationships and subsequent molecular interactions among individual species within the biofilm. In this thesis, I have isolated a pure bacteria species from a single donor's dental plaque and …

Growth Of Diatom Fistulifera Alcalina In Bacterial Co-Culture And Comparative Mitogenomics Of Fistulifera Species, Erwin David Berthold

FIU Electronic Theses and Dissertations

Diatoms are excellent biological models of growth and intracellular oil generation. The productivity and compounds of diatoms, especially oils, support aquatic food chains and human medical and industrial needs. The qualities that made diatoms prolific producers, specifically diatom physiological features such as growth rates with intracellular lipid storage in alkaline environments, are however poorly understood. Another physiological aspect that remains unexplored is the effects of bacteria on the growth and lipid production of alkaliphilic diatoms. More studies, especially co-cultures, are needed for advances in diatom biology and strain performance for the algal biotechnological field. Besides physiology, diatom genetics using next-generation …

Characterization Of Microbial Populations In Landfill Leachate, Umut M. Bicim, Hanna Fulford, Lori A. Hoagland, Alejandro R. Sanchez, Amisha D. Shah, Inez Hua

Discovery Undergraduate Interdisciplinary Research Internship

In the United States, municipal solid waste (MSW) landfills remain a potential mining source of recoverable materials, including but not limited to critical, precious, and rare earth metals found in electronic waste. This is possible due to collectible leachate that filters through MSW landfills, carrying metals, nutrients of value, and microbes—some of which may hold key metal bioleaching properties—within. The purpose of this study is to begin analyzing leachate from MSW landfills in the American Midwest to understand the composition of microbial communities within these landfills. Landfill leachate samples sourced in northern Indiana, representing the landfill process during unique times …

Diverse Community Of Arsenic Resistant Bacteria Display Arsenate Reducing Capabilities, Stephanie Maeda

Undergraduate Honors Theses

Naturally found in soil and water environments arsenic is toxic to many organisms, carcinogenic to humans, and poses a significant public health risk. Yet communities of bacteria found thriving in arsenic ridden environments have evolved mechanisms to tolerate and exploit both oxidation states of this heavy metal (arsenite and arsenate). As the site of an old arsenic mine, Black Mountain Open Space Park in San Diego, California has yielded concentrations of arsenic in the soil between 111-14,800 ppm. Exceeding average arsenic soil concentrations and levels considered safe in the environment by the World Health Organization, we sought to characterize the …

Investigation Of An Elevational Gradient Reveals Strong Differences Between Bacterial And Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata, Kadeem J. Gilbert, Leonora S. Bittleston, Mark Arcebal K. Naive, Anthony E. Kiszewski, Perry Archival C. Buenavente, David J. Lohman, Naomi E. Pierce

Biology Faculty Publications and Presentations

Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and …

Antimicrobial Properties Of An Unknown Microorganism Isolated From The Local Environment, Danielle Duryea

Undergraduate Honors Thesis Projects

Bacterial species that cause disease can usually be combatted with antibiotics; but as the years pass, more and more bacterial pathogens are becoming resistant to these treatments. In fact, the Center for Disease Control has identified eighteen classes of bacteria ranging from urgent to concerning threats due antibiotic resistance (2019), warning the advance of an antibiotic resistance crisis in which untreatable bacterial infections will become a leading cause of death (Bennadi, 2014). The Small World Initiative is a program created in 2012 at Yale University to address the antibiotic crisis through a crowdsourcing effort where undergraduate students are encouraged to …

Effects Of A Neonicotinoid Insecticide On The Growth Of Honey Bee Gut Microbes, Macee Mitchell, Daniel Franzese, Taylor Morales, Shane Lucht, Jesse Steele, Jenifer Walke

2020 Symposium Posters

The gut microbiome plays an essential role in the overall health of organisms. However, the presence and abundance of these microbes may be altered by environmental factors, such as exposure to pesticides. The goals of this project were to understand 1) the prevalence of pesticide residues in honey bees in eastern Washington, and 2) the impact of pesticides to the honey bee gut microbiome. Accordingly, we tested bees from 24 hives among six sites across eastern Washington. High-performance liquid chromatography-mass spectrometry (HPLC-MS) was used to detect the presence and concentration of six commonly used agricultural pesticides: Carbaryl, Chlorpyrifos, Coumaphos, Cypermethrin, …

An Evaluation Of Co-Culture Parameters Effecting Antibiotic Production In Soil Microbes, Rebecca Lindow

Master's Theses and Doctoral Dissertations

The rise of infections caused by antibiotic resistant bacteria, compounded by a reduction in antibiotic discovery and development, jeopardizes human health. Historically, antibiotics derive from secondary metabolites produced by soil microbes in pure culture, but recent genetic evidence suggests that microbes can produce more secondary metabolites than are currently observed. The modified crowded plate technique directly identifies antibiotic-producing soil microbes that were co-plated with a target pathogen. Here, this technique was refined by testing the effect of a D-alanine auxotrophic target pathogen rather than a prototrophic pathogen as well as investigating conditions most conducive to antibiotic production. Antibiotic producing conditions …

