Microbiology Commons^™

Novel Microbial Guilds Implicated In N2o Reduction, Guang He

Doctoral Dissertations

N₂O is a long-recognized greenhouse gas (GHG) with potential in global warming and ozone depletion. Terrestrial ecosystems are a major source of N₂O due to imbalanced N₂O production and consumption. Soil pH is a chief modulating factor controlling net N₂O emissions, and N₂O consumption has been considered negligible under acidic conditions (pH <6). In this dissertation, we obtained solids-free cultures reducing N₂O at pH 4.5. Furthermore, a co-culture (designated culture EV) comprising two interacting bacterial population was acquired via consecutive transfer in mineral salt medium. Integrated phenotypic, metagenomic and metabolomic analysis dictated that the Serratia population excreted certain …

Identification Of The Type Eleven Secretion System (T11ss) And Characterization Of T11ss-Dependent Effector Proteins, Alex S. Grossman

Doctoral Dissertations

Host-associated microbes live in dangerous environments as a result of host immune killing, nutrient provisioning, and physiological conditions. Bacteria have evolved a host of surface and secreted proteins to help interact with this host environment and overcome nutrient limitation. The studies included within this dissertation describe the identification of a novel bacterial secretion system which has evolved to transport these symbiosis mediating proteins. This system, termed the type eleven secretion system (T11SS), is present throughout the Gram negative phylum Proteobacteria, including many human pathogens such as Neisseria meningitidis, Acinetobacter baumanii, Haemophilus haemolyticus, and Proteus vulgaris. Furthermore, …

Enterobactin-Based Immune Interventions Against Gram-Negative Bacterial Infections, Huiwen Wang

Doctoral Dissertations

Enterobactin (Ent)-mediated iron acquisition is critical for many Gram-negative bacteria to survive in the host. Given the bacteriostatic effect of lipocalin-2 resulting from its potent Ent-binding ability, immune interventions directly targeting Ent is a promising antimicrobial strategy against Gram-negative bacterial infections. Moreover, hyperimmune egg yolk antibody is an emerging passive immune agent for the control of bacterial infections. Oral administration of anti-Ent egg yolk antibody may confer passive immune protection against Ent-dependent enteric pathogens. In this dissertation study, multidisciplinary approaches in conjunction with different model systems (in vitro, in vivo, and ex vivo) were used to …

Mechanisms By Which Xenorhabdus Nematophila Interacts With Hosts Using Integrated -Omics Approaches, Nicholas C. Mucci

Doctoral Dissertations

Nearly all organisms exist in proximity to microbes. These microbes perform most of the essential metabolic processes necessary for homeostasis, forming the nearly hidden support system of Earth. Microbial symbiosis, which is defined as the long-term physical association between host and microbes, relies on communication between the microbial community and their host organism. These interactions among higher order organisms (such as animals, plants, and fungi) and their bacteria links metabolic processes between interkingdom consortia. Many questions on microbial behavior within a host remain poorly understood, such as the colonization efficiency among different microbial species, or how environmental context changes their …

Regulation, Mechanism Of Action, And Function Of A Small Toxin Protein In Ehec, Bikash Bogati

Doctoral Dissertations

The zor-orz locus identified in the chromosome of Escherichia coli O157:H7 EDL933 is a type I toxin-antitoxin system that consists of two homologous gene pairs zorO-orzO and zorP-orzP. The zor genes encode for small toxin proteins and the orz genes encode for small RNAs. Previously it was shown that overproduction of ZorO results in cell growth stasis whereas co-expression of orzO rescues cellular growth. Within, I demonstrate that in addition to growth inhibition, ZorO overproduction results in membrane depolarization and ATP depletion but does not impact the gross morphology of E. coli. In vivo translation and subsequent impacts …

Insights Into Steinernema Carpocapsae-Xenorhabdus Nematophila Specificity And The Role Of Adult Nematode Colonization, Erin Mans

Doctoral Dissertations

The gut microbiota can provide the host with several benefits such as the production of secondary metabolites, essential amino acids, as well as the breakdown of food or protection from pathogens. The host in turn provides the microbiota with shelter and nutrients. Given the benefits that the host and microbiota receive from their association, humans and the microbiota have evolved mechanisms of selection and specificity to assure the proper symbionts colonize a host with high fidelity. Chapter two will explore mechanisms by which Xenorhabdus nematophila nematode intestinal localization (nil) genes interact with and adhere to the nematode intestinal …

Applications Of Comparative Genomics And Data Science To Agricultural And Clinical Research, Katrina A. Schlum

