Life Sciences Commons^™

Using Single Cell Genomics To Explore The Impact Of Marine Viruses On Microbial Respiration., Paxton Tomko

MCB Articles

Viral metabolic reprograming of marine prokaryotes, through the use of virally encoded auxiliary metabolic genes (AMGs), plays a critical role in marine ecosystem function by influencing biochemical cycles and genetic diversity in these environments. Despite the fundamental role viruses play in global environmental ecosystems, they remain an understudied aspect of microbial ecology and evolution, in part due to the methods available for studying virus host interactions in natural systems. Thus far, metagenomic analyses have been used to study the interactions of virus host pairs, but these types of analyses have their limitations in accurately linking viruses to hosts, or culture-based …

Identification Of Novel Biosynthetic Gene Clusters Encoding For Polyketide/Nrps-Producing Chemotherapeutic Compounds From Marine-Derived Streptomyces Hygroscopicus From A Marine Sanctuary, Hannah Ruth Flaherty

Honors Theses and Capstones

Nearly one out of six deaths in 2020, around ten million people, were caused by cancer, making it a leading cause of death worldwide (WHO, 2022). This major public health issue, in addition to the rise of multidrug-resistant (MDR) pathogens, provides a high demand for the discovery of new pharmaceutical drugs to be used clinically to treat these conditions. The Streptomyces genus accounts to produce 39% of all microbial metabolites currently approved for human health, indicating its potential as an important species to study for antimicrobial and anticancer agents. The long linear genome of Streptomyces contains specialized sequences known as …

The Expanding Marine Built Environment And Biofilm Formation Processes, Rachel Mugge

Dissertations

The marine built environment (i.e., places or things made or modified by humans) in the northern Gulf of Mexico is rapidly expanding and includes over 2,000 known historic shipwrecks, nearly 4,100 artificial reefs, and other built structures for natural resource extraction, marine aquaculture, renewable energy generation, munitions dumping areas, and commercial and recreational activities. While these structures have the potential to develop into artificial reefs, acting as biodiversity hotspots that provide food and shelter and facilitate organism transport, it is unclear how they affect biodiversity and ecosystem function in the marine environment. The success of artificial reefs to become ecosystems …

Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris

Electronic Thesis and Dissertation Repository

Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.

Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …

Alterations Of The Gut Mycobiome In Patients With Ms - A Bioinformatic Approach, Saumya Shah

Honors Scholar Theses

The mycobiome is the fungal component of the gut microbiome and is implicated in several autoimmune diseases. However, its role in multiple sclerosis (MS) has not been studied. We performed descriptive and formal statistical tests using the R language to characterize the gut mycobiome in people with MS (pwMS) and healthy controls. We found that the microbiome composition of multiple sclerosis patients is different from healthy people. The mycobiome had significantly higher alpha diversity and inter-subject variation in pwMS than controls. Additionally, Saccharomyces and Aspergillus were over-represented in pwMS. Different mycobiome profiles, defined as mycotypes, were associated with different bacterial …

High Arctic Permafrost Microbial Characterizations: Siberian And Svalbard Microbiology Of Ancient And Active Layer Permafrost, Katie Sipes

Doctoral Dissertations

Permafrost is soil that has remained frozen for at least two years. The active layer is a surface portion above the permafrost that experiences seasonal thaw and refreezing. The environmental characteristics of permafrost and active layer are different but are directly related to each other. As the climate continues to warm, the active layer will expand into the permafrost and the continuously frozen soil will be subjected to seasonal thawing. The organisms that inhabit both the active layer and the permafrost soil will respond differently to the climate based on where in the soil they are present and the soil …

Response Of The Soil Bacterial Community, Resistome, And Mobilome To A Decade Of Macrolide Antibiotic Contamination, Liam Paul Brown

Electronic Thesis and Dissertation Repository

Biosolids (treated sewage sludge) are used as agricultural fertilizer but are frequently contaminated with macrolide antibiotics, to which resistance is rising among historically susceptible bacteria. To determine if the land-application of macrolides carried in biosolids could promote antibiotic resistance in soil bacteria, soil plots were exposed annually to environmentally realistic or high doses of macrolides for ten years. I sequenced the bacterial 16S ribosomal DNA, metagenomic DNA, and integron gene cassettes within the treated and antibiotic-free soil to compare the compositions and diversities of the bacterial communities, antibiotic resistance genes, and mobile genetic elements. I determined that the high dose …

