Life Sciences Commons^™

Changes In Antibiotic Resistance Of Soil Microbes During Human Decomposition, Victoria N. Beard

Chancellor’s Honors Program Projects

No abstract provided.

Isolation And Identification Of A Chloromethane-Degrading Bacterium From A Strictly Anaerobic Mixed Culture, Samiha Sadruddin

Chancellor’s Honors Program Projects

No abstract provided.

Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer

Doctoral Dissertations

The coupling of high performance multi-dimensional liquid chromatography and tandem mass spectrometry for characterization of microbial proteins from complex environmental samples has paved the way for a new era in scientific discovery. The field of metaproteomics, which is the study of protein suite of all the organisms in a biological system, has taken a tremendous leap with the introduction of high-throughput proteomics. However, with corresponding increase in sample complexity, novel challenges have been raised with respect to efficient peptide separation via chromatography and bioinformatic analysis of the resulting high throughput data. In this dissertation, various aspects of metaproteomic characterization, including …

Detection, Diversity, And Evolution Of Fungal Nitric Oxide Reductases (P450nor), Steven Adam Higgins

Doctoral Dissertations

Nitrous oxide (N₂O) is a gas responsible for significant ozone layer depletion and contributes to greenhouse effects in Earth’s atmosphere. N₂O is primarily generated by denitrification, whereby nitrate (NO_3-) or nitrite (NO_2-) is converted to gaseous N₂O or N2. Teragram quantities of N₂O are emitted annually from agricultural soils treated with nitrogenous fertilizers due to the activity of soil microbiota. Although bacteria and fungi harbor genes permitting denitrification, fungi lack NosZ, an enzyme responsible for reducing N₂O into inert N2 gas. Historically, scientists have linked fungi …

Managing Exoelectrogenic Microbial Community Development Through Bioprocess Control For Conversion Of Biomass-Derived Streams, Alex James Lewis

Doctoral Dissertations

Bioelectrochemical systems are an emerging technology capable of utilizing aqueous waste streams generated during biomass conversion of lignocellulosic feedstocks to produce valuable co-products and thus, have potential to be integrated into biorefineries. In a microbial electrolysis cell, organic compounds are converted to electrons, protons, and CO₂ by fermentative and exoelectrogenic bacteria in the anode compartment. By having the ability to extract electrons from waste streams, these systems can treat water while also producing hydrogen, and thus can improve the efficiency of biomass to fuel production by minimizing external hydrogen requirement and enabling water recycle. The overall goal of this …

Ecological And Evolutionary Dynamics Of Plant-Soil Feedbacks: Influences On Evolution And Range Dynamics, Michael E. Van Nuland

Doctoral Dissertations

Plants interact with, modify, and are affected by their soil environments. Though plant-soil interactions are well known to be important and active regulators of ecosystem function and community structure, much less is known about how these interactions affect plant evolution. The primary goal of my dissertation was to examine plant-soil interactions under a range of ecological and evolutionary contexts to better understand patterns of biodiversity, ecosystem function, and whole system responses to environmental change. Taking such an eco-evolutionary perspective allows for a holistic understanding of the causes and consequences of complex abiotic and biotic interactions that link ecosystem ecology and …

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 …

A Bug’S Life: Integration Of Anaerobic Digestion And Bioelectrochemical Systems For Enhanced Energy Recovery From Wastewater Solids And Other Waste Substrates, Jeff Ryan Beegle

Masters Theses

Organic waste streams, like domestic wastewater and municipal solid waste, have the potential to be used as feedstocks for biotechnology processes to produce high value products and energy. This thesis investigated the technological, economical, and environmental potential for integrated anaerobic digestion (AD) and bioelectrochemical system (BES) platforms as they were theoretically and physically evaluated for energy recovery from domestic wastewater. The first chapter of this thesis compared the theoretical energy efficiencies of converting waste directly into electricity, using AD and BES alone and in various combinations. This chapter reviewed the experimentally demonstrated energy efficiencies reported in the literature with comparisons …

Ecology Of Organohalide-Respiring Dehalococcoides Mccartyi: Corrinoid Cofactor-Related Community Interactions And Controls Over Strain Selection, Burcu Şimşir