Analysis Of Bacterial Dna And Water Quality: Surface Water Sampling At Gardner-Webb University, Celsea Reeder

Undergraduate Honors Theses

Part 1 of this experiment was to explore the bacterial types within the surface water on the campus of Gardner-Webb University, located in Boiling Springs, NC. Two water samples were collected from four locations on campus, including the boiling spring, Lake Hollifield, and an adjacent creek. Using the Zymo Research “Quick-DNA^™ Fungal/Bacterial Miniprep Kit,” the bacterial DNA within these samples was isolated and sent to Psomagen, Inc. for analysis. The resulting DNA sequences were analyzed through BLAST, and subsequently interpreted. For the second part of this experiment, one surface water sample was taken from the boiling spring, and another …

Factors Affecting The Microbiome Of Ixodes Scapularis And Amblyomma Americanum, R. Jory Brinkerhoff, Chris Clark, Kelly Ocasio, David T. Gauthier, Wayne L. Hynes

Biological Sciences Faculty Publications

The microbial community composition of disease vectors can impact pathogen establishment and transmission as well as on vector behavior and fitness. While data on vector microbiota are accumulating quickly, determinants of the variation in disease vector microbial communities are incompletely understood. We explored the microbiome of two human-biting tick species abundant in eastern North America (Amblyomma americanum and Ixodes scapularis) to identify the relative contribution of tick species, tick life stage, tick sex, environmental context and vertical transmission to the richness, diversity, and species composition of the tick microbiome. We sampled 89 adult and nymphal Ixodes scapularis (N …

Glycolic Acid Utilization In Two Species Of Marine Bacteria, Erik S. Timsak

STAR Program Research Presentations

Interactions between bacteria and phytoplankton are crucial for the cycling of organic matter in marine environments. Around 50% of organic carbon taken up by marine bacteria is converted into inorganic carbon. The uptake of organic carbon by marine bacteria exuded from phytoplankton is a key factor in regulating the marine carbon cycle. One such molecule that is exuded by phytoplankton and then uptaken by marine bacteria is called glycolate - the anion of glycolic acid, a two caron molecule. Glycolate is exuded by phytoplankton during photorespiration and 10-50% of dissolved organic carbon in marine environments is comprised of glycolate. Additionally, …

Green Infrastructure Design Influences Communities Of Urban Soil Bacteria, Jessica Lee Joyner, Jordan Kerwin, Maha Deeb, George Lozefski, Bharath Prithiviraj, Anna Paitseva, John Mclaughin, Peter M. Groffman, Zhongqi Cheng, Theodore R. Muth

Publications and Research

The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree …

The Effects Of A Bacterial Endotoxin On Behavior And Sensory-Cns-Motor Circuits In Drosophila Melanogaster, Oscar Istas, Abigail Greenhalgh, Robin L. Cooper

Biology Faculty Publications

The effect of bacterial sepsis on animal behavior and physiology is complex due to direct and indirect actions. The most common form of bacterial sepsis in humans is from gram-negative bacterial strains. The endotoxin (lipopolysaccharide, LPS) and/or associated peptidoglycans from the bacteria are the key agents to induce an immune response, which then produces a cascade of immunological consequences. However, there are direct actions of LPS and associated peptidoglycans on cells which are commonly overlooked. This study showed behavioral and neural changes in larval Drosophila fed commercially obtained LPS from Serratia marcescens. Locomotor behavior was not altered, but feeding …

Diverse Microbial Communities Hosted By The Model Carnivorous Pitcher Plant Sarracenia Purpurea: Analysis Of Both Bacterial And Eukaryotic Composition Across Distinct Host Plant Populations, Jacob J. Grothjan, Erica B. Young

Biological Sciences Faculty Articles

Background. The pitcher plant Sarracenia purpurea supplements nutrient acquisition through carnivory, capturing insect prey which are digested by a food web community of eukaryotes and bacteria. While the food web invertebrates are well studied, and some recent studies have characterized bacteria, detailed genetic analysis of eukaryotic diversity is lacking. This study aimed to compare eukaryotic and bacterial composition and diversity of pitcher communities within and between populations of host plants in nearby but distinct wetland habitats, and to characterize microbial functions across populations and in comparison with another freshwater community.

Methods. Pitcher fluid was sampled from the two …

The Gut Microbiome: Is Fecal Matter Microbial Composition A Proxy For Intestinal Microbial Composition In Studies Of The Microbiome, Enique Reyes

All Master's Theses

As many health phenomena seem to be affected directly and indirectly by the microbiome, gut microbiome research has increased in the last decade. Issues such as allergies, cancer, obesity, and other health complications have been shown to be influenced by the microbiome. Most of gut microbiome research is done by collecting and sequencing the DNA of the microbiome of the fecal matter from model organisms or human subjects. Studies that use this method of sample collection and analysis assume that fecal matter microbiomes are similar to intestinal microbiomes, and that it can be used as a proxy. At present, no …