Doctoral Dissertations

The advent of inexpensive, high-throughput whole genome sequencing (WGS) technologies has led to the generation of thousands of related genomes, even from a single study. Large-scale genome analysis has resulted in hypothesis-generating approaches in the fields of clinical, human and agriculture genomics. Additionally, population-level genomic sampling has resulted in a decrease in false positives in genotype-phenotype associations and an increase in understanding of the basis of disease, antibiotic and pesticide resistance. Deeper understanding of migration, genetic divergence and evolution has also been made possible due to WGS. This research applies comparative genomics, population genomics and data science approaches to whole …

Approaches To Studying Bacterial Biofilms In The Bioeconomy With Nanofabrication Techniques And Engineered Platforms., Michelle Caroline Halsted

Doctoral Dissertations

Studies that estimate more than 90% of bacteria subsist in a biofilm state to survive environmental stressors. These biofilms persist on man-made and natural surfaces, and examples of the rich biofilm diversity extends from the roots of bioenergy crops to electroactive biofilms in bioelectrochemical reactors. Efforts to optimize microbial systems in the bioeconomy will benefit from an improved fundamental understanding of bacterial biofilms. An understanding of these microbial systems shows promise to increase crop yields with precision agriculture (e.g. biosynthetic fertilizer, microbial pesticides, and soil remediation) and increase commodity production yields in bioreactors. Yet conventional laboratory methods investigate these micron-scale …

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

Subaerial biofilms (SABs) grow at the interface between the atmosphere and rock surfaces in terrestrial and subterranean environments around the world. Multi-colored SABs colonizing relatively dry and nutrient-limited cave surfaces are known to contain microbes putatively involved in chemolithoautotrophic processes using inorganic carbon like carbon dioxide (CO₂) or methane (CH₄). However, the importance of CO₂ and CH₄ to SAB biomass production has not been quantified, the environmental conditions influencing biomass production and diversity have not been thoroughly evaluated, and stable carbon and nitrogen isotope compositions have yet to be determined from epigenic cave SABs. …

Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, Abigail Amina Edwards

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Through their transformation of naturally occurring organic matter, coastal marine bacteria play an essential role in carbon cycling. A phenomenon termed the priming effect (PE) occurs when microbial communities remineralize recalcitrant organic matter faster in the presence of labile organic matter and may be prevalent in coastal systems. To understand how microbial community members interact to induce PE, it is essential to first understand the mechanisms underlying PE in single strains and simplified bacterial communities. The effect to which different concentrations and sources of labile carbon stimulated the production of bacterial biomass from riverine organic matter by two marine bacteria …

Characterization Of The Chea2 Chemotaxis Operon In Azospirillum Brasilense, Erin Lutz

Chancellor’s Honors Program Projects

No abstract provided.

Whole Genome Sequencing As A Tool For Identifying Phenotypic Properties And Underlying Genetic Mechanisms In Staphylococcus Pseudintermedius, Matthew C. Riley

Doctoral Dissertations

Staphylococcus pseudintermedius is a Gram-positive bacterial opportunistic pathogen commonly associated with dermal infections in canines, but capable of causing serious disease in other species. Reports of human infections caused by S. pseudintermedius along with an increase in resistance to multiple antibiotics highlights the importance of this organism. Whole genome sequencing can allow large scale investigation of genetic mechanisms underlying phenotypic properties that contribute to the expansion of successful S. pseudintermedius clonal lineages.

The increase in multidrug and methicillin-resistant S. pseudintermedius (MRSP) may result from horizontal transfer of genetic material between bacterial isolates, yet is thought to be rare in Staphylococci …

Switchgrass Extractives Have Potential As A Value-Added Antimicrobial Against Plant Pathogens And Foodborne Pathogens, Alexander Ian Bruce

Masters Theses

Panicum virgatum (switchgrass), a perennial grass native to North America, is a leading biomass feedstock candidate for the manufacture of cellulosic ethanol. Switchgrass is considered a viable option for biofuel production due to its cheap production cost and ability to grow on marginal land. Biofuel derived from switchgrass has been shown to be very energy efficient, producing 540% more renewable energy versus nonrenewable energy expended. Switchgrass-derived biofuel is also estimated to have greenhouse gas emissions that are 94% lower than emissions from gasoline (Schmer et al 2008). Biofuels are created through biochemical processes that utilize various enzymes and microorganisms for …

The Effects Of Exogenous Fatty Acids On Enterococcus Faecalis Og1rf, Holly Elizabeth Johnson Saito

