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Microbiology

University of Tennessee, Knoxville

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The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles Apr 2019

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 ...


What’S For Dinner? Different Carbon Compounds Influence Host Metabolism In A Model Roseobacter-Roseophage System, Kaylee Rae Jacobs Apr 2019

What’S For Dinner? Different Carbon Compounds Influence Host Metabolism In A Model Roseobacter-Roseophage System, Kaylee Rae Jacobs

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Viruses that infect bacteria (temperate phages) engage in complex interactions with their hosts. These phages can have two life cycles: lytic and lysogenic. For the latter, the phage can integrate its genome into that of its host and harmlessly replicate alongside with it. Conversely, upon induction, these integrated viruses can excise from their host genome and initiate the lytic cycle. A current paradigm is that phage induction is in response to host cell stress. However, in the absence of stressors, a low level of induction in a population occurs. This poorly understood phenomenon is referred to as spontaneous prophage induction ...


Microbe Hunters: Searching For Anammox Bacteria In The Tennessee Aquarium, Claire Elbon Apr 2019

Microbe Hunters: Searching For Anammox Bacteria In The Tennessee Aquarium, Claire Elbon

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ammonium and nitrite are toxic metabolic waste products generated by aquatic macroorganisms. They are of particular concern in closed systems, such as commercial aquaria. Typically, biological filtration systems are employed to regulate levels of toxic N species as they are more cost-efficient compared to water removal and replacement. Microbial communities that reside in these systems play vital roles in transformation of toxic N species. Commonly, nitrite and ammonium are converted into nitrate via nitrification. However, even nitrate is toxic at higher concentrations. Bacteria belonging to the phylum Planctomycetes can transform ammonium and nitrite to N2 via anaerobic ammonium oxidation (anammox ...


Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen Apr 2019

Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ultramicrobacteria (UMB) are a largely uncultured, globally abundant, and metabolically active group of bacteria. UMB have cell diameters ≤0.3μm, cell volumes ≤0.1 μm3, and small streamlined genomes. Recent findings indicate that UMB aid in bioremediation and nutrient cycling, but future investigations and comprehension of current findings are skewed by highly variable nomenclature and a lack of databases for functional, genomic, geochemical, or spatial data specific to candidate UMB. We aim to develop a user-friendly open-access database of various UMB candidates linked to an open-access online map where researchers can gather genomic, spatial, and geochemical data. Our comprehensive review ...


Improving The Analysis Of T Cell Movement, Viktor Zenkov May 2018

Improving The Analysis Of T Cell Movement, Viktor Zenkov

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Vaccine-induced T cells play an important role in combating malaria by eliminating infection in the liver stage. However, as millions of hepatocytes inhabit a mouse liver and only some are infected, how T cells locate the infection site and eliminate infection remains poorly understood. Are T cells moving intentionally toward parasites, or randomly successful? To answer this, I used timed position data of malaria-specific T cells, non-specific control T cells, and a parasite, obtained from experiments in a mouse liver; I performed analyses with the null hypothesis that T cells move randomly. I used two metrics, based on distances from ...


Synechococcus As An Hooh-Consuming Helper For Prochlorococcus, Abigail Mcgettigan Jarratt May 2018

Synechococcus As An Hooh-Consuming Helper For Prochlorococcus, Abigail Mcgettigan Jarratt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

The marine cyanobacterium Prochlorococcus is an abundant and globally important microbe that contributes an estimated 40% of bacterial production in the oligotrophic ocean. The success of this photosynthetic bacterium is largely a consequence of its small cell size and streamlined genome, which are advantageous in nutrient-limited environments. However, this genomic streamlining has also led to the loss of the gene (katG) encoding catalase, an enzyme that is essential for the degradation and detoxification of the reactive oxygen species hydrogen peroxide (HOOH). HOOH is naturally present in the illuminated waters of the ocean, and in the absence of catalase, Prochlorococcus is ...


Determining If Host Serum Igg Titer Is Associated With Toxoplasma Gondii Virulence, Riley E Byrd May 2018

Determining If Host Serum Igg Titer Is Associated With Toxoplasma Gondii Virulence, Riley E Byrd

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Toxoplasma gondii is a protozoan parasite that causes the disease toxoplasmosis in animals and humans. One third of the world’s human population is chronically infected with this parasite (1). Toxoplasma gondii has two infectious forms: oocysts shed in the feces of felids (domestic and wild cats) and tissue cysts in chronically infected animals (Figure 1). Humans may become infected via ingestion of food or water contaminated with oocysts, the consumption of tissue cysts in undercooked meats, or vertical transmission from the mother to the fetus. Previous studies have found that T. gondii strains from South America are genetically diverse ...


Isolation And Identification Of A Chloromethane-Degrading Bacterium From A Strictly Anaerobic Mixed Culture, Samiha Sadruddin May 2018

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

Chancellor’s Honors Program Projects

No abstract provided.


Determining If Host Serum Igg Titer Is Associated With Toxoplasma Gondii Virulence, Riley E Byrd May 2018

Determining If Host Serum Igg Titer Is Associated With Toxoplasma Gondii Virulence, Riley E Byrd

Chancellor’s Honors Program Projects

No abstract provided.


Interactions And Growth Dynamics Of Prochlorococcus, Rhodospirilaceae, And Alteromonas In A Coculture Environment, Vasily Giovanni Carniello Apr 2018

Interactions And Growth Dynamics Of Prochlorococcus, Rhodospirilaceae, And Alteromonas In A Coculture Environment, Vasily Giovanni Carniello

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Interactions between different species of microorganisms have a significant role in the growth dynamics within the environment. (Morris 08) The specifics mechanisms of these interactions, however, are overall poorly understood. The purpose of this study is to study the interactions between the heterotrophs Rhodospirilaceae (EZ54), and Alteromonas (EZ55) and the cyanobacterium Prochlorococcus (Vol 1). Here we establish the effects the cyanobacterium has on the growth dynamics of each of the heterotrophs as well as the effect the two heterotrophs have on one another.