Better Living Through Chemistry: Addressing Emerging Antibiotic Resistance, Nathan P. Coussens, Ashley L. Molinaro, Kayla J. Culbertson, Tyler Peryea, Gergely Zahoránszky-Köhalmi, Matthew D. Hall, Dayle A. Daines

Biological Sciences Faculty Publications

The increasing emergence of multidrug-resistant bacteria is recognized as a major threat to human health worldwide. While the use of small molecule antibiotics has enabled many modern medical advances, it has also facilitated the development of resistant organisms. This minireview provides an overview of current small molecule drugs approved by the US Food and Drug Administration (FDA) for use in humans, the unintended consequences of antibiotic use, and the mechanisms that underlie the development of drug resistance. Promising new approaches and strategies to counter antibiotic-resistant bacteria with small molecules are highlighted. However, continued public investment in this area is critical …

Best Practices For Healthy Beaches And Watersheds In Maine: Potential Bioremediation Strategies For Improving Water Quality, Elyse Defranco

Maine Sea Grant Publications

Maine’s watersheds face many challenges from human inputs, with pollution threatening the health of our beaches, rivers, and aquaculture operations. Maine’s rural communities often lack the resources to update aging sewer infrastructure or to adequately maintain septic systems, and these sources of pollution impact watershed health. In addition to addressing sources of pollution, which can be difficult to ascertain and challenging to address when located, bioremediation practices have the potential to aid in clean-up efforts. New technological advances and research discoveries in creative forms of bioremediation are being developed and are producing promising case studies around the world. These new …

The External Microbiome Of Bats: Effects Of Season, Site, Host Species, And Body Region, Kyle G. George

Master's Theses and Doctoral Dissertations

White-nose syndrome is a cutaneous fungal disease that has been detrimental to North American bats for over 10 years, but few investigators have examined the natural microbiota living on these mammals. I explored the influence of season, geographic site, host species, and body region on the external microbiome of four cave-hibernating and two migratory species. Automated ribosomal intergenic spacer analysis was used to profile bacterial communities from three cutaneous regions of 222 bats across winter and summer sites in Michigan, Illinois, and Kentucky. Season, site, host species, and body region all influenced the composition of external bacterial communities, but geographic …

A Study On The Dissolution Of Autunite Minerals By Facultative Bacteria In Bicarbonate Media, Sandra C. Herrera Landaez

FIU Electronic Theses and Dissertations

Uranium (U) is a key contaminant at the Hanford site. The formation of uranyl-phosphate bearing minerals such as autunite as a result of tripoliphosphate injections has been used as a U immobilization strategy. Bacteria are known as key factors governing the fate and transport of soil contaminants. This research evaluated the interaction of facultative bacteria Shewanella Oneidensis MR-1 with autunite mineral in bicarbonate-amended media solutions. The concentration of several elements such as U, calcium (Ca) and phosphorous (P) released as a result of autunite mineral biodissolution were determined as a function of time; changes in cell density and protein assay …

An Analysis Of Bacterial Contamination Of Chicken Eggs And Antimicrobial Resistance, Holly Spitzer

All College Thesis Program, 2016-2019

Chicken eggs are a major component of American diets, with an average yearly consumption of approximately 250 eggs per person (American Humane Society). While highly nutritious, eggs are also one of the leading causes of food poisoning and food borne illness in the United States. Eggs may become contaminated by a number of different types of bacteria during production, including Salmonella, a group of bacteria that, according to the CDC, causes more than 1.2 million cases of food borne illness in the United States every year. In an effort to decrease the frequency of bacterial contamination, many food producers …

Isolation And Characterization Of Microbial Community Associated With Diadumene Lineata, The Orange-Striped Sea Anemone, Tiffany Lin, Andrew Weir

Student and Faculty Research Days

The orange-striped sea anemone, Diadumene lineata, is a marine invertebrate that can be found in the Northern Hemisphere. Distribution of Diadumene lineata ranges from Japan to the Gulf of Argentina. This invasive anemone originated from the Pacific Coast of Asia and serves as a host for a diverse microbial community including a photosynthetic alga. The epiphytic bacteria adhere to the outer surface as well as to the gastrovascular cavity of the host. The microbial community associated with Diadumene lineata is relatively unknown. This study attempted to isolate and identify bacteria commonly associated with this invasive marine invertebrate. Diadumene lineata was …

Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford

Honors Theses and Capstones

Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …

Engineering Novel Detection And Treatment Strategies For Bacterial Therapy Of Cancer, Jan T. Panteli

Doctoral Dissertations

Finding and treating cancer is difficult due to limited sensitivity and specificity of current detection and treatment strategies. Many chemotherapeutic drugs are small molecules that are limited by diffusion, making it difficult to reach cancer sites requiring high doses that lead to systemic toxicity and off-target effects. Tomographic detection techniques, like PET, MRI and CT, are good at identifying macroscopic lesions in the body but are limited in their ability to detect microscopic lesions. Biomarker detection strategies are extremely sensitive and able to identify ng/ml concentrations of protein, but are poor at discriminating between healthy and disease state levels due …