Doctoral Dissertations

Organohalides such as tetrachloroethene (PCE) and trichloroethene (TCE) are among the most prevalent toxic groundwater contaminants. Remediation of organohalide-contaminated sites has high priority, and efficient and cost-effective remedies are needed to prevent environment and human exposure through contaminated water. Bacterial organohalide-respiration plays a major role in organohalide detoxification. Dehalococcoides mccartyi (Dhc) are key mediators in bioremediation, since only Dhc strains have been documented in complete detoxification of chlorinated ethenes to benign ethene. Dhc depends on other microorganisms in the environment for essential growth requirements (e.g., hydrogen and vitamins). For successful implementation of the reductive dechlorination to remediate contaminated …

Bioremediation Of Chlorinated Ethenes: Ph Effects, Novel Dechlorinators And Decision-Making Tools, Yi Yang

Doctoral Dissertations

Chlorinated solvents have been widely used in different areas of modern society. Usage of these chlorinated solvents was not necessarily accompanied with proper handling and disposal of these hazardous compounds, which caused a variety of environmental problems and continues to affect human health. Remediation of chlorinated ethenes contaminated sites has high priority for state regulators and site owners. Among the available treatment technologies, bioremediation shows great promise as a cost-effective corrective strategy for a variety of environmental pollutants. Prerequisites are that the microbiology involved in contaminant degradation and geochemical factors, such as pH, are understood, so that bioremediation technologies can …

Molecular And Ecological Aspects Of The Interactions Between Aureococcus Anophagefferens And Its Giant Virus, Mohammad Moniruzzaman

Doctoral Dissertations

Viruses are increasingly being recognized as an important biotic component of all ecosystems including agents that control the rapid ecological events that are harmful algal blooms (HABS). Aureococcus anophagefferens is a pelagophyte which causes recurrent ecosystem devastating brown tide blooms along the east coast of the USA and has recently spread to China and South Africa. It has been suggested that a large virus (AaV) is possibly an important agent for demise of brown tide blooms. This observation is consistent with the recognition of a number of other giant viruses modulating algal blooms in marine systems. In this dissertation, we …

Microbial Respiration And Community Response To Crude Oil In Deep Eastern Mediterranean And The Great Australian Bight, Jiang Liu

Doctoral Dissertations

The Deep Water Horizon (DWH) oil spill in 2010 was the largest deep ocean oil spill in world history. Very limited information about oil biodegradation is available in deep oceans other than GOM since DWH. In this study, we investigate the microbial communities’ response to crude oil contamination in the deep Eastern Mediterranean sea (E.Med) and Great Australian Bight (GAB). In addition, we will assess feasible methods for oil bioremediation in those locations.

First, we discovered the fast adaption of the E.Med deep water microbial community to oil contamination in terms of phylogeny and functional genes. Based on the 16S …

Exploring Enrichment Cultures Of Denitrifying Microorganisms From El Yunque National Forest, Samiha Ahsan, Jenny Onley, Frank Loeffler

Chancellor’s Honors Program Projects

No abstract provided.

Microbial Extracellular Enzymes In Marine Sediments: Methods Development And Potential Activities In The Baltic Sea Deep Biosphere, Jenna Marie Schmidt

Masters Theses

The deep biosphere is defined as the subsurface ecosystem in which little energy is available to microorganisms and microorganisms can live for thousands of years. Heterotrophic microbes survive in the deep biosphere even though organic matter is limited and highly recalcitrant in nature. Measuring microbial extracellular enzyme activity provides a potential means to evaluate the rate at which microorganisms are performing carbon remineralization in the energy limited sediment beneath the seafloor. Extracellular enzymes breakdown organic compounds so that the nutrients can move inside the cell and be used for energy. This study explored the role extracellular enzymes play in the …

Aerobic Bacterial Transformations Of Lignin-Derived Aromatic Compounds, Ashley Marie Frank

Doctoral Dissertations

Lignin, the most abundant aromatic polymer on earth, has been estimated to contribute ~20% of the total carbon deposited in nature and thus imparts a large influence on carbon cycling in the environment. The extraordinary abundance of carbon stored in this material renders it a desirable source of renewable carbon for a variety of applications including hydrocarbon fuels and industrial chemicals. Due to its incredibly stable architecture and entanglement with cell wall polysaccharides, however, efforts toward the conversion of lignin to high value commodities have historically been impeded. Despite this obstacle, many microbes in nature are capable of degrading lignin …

Computational Perspective For Developing Bioluminescent Yeast Estrogen Screens For Environmental Toxicology, Jun Wang

Doctoral Dissertations

The impact of endocrine disruptive chemicals to human and wild life health has raised serious public health concerns through the past decades. To address this concern, much research was involved to develop tools for screening and assessing the hormonal potential of these compounds. Yeast bioluminescent bioreporter assay was one of the tools developed as the result of these past research endeavors. In this dissertation, a yeast bioluminescent bioreporter assay system was evaluated for the screening of endocrine disruptors from both experimental and computational perspectives. The yeast bioluminescent bioreporters were first standardized and applied in the comparative study of traditional activated …

