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Articles 1 - 9 of 9
Full-Text Articles in Ecology and Evolutionary Biology
Mathematical Modelling Of Prophage Dynamics, Tyler Pattenden
Mathematical Modelling Of Prophage Dynamics, Tyler Pattenden
Electronic Thesis and Dissertation Repository
We use mathematical models to study prophages, viral genetic sequences carried by bacterial genomes. In this work, we first examine the role that plasmid prophage play in the survival of de novo beneficial mutations for the associated temperate bacteriophage. Through the use of a life-history model, we determine that mutations first occurring in a plasmid prophage are far more likely to survive drift than those first occurring in a free phage. We then analyse the equilibria and stability of a system of ordinary differential equations that describe temperate phage-host dynamics. We elucidate conditions on dimensionless parameters to determine a parameter …
Anthropogenic Influences On Bacterial Assemblages In Stream Biofilms, Elizabeth M. Ogata
Anthropogenic Influences On Bacterial Assemblages In Stream Biofilms, Elizabeth M. Ogata
All Graduate Theses and Dissertations, Spring 1920 to Summer 2023
Bacteria within biofilms are an essential component of stream ecosystems, influencing the movement of carbon (C), nitrogen (N), and phosphorus (P) in watersheds. To better understand the ecological effects of human activities on stream ecosystems, my research examined how nutrients and pharmaceuticals, common pollutants in streams worldwide, influence bacterial assemblages in stream biofilms. First, I tested how nutrients (N, P, iron) and pharmaceuticals (caffeine, diphenhydramine) influenced biofilm bacterial microbiomes (taxa present in at least 75% of samples of a contaminant treatment). Nutrients allowed taxa known for their ability to thrive in nutrient-rich environments to dominate microbiomes, pharmaceuticals supported a rich …
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
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. …
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
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 …
Phage-Bacteria Interaction And Prophage Sequences In Bacterial Genomes, Amjad Khan
Phage-Bacteria Interaction And Prophage Sequences In Bacterial Genomes, Amjad Khan
Electronic Thesis and Dissertation Repository
In this investigation, we examined the interaction of phages and bacteria in bacterial biofilm colonies, the evolution of prophages (viral genetic material inserted into the bacterial genome) and their genetic repertoire. To study the synergistic effects of lytic phages and antibiotics on bacterial biofilm colonies, we have developed a mathematical model of ordinary differential equations (ODEs). We have also presented a mathematical model consisting of a partial differential equation (PDEs), to study evolutionary forces acting on prophages. We fitted the PDE model to three publicly available databases and were able to show that induction is the prominent fate of intact …
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
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, …
Nitrogen Fertilization Decouples Roots And Microbes In Temperate Forests: Impacts On Soil Carbon And Nitrogen Cycling, Joseph E. Carrara
Nitrogen Fertilization Decouples Roots And Microbes In Temperate Forests: Impacts On Soil Carbon And Nitrogen Cycling, Joseph E. Carrara
Graduate Theses, Dissertations, and Problem Reports
Since the start of the industrial revolution the burning of fossil fuels has resulted in enhanced nitrogen (N) inputs into temperate forests through atmospheric deposition. As N is the limiting nutrient for tree growth across most forests, these inputs have generally enhanced above-ground biomass accumulation. However, the impacts of added N on soil carbon storage (C) are less straightforward. While the mean N response across studies is an enhancement of soil C, these results are variable with some studies reporting net C losses. The classic paradigm posits that N enhances soil C through negative effects on fungal decomposers. However, some …
Determination Of Iron-Reducing Bacterial Activities In Lake Sediments., Alexandra Kahn
Determination Of Iron-Reducing Bacterial Activities In Lake Sediments., Alexandra Kahn
Williams Honors College, Honors Research Projects
Algal blooms are growing rampantly in lacustrine systems due to an increase of phosphorus, a nutrient for algae. Phosphorus is being released into the environment causing overpopulation and eutrophication which damages the ecosystem. The availability of phosphorus is affected by the solubility of iron which is regulated through iron reducing and iron oxidizing bacteria. Phosphorus adheres to insoluble Fe(III), which prohibits algae from utilizing it, while phosphorus does not attach to soluble Fe(II) and therefore it remains available to algae. The purpose of this study was to determine how bacteria influence iron solubility and what are the ideal environmental conditions …
The Effect Of Plastic On Leaf Litter Breakdown In Urban Streams, Lisa Haneul Kim
The Effect Of Plastic On Leaf Litter Breakdown In Urban Streams, Lisa Haneul Kim
Master's Theses
The plastic component of anthropogenic litter (AL) is an emerging ecological concern and has been a focus of research, as it is long-lived, mobile, interacts with physical and chemical components of aquatic ecosystems, and breaks down into smaller pieces (i.e., microplastic, <5mm particles). Rivers are considered a major source of plastic to oceans, but little is known about plastic's abundance, distribution, and effects on ecological processes in urban streams. Previous studies report plastic is abundant in freshwater systems, especially in naturally occurring debris dam structures and overhanging vegetation which accumulate high quantities of AL, especially plastic items (i.e. bags, wrappers, packaging material), along with leaf litter and other coarse particulate organic matter. in temperate, forested streams, leaf litter is a critical food source and plays an essential role in the stream food web. the rate at which leaves break down is affected by many variables such as hydrology, water chemistry, and macroinvertebrate and microbial communities. We predicted that plastic accumulation along with leaf litter can slow leaf breakdown by reducing diversity and abundance of microbial decomposers, as well as macroinvertebrate consumers. We measured leaf breakdown, and characterized macroinvertebrate and microbial (i.e., bacterial, fungal, algal) communities in 3 litter bag treatments: leaves alone, plastic alone, and leaves mixed with plastic. Although plastic did not reduce leaf breakdown rates or have a significant effect on macroinvertebrate consumer communities, it showed distinct microbial communities compared to leaf substrates. Results will provide a new understanding of how plastic and microbial communities interact, and set the framework for future studies to look at microbial succession and macroinvertebrate diversity on other synthetic substrates in freshwater systems.