Microbiology Commons^™

Impact Of Endangered Animal Protection Rights, Policies, And Practices On Zoonotic Disease Spread, Daniella Fedak-Lengel

Honors Projects

Building on field research in Costa Rica and Belize, this honors project analyzes environmental and endangered animal protection policies, rights, and practices in Central America and the Caribbean, and assesses the impact of veterinary science and biological research and practice, particularly conservation biology, on animal welfare concerns. Informed by the recent surge in awareness regarding zoonoses and zoonotic disease transmission, prevention and control, resulting from the current global pandemic of SARS-CoV-2, the project assesses the need for new and innovative types of collaboration, particularly involving conservation biologists, environmental scientists, public health experts, law and policy makers, and global trade and …

Climate Warming’S Alteration Of Host-Parasite Dynamics, Ting-Hsuan Wu

Binghamton University Undergraduate Journal

Parasites and pathogens have significant roles in host population control, and thus host-parasite interactions affect biodiversity. The important question reviewed in this paper is how changes in temperature due to climate change affect host-parasite interactions. There is mounting evidence that elevated temperatures have both beneficial and detrimental effects on parasites and independently on hosts. These independent changes result in altered host-parasite dynamics through various mechanisms. If elevated temperatures enhance parasite survival, risk of disease transmission among hosts is enhanced as well. This enhancement is dependent on temperature-induced shifts in the host lifecycle, as asynchrony in host and parasite development can …

Mosquito Microbiomes: Understanding The Interface Between Microbiome, Environment, And Human Pathogens, Amanda G. Tokash-Peters

Graduate Doctoral Dissertations

The study of mosquito microbiomes promises a deeper understanding of factors influencing interactions between mosquito hosts, human pathogens, and the environment. While several studies have focused on tripartite interactions between host, pathogen, and microbiome, far fewer have analyzed the environmental factors that shape these interactions and provide the basis for the formation of microbial communities in the mosquito host. Additionally, the use of Wolbachia and similar anti-arboviral symbionts in mosquitoes to control pathogen transmission has emerged as a popular idea for mosquito control and requires further investigation. The works presented here address changes in mosquito microbiomes, including the abundance of …

Drivers Of Rickettsial Pathogen Transmission And Spillover In Local Tick Populations In Southeastern Virginia, Alexandra Cumbie

Biomedical Sciences Theses & Dissertations

Cases of spotted fever group rickettsiosis are becoming more prevalent in the United States. In Virginia, there are three human-biting ticks which are largely responsible for the spread of rickettsial pathogens and the increase in disease cases. These species include Dermacentor variabilis, Amblyomma americanum, and Amblyomma maculatum; all of which are vectors of rickettsial agents to vertebrate hosts. These species are sympatric as adults and have the potential to share large and small mammal hosts. Their interactions on and off host and their associated rickettsiae were the focus of this dissertation work. Amblyomma americanum is the vector …

Effects Of Nitrogen Fertilization And Bioenergy Crop Species On Central Tendency And Spatial Heterogeneity Of Soil Glycosidase Activities, Min Yuan, Jianjun Duan, Jianwei Li, Siyang Jian, Lahiru Gamage, Kudjo E. Dzantor, Dafeng Hui, Philip A. Fay

Agricultural and Environmental Sciences Faculty Research

Extracellular glycosidases in soil, produced by microorganisms, act as major agents for decomposing labile soil organic carbon (e.g., cellulose). Soil extracellular glycosidases are significantly affected by nitrogen (N) fertilization but fertilization effects on spatial distributions of soil glycosidases have not been well addressed. Whether the effects of N fertilization vary with bioenergy crop species also remains unclear. Based on a 3-year fertilization experiment in Middle Tennessee, USA, a total of 288 soil samples in topsoil (0–15 cm) were collected from two 15 m2 plots under three fertilization treatments in switchgrass (SG: Panicum virgatum L.) and gamagrass (GG: Tripsacum dactyloides L.) …

Spatio-Temporal Dynamics Of Fungal Communities And Their Effects On Plants, Kel Cook

Biology ETDs

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, …

Environmental Influences On Expression Of Virulence- And Survival-Associated Genes And Epigenetic Modifications Of Dna In Vibrio Vulnificus, James W. Conrad