Environmentally Driven Orchestration Of Metabolisms By Prochlorococcus Spp., Martin James Szul

Doctoral Dissertations

In the oligotrophic waters of the world’s open oceans physical factors such as pH, salinity, and temperature are generally stable. The nutrient limited conditions as well as the low environmental variability endemic to these ecosystems select for specialists that gain fitness advantages through minimalism, efficiency, and thrift. These physical characteristics are thought to reduce nutrient demand while allowing for constant metabolic activity and growth, but the mechanisms that promote these fitness advantages are currently unknown. To better understand how these physiologies improve selective fitness for the dominant phytoplankton, we observed metabolic parameters under environmental conditions typical to these waters. In …

Isolation And Characterization Of Microbial Communities From Hydraulic Fracturing Fluids, Sheridan S. Brewer 6284984

Chancellor’s Honors Program Projects

No abstract provided.

Physiological Characterization Of Prochlorococcus Under Abiotic Stressors Temperature And Hydrogen Peroxide, Lanying Ma

Doctoral Dissertations

Cyanobacteria of the genus Prochlorococcus are the smallest and most abundant phytoplankters in the ocean. Temperature is a major influence on Prochlorococcus abundance and distribution in the ocean, but the physiological basis for this relationship is not well understood. In other microbes, lipid and fatty acid composition have been shown to be influenced by temperature, and temperature has also been proposed as a relevant factor for setting the elemental allocation in marine phytoplankton. In this study, we found that percentage of fatty acids unsaturation was negatively related with temperature in some Prochlorococcus strains, but this was not universal. Temperature had …

Bacterial Diversity And Function Within An Epigenic Cave System And Implications For Other Limestone Cave Systems, Kathleen Merritt Brannen-Donnelly

Doctoral Dissertations

There are approximately 48,000 known cave systems in the United States of America, with caves formed in carbonate karst terrains being the most common. Epigenic systems develop from the downward flow of meteoric water through carbonate bedrock and the solutional enlargement of interconnected subsurface conduits. Despite carbonate karst aquifers being globally extensive and important drinking water sources, microbial diversity and function are poorly understood compared to other Earth environments. After several decades of research, studies have shown that microorganisms in caves affect water quality, rates of carbonate dissolution and precipitation, and ecosystem nutrition through organic matter cycling. However, limited prior …

Identification Of Purinyl-Cobamide As A Novel Corrinoid Cofactor Of Tetrachloroethene Reductive Dehalogenases In Desulfitobacterium Spp., Meng Bi

Masters Theses

Corrinoids (e.g. vitamin B₁₂) [cyanocobalamin] are a group of structurally similar, cobaltcontaining tetrapyrrole compounds involved in a number of important biochemical reactions. In organohalide respiration, vitamin B₁₂ analogues carrying different lower bases are obligate cofactors for the reductive dehalogenases (RDases) that catalyze reductive dechlorination reactions. The focus of this research was on the isolation and characterization of a novel natural corrinoid cofactor that enables the dechlorination-coupled energy conservation in organohaliderespiring Desulfitobacterium strains. Analysis of the purified corrinoid in the cyano form using a combination of high-performance liquid chromatography (HPLC), UV-Vis [Ultraviolet–visible spectroscopy] and ultra-performance liquid chromatography-high-resolution mass …

Rare Occurrences Of Free-Living Bacteria Belonging To Sedimenticola From Subtidal Seagrass Beds Associated With The Lucinid Clam, Stewartia Floridana, Aaron M. Goemann

Masters Theses

Lucinid clams and their sulfur-oxidizing endosymbionts comprise two compartments of a three-stage, biogeochemical relationship among the clams, seagrasses, and microbial communities in marine sediments. A population of the lucinid clam, Stewartia floridana, was sampled from a subtidal seagrass bed at Bokeelia Island Seaport in Florida to test the hypotheses: (1) S. floridana, like other lucinids, are more abundant in seagrass beds than bare sediments; (2) S. floridana gill microbiomes are dominated by one bacterial operational taxonomic unit (OTU) at a sequence similarity threshold level of 97% (a common cutoff for species level taxonomy) from 16S rRNA genes; …

Geochemical Control Of Methanogenesis In Cape Lookout Bight, North Carolina, Richard Kevorkian