Exploration Of The Role Of Microbiome Structure, Metabolism, And Modification In Black Band Disease Etiology, Patricia Waikel

FIU Electronic Theses and Dissertations

The coral microbiome plays an integral role in coral health. Modification of the microbiome is thought to alter susceptibility to disease. Black Band Disease (BBD), is polymicrobial, mat forming, and affects reef building coral globally. Dominated by the cyanobacterium Roseofilum reptotaenium, it has been noted to increase in virulence with increasing temperatures, making BBD of particular concern in the face of climate change-induced warming seas. The active sulfur cycle of BBD makes dimethylsulfoniopropionate (DMSP), a widely available source of sulfur in the marine environment, of particular interest in the study of BBD. Traditional infection studies require field collection and …

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 …

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, …

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen

Senior Honors Projects, 2010-2019

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also …

Fungi Of Forests: Examining The Diversity Of Root-Associated Fungi And Their Responses To Acid Deposition, Donald Jay Nelsen

Graduate Theses and Dissertations

Global importance of forests is difficult to overestimate, given their role in oxygen production, ecological roles in nutrient cycling and supporting numerous living species, and economic value for industry and as recreational zones. Fitness of the forest-forming trees strongly depends on microbial communities associated with tree roots. In particular, fungi impact tree fitness: mycorrhizal species provide water and nutrients for the trees in exchange for C, endophytic fungi play key roles in host defense against pathogenic organisms, and saprotrophic fungi decompose dead organic matter and facilitate nutrient cycling. In addition, pathogenic fungal species strongly affect forest fitness. Despite their importance, …

The Microbial Ecology Of Bacterial Lignocellulosic Degradation In The Ocean, Hannah Laing Yee Woo

Doctoral Dissertations

The overarching theme of my dissertation is to study the role of bacteria in lignocellulose degradation. In recent years, more research has investigated the biodegradability of lignocellulose for biofuel production. The components of the lignocellulosic plant cell wall are considered intrinsically recalcitrant due to their structure. However, we hypothesize that these components are not intrinsically recalcitrant but their biodegradation is contingent on the environmental conditions, particularly the bacterial diversity. We believe bacteria will become especially important in lignocellulose degradation in conditions that are unfavorable for white-rot fungi. Therefore, we investigated the potential for lignin degradation by bacteria in the ocean …

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Elucidating The Impact Of Roseophage On Roseobacter Metabolism And Marine Nutrient Cycles, Nana Yaw Darko Ankrah

Doctoral Dissertations

As the most abundant biological entities in marine environments, viruses are an important component of marine food webs. The activity of viruses contributes significantly to the mortality of marine microorganisms, ultimately influencing biological function and chemical composition of aquatic systems by impacting species composition and flow of carbon, nitrogen and other nutrients. Despite the growing recognition that viral activity contributes to marine biogeochemical cycles, the extent to which virus infection reshapes host metabolism and the effect of this alteration on the composition of host lysate remains poorly understood. Additionally, the degree to which natural bacterioplankton communities metabolise the released lysate …

Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood

Doctoral Dissertations

Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …

Characterization Of The Extracellular Proteome Of A Natural Microbial Community With An Integrated Mass Spectrometric / Bioinformatic Approach, Brian Keith Erickson

Doctoral Dissertations

Proteomics comprises the identification and characterization of the complete suite of expressed proteins in a given cell, organism or community. The coupling of high performance liquid chromatography (LC) with high throughput mass spectrometry (MS) has provided the foundation for current proteomic progression. The transition from proteomic analysis of a single cultivated microbe to that of natural microbial assemblages has required significant advancement in technology and has provided greater biological understanding of microbial community diversity and function.

To enhance the capabilities of a mass spectrometric based proteomic analysis, an integrated approach combining bioinformatics with analytical preparations and experimental data collection was …