Browsing by Author "Wrighton, Kelly C., advisor"

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Open Access
Deciphering the biological determinants on methane cycling from Gulf Coast wetlands
(Colorado State University. Libraries, 2024) de Melo Ferreira, Djennyfer Karolaine, author; Wrighton, Kelly C., advisor; von Fischer, Joseph, committee member; Melzer, Suellen, committee member; Wilkins, Michael, committee member
In Chapter 1, I introduce the importance of coastal wetlands for ecosystem services, including carbon storage, physical barrier for natural disasters, and habitat for diverse fauna and flora. Sea level rise is one of the main environmental risks affecting coastal wetlands, because of their geographic position. The effects of saltwater intrusion into freshwater wetlands can change established environmental conditions and vegetation coverage, which affects the functionality of various ecosystem functions they provide. These changes can also affect the methane emissions from coastal wetlands, which are major sources of this potent greenhouse gas. In this chapter, I evaluate the current knowledge of microbial methane production and consumption, including aspects of the ecophysiological adaptation to salinity, and the changes in the microbial ecological interactions modulated by increased salinity from marine water intrusion. In Chapter 2, I conducted a study to characterize the microbial communities and geochemistry of soil and water compartments in three coastal wetlands following a salinity gradient from Barataria Bay, Louisiana. To investigate the methane cycling microbial communities and their distribution on a freshwater flotant, Jean Lafitte swamp, and saltwater marsh wetlands, I collected soil and water samples under different vegetation coverage from each wetland. I analyzed the 16S rRNA gene sequencing and paired this data within situ methane fluxes and porewater concentrations. I also analyzed the geochemistry of the soil samples including profiling the anions, cations, pH, and redox conditions of soil and water samples across wetlands. The analysis showed that the diversity of methane cycling microbial communities decreased with increased salinity. Although the distribution and relative abundance of methanogen functional types was not impacted, with hydrogenotrophic methanogens being the most abundant across all wetlands. Looking at the methanotroph abundance and taxonomy in soil and water samples, I observed that swamp and saltwater wetlands share more methanotroph members in the water column, while the soils had more site-specific similarities. My research findings contribute to the understanding of methane cycling microbial tolerance to saltwater and may be used in future works to create more robust methane prediction models. In Chapter 3, I summarize the key aspects of microbial methane cycling in coastal wetlands and offer future directions for pairing geochemical and microbial data, including using an 'omics' approach and expanding investigation to more wetlands. We discuss the valuable findings these tools can give, contributing to a more accurate prediction of the metabolisms behind the ecophysiology and ecology of methane fluxes in coastal wetlands, and how targeting specific genes and metabolism can better help climate model efforts. In the Appendix sections, I give an expanded characterization of the wetlands site description, hydrology, vegetation and topological heterogeneity. I observed that, although relatively close in geographical position, each wetland has a different salinity range, vegetation type and microtopography that can influence the distribution of microorganisms in the soil and water. Here, we also analyzed the redox potential, dissolved oxygen, pH and geochemical compounds (bromide, nitrate, ammonium, acetate, sodium, potassium, magnesium, sulfate, chloride, and iron (II)) of these wetlands. We found no correlation between geochemistry with depth, but noticed higher salt contents in the saltwater marshes, and shared geochemistry between the swamp and freshwater flotant wetlands, as expected. Conclusively, this thesis contributes to the understanding of microbial communities to natural fluxes of methane in coastal wetlands and their interaction with the geochemistry of these ecosystems.
Open Access
From computation to communication: unveiling Salmonella metabolic plasticity and public perceptions of the microbial world using multi-omics and thematic analysis
(Colorado State University. Libraries, 2024) Kokkinias, Katherine, author; Wrighton, Kelly C., advisor; Kelp, Nicole, committee member; Borlee, Brad, committee member; Weir, Tiffany, committee member
Research and communication on microorganisms and microbiomes has become increasingly important in recent decades due to evolving threats posed by infectious diseases and microbial contributions to ecological systems. Antibiotic resistance presents a significant challenge to global health equity, with nontyphoidal Salmonella infections being a prominent concern. Despite its prevalence and impact, Salmonella infections lack effective vaccines, posing a serious threat to vulnerable populations. Concurrently, misconceptions and misinformation about microorganisms and microbiomes can arise given the dynamic nature of scientific research which can hinder effective science communication and health outcomes. Despite this, little is known about public perceptions of microorganisms and microbiomes, impeding our ability to create effective, tailored science messaging. Both basic pathogen research and science communication research are essential to identify targeted prevention strategies and to understand public perceptions of microorganism and microbiomes. This dissertation spans microbiome and science communication research, employing both qualitative and quantitative methods. The overarching research goals of this dissertation are to 1) lay the groundwork for therapeutics by studying Salmonella metabolism and metabolic plasticity, 2) develop a multi-omics repository to expand the usability of our omics datasets, and 3) understand public perceptions of microorganisms and microbiomes to improve future microbial science communication efforts. Chapter 1 as the introductory chapter reviews the current state of Salmonella and science communication research, providing a context for the new research presented in this dissertation. Through a multi-omics approach, Chapter 2 explores the metabolic strategies of Salmonella under different diet backgrounds and over time, offering insights into potential therapeutic targets. Chapter 3 introduces the CBA_DREAMM database, facilitating centralized storage and sharing of multi-omics datasets to enhance communication of our research and collaboration in microbiome research. Chapter 4 investigates public perceptions of microbes and microbiomes in the United States, revealing a need for tailored science communication efforts. Additionally, the study emphasizes the importance of clear communication, trust, and emotions, like apathy, in science communication. Chapter 5 is the conclusion, summarizing findings from Chapter 2, 3, and 4 and describing future directions. By bridging natural and social sciences, this dissertation aims to inform strategies for tackling global issues by advancing microbiome and science communication research.