Masters Theses

Hydrogen exerts thermodynamic control over the exclusion of methanogens by sulfate reducers in Cape Lookout Bight, NC, marine sediments. This has been demonstrated by previous in situ measurements, but has never been demonstrated in a batch incubation of unamended sediments and has never been combined with identification of the microorganisms involved in this process. We made triplicate anoxic incubations of sediments from the upper 3 cm of sediment over 122 days while taking weekly samples for DNA extraction, cell counts, and measurements of methane, sulfate, and hydrogen. The headspaces of the bottles were initially gassed with nitrogen and the third …

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 …

Long-Term Impacts Of Tillage, Cover Crops, And Nitrogen Rates On Microbial Community Dynamics And Soil Quality Parameters Under Continuous Cotton Production In West Tennessee, Lilian Wanjiru Mbuthia

Doctoral Dissertations

Microbial communities play a central role in nutrient cycling and soil quality in agro-ecosystems. This research focused on a comparative analysis of the microbial community structure and activity of soils on long-term (31 years) continuous cotton- Gossypium hirsutum L., production in West Tennessee under conservation agricultural (CA) and conventional tillage practices that included: Nitrogen (N) fertilizer rates (N-rates) (0, 34, 67 and 101 kg N per ha); Cover crops (Hairy vetch-Vicia villosa and winter wheat- Triticum aestivum, and a No Cover control); and Tillage (Till and No-till). It was expected that microbial diversity, activity and soil quality would be …

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 …

Diversity And Function Of Sulfur Cycling Microorganisms In Sediments From Subglacial Lake Whillans, Antarctica, Alicia Marie Purcell

Masters Theses

There is a growing consensus that metabolically and phylogenetically diverse assemblages of microorganisms mediate subglacial nutrient and elemental cycling. Subglacial Lake Whillans (SLW), located under 801 m of glacial ice, was recently penetrated using environmentally clean protocols. SLW is a permanently dark, cold (-0.5 °C [degrees Celsius]), and shallow (~2.2 m) freshwater lake beneath the West Antarctic Ice Sheet. The presence and diversity of key functional genes involved in dissimilatory sulfur oxidation and reduction were examined at various depths in two sediment cores taken from SLW. Our data show a diversity of sulfur transformation genes throughout the top 34 cm …

Systems Biology Of Microcystis Blooms, Morgan Michelle Steffen

Doctoral Dissertations

Cyanobacterial harmful algal blooms (cHABs) degrade freshwater lakes worldwide. Accumulation of nuisance biomass and production of noxious secondary metabolites can result in an expansive impact on both lake ecology and the surrounding communities. The cHAB forming organism Microcystis aeruginosa is known to produce the toxin microcystin, a compound nicknamed “fast death factor,” which has been implicated in animal poisonings and human liver failure and cancers. M. aeruginosa inhabits a wide range of freshwater lakes around the world, such as Lake Erie (USA/Canada) and Lake Tai (Taihu, China), and is often a dominant member of bloom communities. Such systems are well-studied …

Relationships Among Prochlorococcus Ecotypes Across Oceanic Temperature Ranges, Jeremy Werner Chandler

Doctoral Dissertations

Prochlorococcus, the world’s smallest known photosynthetic organism, is an open ocean cyanobacterium, thought to be globally significant in nutrient cycling. Genetically and physiologically distinct “ecotypes” of Prochlorococcus populate the world’s subtropical and tropical oceans. A few of these key ecotypes comprise the majority of these populations, with the dominant ecotypes frequently varying as a function of depth and latitude. The mechanisms underlying the specific distributions of the ecotypes remain poorly understood, but temperature was believed to play a key role in latitudinal partitioning. Quantitative PCR (Q-PCR) was used to assess ecotypic abundances across transects spanning the Pacific Ocean from 27°N …

Development Of An Experimental And Computational Platform For Enhanced Characterization Of Modified Peptides And Proteins In Environmental Proteomics, Ritin Sharma

Doctoral Dissertations

Over the last decade, mass spectrometry based proteomics has been established as the front-runner in systems-level protein expression studies. However, with the field progressing into research of more and more complex samples, novel challenges have been raised with respect to efficient protein extraction and computational matching. In this dissertation, various aspects in the proteomics workflow, including experimental and computational approaches, have been developed, optimized and systematically evaluated. In this work, some of the critical factors with respect to proteomics sample preparation, like available biomass, detergent removal methods, and intact protein fractionation to achieve deeper proteome measurements were evaluated. The presented …