USF Tampa Graduate Theses and Dissertations

Vibrio vulnificus is an autochthonous inhabitant of warm, brackish coastal waters and is an opportunistic pathogen that causes the highest mortality of all seafood-related illnesses (1). These fatal infections are generally caused by the clinically-associated vcgC/16S rRNA type B genotypes within the biotype I group (2–5). However, the reasons for the heightened infectiousness of the clinically-associated strains over environmentally-associated ones remains elusive, as no unique clinically-associated virulence genes have been identified through genomic sequencing or other strategies. DNA methylation may contribute to regulation of virulence by affecting gene transcription, and was investigated in the highly virulent V. vulnificus strain CMCP6. …

Potential Virus-Mediated Nitrogen Cycling In Oxygen-Depleted Oceanic Waters, M. Consuelo Gazitúa, Dean R. Vik, Simon Roux, Ann C. Gregory, Benjamin Bolduc, Brittany Widner, Margaret R. Mulholland, Steven J. Hallam, Osvaldo Ulloa, Matthew B. Sullivan

OES Faculty Publications

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ …

Shifts In The Microbiota Associated With Male Mosquitoes (Aedes Aegypti) Exposed To An Obligate Gut Fungal Symbiont (Zancudomyces Culisetae), Jonas Frankel-Bricker

University Author Recognition Bibliography: 2020

Research characterizing arthropod-associated microbiota has revealed that microbial dynamics can have an important impact on host phenotypic traits. The influence of fungi on these interactions are emerging as targets for research, especially in organisms associated with global human health. A recent study demonstrated colonization of a widespread gut fungus (Zancudomyces culisetae) in a larval mosquito (Aedes aegypti) digestive tract affected microbiomes in larvae and newly emerged adult females (Frankel-Bricker et al. Appl Environ Microbiol, 2020. https://doi.org/10.1128/AEM.02334-19) but did not investigate these processes in males. The objective of the study presented here was to assess fungal influences …

Microbiome Shifts Associated With The Introduction Of Wild Atlantic Horseshoe Crabs (Limulus Polyphemus) Into A Touch-Tank Exhibit, Ariel D. Friel, Sean A. Neiswenter, Cale O. Seymour, Lauren Rose Bali, Ginger Mcnamara, Fabian Leija, Jack Jewell, Brian P. Hedlund

Life Sciences Faculty Research

The Atlantic horseshoe crab (Limulus polyphemus) is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adult L. polyphemus in a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. …

Plankton Dynamics In An Urban, Subtropical Lake Prior To Lake Restoration, Jennifer C. Pulsifer

LSU Master's Theses

This research assessed plankton dynamics in two urban, subtropical lakes (University Lake and City Park Lake) shortly before a proposed and approved lake restoration project. Plankton dynamics were determined in University Lake by the dilution method to attempt to quantify growth rates of phytoplankton and grazing rates of zooplankton. Landry and Hassett’s (1982) dilution method has been widely used in marine systems to estimate rates of growth and grazing. In many marine systems, nutrients must be added to prevent nutrient limitation. However, it is assumed, due to the hypereutrophic conditions, that nutrients would not be a limitation in University Lake. …

Using Soil Geospatial Properties And Environments To Explore Microbial Diversity, Sharon Faye Smith

Graduate Theses and Dissertations

Soil microorganisms help maintain nutrient cycling, control carbon sequestration, impact plant productivity, and influence several soil chemical and physical properties; yet, the processes that control the microbial composition of soil and how environmental changes may affect the composition and activity of these organisms at different scales remains a difficult and intriguing puzzle for soil scientists, ecologists, and modelers. Wetlands are endangered and important ecosystems that provide several services, which are directly linked to soil function. However, few wetland assessments consider the soil environment and microbial ecology. Linking soil microbial community composition and distribution patterns to soil physio-chemical properties would provide …