Open Access
Multi-omics investigation of interactions between persistent bacteria and Salmonella in the inflamed gut
(Colorado State University. Libraries, 2023) Leleiwi, Ikaia, author; Wrighton, Kelly C., advisor; Prenni, Jessica, committee member; Szymanski, Erika, committee member; Weir, Tiffany, committee member
Salmonella is a globally relevant enteric pathogen responsible for numerous outbreaks and debilitating illness yearly. Expansive tropism allows Salmonella to find bastion in zoonotic reservoirs including prominent food animals. Continued prophylactic antibiotic use in livestock and therapeutic antibiotic use in humans has increased selection for multi-drug resistant Salmonella varieties. Most of the current research on Salmonella enteric disease is performed absent complete native gut microbiota. Further, common murine models that could facilitate study of Salmonella in a robust community setting lack model-specific microbiome resources to accomplish the feat. Presented in this dissertation is a comprehensive catalogue of CBA/J mouse gut microbial genomes created as a resource for the research community. The genome database was used to recruit various omics data types to expand the current knowledge of Salmonella infection in a complex community setting, identifying community members robust to inflammation and with potential to further explore as probiotics. In Chapter 1, I review the current state of Salmonella pathogenesis in the context of the gut microbiome. The focus here is to survey the literature for prominent Salmonella mechanisms of infection and how they relate to both host and commensal microbes. I explore host responses to Salmonella and microbial metabolites capable of affecting Salmonella pathogenesis. This microbiome-centric take on Salmonella infection implies a need for comprehensive methods to examine microbes and their processes in vivo, including queries of genes and gene products. A special emphasis on multi-omics approaches is mentioned in this section as powerful tools to holistically study the complete Salmonella-included gut microbiome and to address deficiencies in prior work, ultimately providing more translatable results impacting human health. Chapter 2 outlines the creation of the CBAJ-DB – a first of its kind bacteria and virus genome collection produced from the gut communities of Salmonella infected and uninfected CBA/J mice. Relevance of this work to Salmonella research is explained, emphasizing the CBA/J model advantages to study enteric infection in unperturbed gut communities. Robust genome recovery from deep sequencing yielded over 2,000 bacterial metagenome-assembled genomes including novel bacteria strains and taxa with implications for other mouse breeds and human microbiomes. Viral genomes reconstructed from metagenomic sequencing were linked to bacteria hosts and mined for genes germane to bacteria function. The complete functional potential of the CBA/J gut community in infected and uninfected mice was also explored, detailing a decrease in immune-modulatory functional potential following Salmonella infection, and implying a potentially important role of Alistipes sp. in butyrate production. Importantly, work from this chapter provides the infrastructure for genome-resolved multi-omics investigations detailed in Chapter 3 that are critical to determine functional links between Salmonella and the commensal microbiota. In Chapter 3 additional metagenomic sequencing is combined with the CBAJ-DB and used to recruit metatranscriptomic and metabolomic data from infected and uninfected CBA/J mice. We reveal expression and metabolites that implicate numerous commensal bacteria with the flow of sulfur in the inflamed intestine, making it available for host oxidation to tetrathionate in support of Salmonella anaerobic respiration. Current dogma surrounding Salmonella lactate utilization from the host is also confronted by our data, which implies potential cross feeding on microbially derived D-lactate by Salmonella during peak infection. These expression data are supported by random forest and logistic regression modeling which determined genes for D-lactate production or utilization are important to Salmonella-association of other bacteria in the inflamed gut. Relatively abundant bacteria observed in Chapter 2 were confirmed to be active in infected communities and to be expressing genes relevant to Salmonella processes like chitinase, lactate dehydrogenase, and sulfatase. Not only does this chapter illustrate the utility of the CBAJ-DB but it highlights how multi-omics investigation in complete ecosystems can unveil results that may be different than claims made based on in vitro or reduced community in vivo studies. The final chapter presented here summarizes the key findings from Chapters 2 and 3 and offers avenues for future research including specific strain isolation from infected communities and subsequent Salmonella competition experiments to determine probiotic therapeutic potential. This dissertation aims to (1) Examine the diversity of the CBA/J mouse gut and provide a genomic resource to the microbiome community, (2) using various omics techniques, discover interactions between Salmonella and commensal bacteria that could impact pathogenesis, and (3) identify members of the inflamed community with probiotic potential that are indifferent to Salmonella or that display niche overlap for substrate competition with Salmonella. Ultimately, this dissertation provides a comprehensive examination of Salmonella infection amidst a whole and robust microbiome identifying important membership in the inflamed community and linking autochthonous processes with pathogenic ones to better understand Salmonella enteric disease.
Open Access
Putting microbial polyphenol metabolism on the map: using microbiome science to revise soil chemical paradigms
(Colorado State University. Libraries, 2022) McGivern, Bridget B., author; Wrighton, Kelly C., advisor; Hagerman, Ann, committee member; Borch, Thomas, committee member; Prenni, Jessica, committee member; Wilkins, Michael J., committee member
To view the abstract, please see the full text of the document.
Open Access
The whole is greater than the sum of the parts: piecing together microbial methylated amine metabolism
(Colorado State University. Libraries, 2020) Borton, Mikayla A., author; Wrighton, Kelly C., advisor; Wilkins, Michael J., committee member; Borch, Thomas, committee member; Chan, Siu Hung Joshua, committee member
To view the abstract, please see the full text of the document.