Doctoral Dissertations

Enterococcus faecalis is a commensal of the mammalian intestine and an opportunistic pathogen that infects various locations in the human host. Specifically, the organism can infect surgical wounds, the urinary tract, and is an agent of endocarditis. Regardless of niche, this organism has access to fatty acid sources in the host, which may influence its ability to survive and cause infection; yet, the effects of exogenous fatty acids were unknown in E. faecalis. We have shown that complex sources of fatty acids such as bile or serum can significantly alter the membrane content and protect E. faecalis from acute …

Thermal Inactivation Of Shiga Toxin-Producing Escherichia Coli In Foods, Malcond David Valladares

Doctoral Dissertations

Emerging non-O157 Shiga toxin-producing Escherichia coli (STEC) were recently added to the zero tolerance policy by the USDA-FSIS. Therefore, the precise characterization of their thermal inactivation kinetics in different foods and the effect of stress on thermal inactivation are needed. This research aimed at determining the heat inactivation kinetics of non-O157 and O157 STECs in buffer and model food matrices and the effects of DnaK levels on thermal resistance after acid and heat-shock. Thermal inactivation was carried out in either in 2-ml glass vials or nylon vacuum-sealed bags for buffer and food (spinach, ground-beef, turkey deli-meat, pasta) samples, respectively. Vials …

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 …

Comparison Of Bacterial Communities Associated Spider Species Occupying Different Physical Environments, Jack Kang

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

No abstract provided.

Diversity And Activity Of Roseobacters And Roseophage, Charles Ryan Budinoff

Doctoral Dissertations

Bacteria of the Roseobacter lineage are dominant bacterioplankton in coastal systems and contribute significantly to secondary production in oceanic environments. Generalities of Roseobacter ecology, diversity, and distributions are known, but the intraspecific differences between species and their dynamics over short temporal periods is not well understood. Bacteriophage that infect Roseobacters (‘roseophage’) have the potential to shunt secondary production into the dissolved carbon pool and through the process of infection alter Roseobacter physiology. Despite their significance, little effort was made prior to the onset of this study to characterize roseophage. Using culture dependent and independent approaches, I describe the diversity and …

Role Of Surface Antigens Of Mycobacterium Spp. In Diagnosis, Ashutosh Wadhwa

Doctoral Dissertations

Mycobacterial species are ubiquitous in nature and a worldwide concern for human and animal health. The major mycobacterial infections in animals are Johne’s disease (JD) and bovine tuberculosis (bTB). Controlling these infections is difficult due to the lack of highly sensitive and sensitive diagnostic test. Currently available diagnostic tests have to be carried out in laboratory settings with well experienced and trained examiners. My goal is to develop a sensitive on-site (in-field) device for diagnosis of Johne’s disease and bovine tuberculosis. The specific aims of this thesis were (1) to review currently-used or recently developed diagnostic tests for mycobacterial infections, …

Genomic And Molecular Analysis Of The Exopolysaccharide Production In The Bacterium Thauera Aminoaromatica Mz1t, Ke Jiang

Doctoral Dissertations

Thauera aminoaromatica MZ1T is an exopolysaccharide (EPS)-producing Gram negative bacterium isolated from the wastewater treatment plant of a major industrial chemical manufacturer as the causal agent for poor sludge dewatering. It shares common features with other known Thauera spp. (i.e. Thauera aromatica, and Thauera selenatis), being capable of degrading aromatic compounds anaerobically and using acetate and succinate as carbon sources. It is unique among the Thauera spp. in its production of abundant EPS which results in viscous bulking and poor sludge dewaterability. In this respect, it is similar to Azoarcus sp. EbN1 and BH72. Thaueran is the proposed …

Mechanisms Of Antimicrobial Peptide Resistance In Campylobacter, Ky Van Hoang

Doctoral Dissertations

Campylobacter is the major bacterial cause of human gastroenteritis in the United States and other developed countries. Poultry are considered a main source of human Campylobacter infections. Thus, reduction of Campylobacter load in poultry is significant in food safety and public health. However, no effective measure is commercially available to prevent Campylobacter colonization in poultry to date. Antimicrobial peptides (AMPs) are short and bactericidal peptides widely present in intestine to limit bacterial infections. Recently, AMPs have been increasingly recognized as a novel class of antibiotics (peptide antibiotics) to control foodborne pathogens. Notably, several potent anti-Campylobacter bacteriocins, a group of AMPs …

A Study Of Some Of The Metabolic Aspects Of Host-Parasite Interaction Using The Baby Chick And Salmonella Pullorum, Elmo Sharber Dooley

Doctoral Dissertations

No abstract provided.