Microbial Community Structures In Three Bahamian Blue Holes, Meghan J. Gordon

USF Tampa Graduate Theses and Dissertations

This study used 16S rDNA metagenomics and water chemistry to conduct an examination of microbial community dynamics and biogeochemistry in three physically adjacent, sunlit blue holes with variable hydrologic regimes on San Salvador Island, Bahamas. Church and Watling’s Blue Holes are holomictic with relatively clear waters, while Inkwell Blue Hole hosts density stratification and waters stained brown with tannins. Based on water color and clarity and physicochemical profiles, I hypothesized Church and Watling’s Blue Holes would be dominated by oxigenic photoautotrophs, and that the bottom layer of Inkwell would be characterized by euxinic (anoxic and sulfidic) conditions and host primarily …

Abundance And Distribution Of Microplastics And Phthalic Acid Esters In Selected Mangrove Areas In Peninsular Malaysia, Anuar Norkhairah

Student Works (2020-2029)

Contamination of microplastics in mangrove has been receiving growing attention as experts reckon 30 billion tonnes of plastics will accumulate in 2050. The vast increase in plastic commodities will increase microplastics abundance in mangroves as mangroves are substantially sinks and traps for plastic debris. Due to persistent properties and high surface to volume ratio of microplastics, Phthalic Acid Esters (PAEs) can be taken up by microplastics, representing a grave threat to the ecosystems. This study investigated the abundance and distribution of microplastics and PAEs in selected mangrove areas in Peninsular Malaysia. The objectives of this study are to identify the …

Influences Of Anti-Bd Bacteria On Amphibians And Their Microbiomes, Emme L. Schmidt

Honors Thesis

The fungal pathogen Batrochochytrium dendrobatidis (Bd) has been threatening amphibian populations across the globe. Recent work has discovered that bacteria isolated from certain populations of amphibians protect hosts from this pathogen. This project focuses on the anti-fungal mechanisms of Serratia marcescens, a species of bacteria isolated from a Costa Rican frog that dramatically inhibited Bd in culture. Wild-type and recombinant S. marcescens was introduced to the microbiomes of a live amphibian host, Acris blanchardi (Blanchard’s Cricket Frog) and then challenged with Bd to examine the protective effects of this bacteria. The experiment includes recombinant S. marcescens with …

The Physiology And Evolution Of Selenite Respiration In Bacteria, Michael Wells

Electronic Theses and Dissertations

The selenium oxyanions selenate (Se(VI)) and selenite (Se(IV)) can be utilized by some bacteria and archaea as terminal electron acceptors in anaerobic respiration. Se(VI) and Se(IV) respiration is mediated by a phylogenetically and ecologically diverse array of organisms, suggesting that selenium respiration is ubiquitous in natural environments. Several respiratory Se(VI) reductases have been characterized in bacteria, revealing that Se(VI) respiration has evolved independently several times in this domain. Se(IV) respiration, in contrast, has yet to be characterized. I have purified and characterized the first respiratory Se(IV) reductase from Bacillus selenitireducens MLS10. The Se(IV) reductase appeared to purify as a single …

Effects Of Light, Nutrients, And Salts On Microbial Biofilm Productivity And Detrital Processing In Aquatic Mesocosms, Bethanie Brooke Howard-Parker

Graduate Theses and Dissertations

Anthropogenic activities associated with urbanization, agriculture, and resource extraction continue to increase to support increasing needs of the growing population. These activities increase the amounts of pollutants entering freshwater streams and put aquatic ecosystems at structural and functional risk. Aquatic microbes play an important role in detrital processing in streams as a key linkage in moving carbon from detrital stocks into aquatic food webs. My research investigates the effects of light, nutrients, and salts on detrital microbes and decomposition in freshwaters using a mesocosm approach. In chapter one, I modified a current priming effect (PE) hypothesis model to include light …

A Comparative Taxonomic And Diversity Study Of Litter-Associated Fungi In Northwest Arkansas Forests, Rajaa Abdulrazzaq Abbas Al Aanbagi

Graduate Theses and Dissertations

Fungi are taxonomically the most species-rich group of organisms on the earth, ecologically occupy distinctive niches and interact with diverse other organisms throughout their biogeographic distributions and functionally play key roles through their various lifestyles. Plant litter, in particular, is a keystone component in ecosystems and provides heterogeneous microhabitats for the often overlooked litter-decomposing fungi and other organisms on the floor of temperate deciduous forests. Litter fungi involve indirect interactions with the plant, soil and whole food web network. However, the community structure and functions of litter-associated fungi as well as patterns of species richness distributed across various litter microhabitats …

Soil Microbial Diversity And Litter Decomposition Increase With Time Since Land Use Disturbance In Tropical Montane Forests Of Malaysian Borneo, Renee Sniegocki

Graduate Theses and Dissertations

Logging and forest conversion are occurring at alarming rates in the tropical forests of Southeast Asia. These disturbances alter soil chemistry, microbial diversity, and disrupt carbon cycling through shifts in litter decomposition. Direct links between microbial diversity and soil properties such as pH are well established; however, the indirect impacts of logging and forest conversion on microbial diversity and litter decomposition are poorly understood. We used surface (5 cm) soil to assess soil physicochemical properties, next-generation DNA sequencing to assess soil microbial diversity, and standardized litterbags to assess litter decomposition stabilization at five sites along a land use disturbance gradient …

Evolutionary Bioethics Advanced By Ernest Everett Just: Implications For Biology, Ethics, And Theology, Theodore Walker

Perkins Faculty Research and Special Events

Ernest Everett Just (1883-1941) is an acknowledged “pioneer” in biology, being honored with a Black Heritage postage stamp in 1996. Here we discover that Just also made pioneering contributions to general evolutionary bioethics (distinct from special medical bioethics) by advancing a cell-biology-rooted theory of the origin and continuing evolution of ethical behavior influenced by the “law of environmental dependence.”

See especially “The Origin of Man’s Ethical Behavior (1941, unpublished book manuscript) by Ernest Everett Just and Hedwig Schnetzler Just, discovered in 2018 among the collected papers of E.E. Just at the Moorland-Spingarn Research Center at Howard University.

Accordingly, evolution is …

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

Publications and Research

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 compare the …

Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates Selected From Five Different States That Use Different Fungicide Treatments, Cristian Wulkop Gil

UCARE: Research Products

Sclerotinia sclerotiorum is a plant pathogenic fungus that causes a disease called white mold that can infect more than 450 plant species including soybeans, dry beans, green beans, canola, and sunflower. This pathogen is capable of up to $252M in losses every year (U.S. Canola Association, 2014). Fungicides are widely used in developed agricultural systems to control disease. However, resistance to the most effective fungicides has emerged and spread in pathogen populations and there have been multiple reports of S. sclerotiorum isolates becoming resistant to certain fungicides. Since different fields in different states use different fungicide treatments on plants and …

Variation In The Microbiota Associated With Daphnia Magna Across Genotypes, Populations, And Temperature, Jonas Frankel-Bricker, Michael J. Song, Maia J. Benner, Sarah Schaack

University Author Recognition Bibliography: 2020

Studies of how the microbiome varies among individuals, populations, and abiotic conditions are critical for understanding this key component of an organism’s biology and ecology. In the case of Daphnia, aquatic microcrustaceans widely used in population/community ecology and environmental science studies, understanding factors that influence microbiome shifts among individuals is useful for both basic and applied research contexts. In this study, we assess differences in the microbiome among genotypes of D. magna collected from three regions along a large latitudinal gradient (Finland, Germany, and Israel). After being reared in the lab for many years, we sought to characterize any …

Diatom Community Composition Shifts Driven By Coherent Cyclonic Mesoscale Eddies In The California Current System, Zuzanna Maria Abdala

OES Theses and Dissertations

The California Current System (CCS) is characterized by an equatorward flowing eastern boundary current, as well as seasonal wind-driven coastal upwelling which supplies nutrient-rich waters to the surface and drives high coastal productivity. Cyclonic mesoscale eddies form off the coast in the CCS where they trap the highly productive upwelled coastal waters, along with their resident planktonic communities, and transport them offshore into the more oligotrophic California Current waters. The interaction between waters within and outside of the eddies is limited, and so the eddies act as natural mesocosms, where the resident phytoplankton population undergo ecological succession as the eddy …

Epidemiological Significance Of Parasitic Infections In Olive Baboons (Papio Anubis) At Gombe National Park, Tanzania, Jared S. Bakuza

Tanzania Journal of Science

Several parasites of significant health importance have been observed in baboons at Gombe National Park in western Tanzania.  However, little is known on impacts these infections have on baboon health. Baboon stools were examined for parasites using formol-ethyl technique and their health and troop membership associated with parasitic infections. Observed nematode parasites were; Streptopharagus sp., Physaloptera sp., unidentified nematodes, hookworms and Trichuris sp. Trematode parasites included Schistosoma mansoni and unidentified trematode, with the latter’s intensity being highest in DB troop baboons. Parasite egg counts (epg) for nematodes ranged from 9 to 12, and that of trematodes from 4 to 40 …

On The Inadequacy Of Species Distribution Models For Modelling The Spread Of Sars-Cov-2: Response To Araújo And Naimi, Joseph D. Chipperfield, Blas M. Benito, Robert B. O'Hara, Richard J. Telford, Colin J. Carlson

United States Public Health Resources

The ongoing pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing significant damage to public health and economic livelihoods, and is putting significant strains on healthcare services globally. This unfolding emergency has prompted the preparation and dissemination of the article “Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate” by Araújo and Naimi (2020). The authors present the results of an ensemble forecast made from a suite of species distribution models (SDMs), where they attempt to predict the suitability of the climate for the spread of SARS-CoV-2 over the coming months. They argue that climate is …

Context-Dependent Dynamics Lead To The Assembly Of Functionally Distinct Microbial Communities, Leonora S. Bittleston, Matti Gralka, Gabriel E. Levanthal, Itzhak Mizrahi, Otto X. Cordero

Biology Faculty Publications and Presentations

Niche construction through interspecific interactions can condition future community states on past ones. However, the extent to which such history dependency can steer communities towards functionally different states remains a subject of active debate. Using bacterial communities collected from wild pitchers of the carnivorous pitcher plant, Sarracenia purpurea, we test the effects of history on composition and function across communities assembled in synthetic pitcher plant microcosms. We find that the diversity of assembled communities is determined by the diversity of the system at early, pre-assembly stages. Species composition is also contingent on early community states, not only because of …

The Ecology And Conservation Of An Urban Karst Subterranean Estuary, Robert J. Scharping

USF Tampa Graduate Theses and Dissertations

Sulphur Springs is an artesian spring and part of the limestone karst topography of metropolitan Tampa, Florida, USA. Underlying this spring is an extensive cave system that hosts saltwater vents and conspicuous microbial biofilm communities. For decades, water from Sulphur Springs has been extracted and used to supplement public water supply and dry season flows in the Hillsborough River Estuary. This dissertation describes research conducted at Sulphur Springs to determine the impacts of urban land use on the underlying cave and downstream estuary ecosystems, and presents the use of this system as a model to fill certain ecological knowledge gaps. …

Diatom Voucher Flora And Comparison Of Collection Methods For Biodiversity Hotspot Upper Three Runs Creek, Katie M. Johnson

Biology Theses

Surface freshwater is a scarce resource. Due to the scarcity and necessity of this resource, it is imperative that its quality is routinely monitored. One way of monitoring water quality is through biological assessments, which include examining algal assemblages. Regionally, little remains known of algal taxa in the southeastern United States. In the past, the Academy of Natural Sciences of Philadelphia (ANSP) conducted biological assessments along the Savannah River finding Gomphonema parvulum (Kützing) Kützing 1849 to be a dominant taxon rendering assessments inconclusive. Recent studies have provided evidence that species complexes and semi-cryptic taxa have been identified within the Gomphonema …

The Gut Microbiota Of A Wild American Black Bear (Ursus Americanus) Population, Sierra Gillman

All NMU Master's Theses

The gut microbiome (GMB), the mutualistic microbial communities located in the gastrointestinal tract (GIT), has co-evolved in vertebrates to perform micro-ecosystem services to facilitate physiological functions. Despite the key role of the GMB in host health, wildlife managers have been slow to consider the ramifications of anthropogenic pressures to wildlife-GMB diversity. For example, although diet is one of the most influential determinants of a host’s GMB, many wildlife agencies allow baiting with human-provisioned foods to facilitate the harvest of wildlife such as American black bear (Ursus americanus). Additionally, much of our knowledge of wildlife-GMB relationships is based on …