Quantatative Analysis Of Microbial Abundance Within Arctic Fjord Sediments Assessed Through Direct Counting, Alex Taylor Swystun Dec 2017

Quantatative Analysis Of Microbial Abundance Within Arctic Fjord Sediments Assessed Through Direct Counting, Alex Taylor Swystun

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbes found in the marine sediments are responsible for the production of nearly half of the carbon dioxide found in the atmosphere (Arrigo, 2005). The fjords of Svalbard (79°N) are not considered typical marine sediments because high iron content influences unique subsurface redox chemistry. Radiotracer studies have shown that these sediments contain active bacterial sulfate-reducing communities (Finke et al., 2016). In addition to bacteria, archaeal cells within these sediments have been in aggregates encompassed by sulfate-reducing bacteria (Ravenschlag et al., 2001). These anaerobic organisms participate in mediating environmental biogeochemical cycles, including the oxidation of methane (Ravenschlag et al., 2001 ...


Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, Abigail Amina Edwards Dec 2017

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 ...


Molecular Classification And Uv Tolerance Of Pigmented Antarctic Extremophiles, Aaron M. Perry Dec 2017

Molecular Classification And Uv Tolerance Of Pigmented Antarctic Extremophiles, Aaron M. Perry

Chancellor’s Honors Program Projects

No abstract provided.


Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), Emma Harrower Dec 2017

Systematics And Biogeography Of The Cortinarius Violaceus Group And Sequestrate Evolution In Cortinarius (Agaricales), Emma Harrower

Doctoral Dissertations

Phylogenetics is a powerful tool used for illuminating the diversity of life on Earth, their evolution and their ecology. I created a multi-gene phylogenetic tree of Cortinarius section Cortinarius and uncovered five previously overlooked species, increasing the number of species in the section from seven to twelve. All members of the clade possess both cheilocystidia and pleurocystidia and possess a pigment known as (R)-39,49-dihydroxybphenylalanine. Ancestral state reconstruction estimated that the ancestral host was most likely an angiosperm, switching hosts when encountering novel host species in new lands, and only C. violaceus associating with the Pinaceae in North America ...


Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks Dec 2017

Design And Synthesis Of Analogs Of Myo-Inositol, Serine, And Cysteine To Enable Chemical Biology Studies, Tanei J. Ricks

Doctoral Dissertations

Phosphorylated myo-inositol compounds including inositol phosphates (InsPs) as well as the phosphatidylinositol polyphosphate lipids (PIPns) are critical biomolecules that regulate many of the most important biological processes and pathways. They are aberrant in many disease states due to their regulatory function. The same is true of the phospholipid phosphatidylserine (PS) which can serve as a marker to begin apoptosis. However, the full scope of activities of these structures is not clear, particularly since techniques that enable global detection and analysis of the production of these compounds spatially and temporally are lacking. With all of these obstacles in ...


Investigating The Regulation Of Indole-3-Acetic Acid Production By The Plant Associated Microbe Pantoea Sp. Yr343, Kasey Noel Estenson Dec 2017

Investigating The Regulation Of Indole-3-Acetic Acid Production By The Plant Associated Microbe Pantoea Sp. Yr343, Kasey Noel Estenson

Doctoral Dissertations

The auxin indole-3-acetic acid (IAA) plays a central role in plant growth and development and many plant-associated microbes produce IAA. Several IAA biosynthetic pathways have been identified in microbes which use the precursor tryptophan. Pantoea sp. YR343, which was isolated from the Populus deltoides rhizosphere, is a robust plant root colonizer that produces IAA. Using genomic and metabolomics analyses, we predicted that the indole-3-pyruvate (IPA) pathway is the major pathway in Pantoea sp. YR343 for IAA production. To better understand IAA biosynthesis and the effects of IAA exposure on cell physiology, we performed proteomics on Pantoea sp. YR343 grown in ...


Bioinformatic And Experimental Approaches For Deeper Metaproteomic Characterization Of Complex Environmental Samples, Ramsunder Mahadevan Iyer Dec 2017

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 Aug 2017

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 (NO3-) or nitrite (NO2-) 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 to ...


Managing Exoelectrogenic Microbial Community Development Through Bioprocess Control For Conversion Of Biomass-Derived Streams, Alex James Lewis Aug 2017

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 ...


Complete Denitrification By The Non-Denitrifier Anaeromyxobacter Dehalogenans: The Role Of Coupled Biotic-Abiotic Reactions, Jenny Rae Onley Aug 2017

Complete Denitrification By The Non-Denitrifier Anaeromyxobacter Dehalogenans: The Role Of Coupled Biotic-Abiotic Reactions, Jenny Rae Onley

Doctoral Dissertations

Nitrous oxide (N2O) is a potent greenhouse gas and ozone-depleting substance produced by many different pathways in the nitrogen cycle, including nitrification, denitrification, and chemodenitrification. Abiotic sources of N2O such as the chemical reaction between nitrite (NO2-) and ferrous ion (Fe[II]) are generally neglected in studies of N turnover in soils. Abiotic controls containing nitrate (NO3-) and ferric iron (Fe[III]) fail to capture potential reactions between intermediates of N cycle pathways (e.g., NO2- as an intermediate in NO3 - reduction to ammonium [NH4+] or nitrogen gas) or replenishment of ...


Evidence For The Priming Effect In Single Strain And Simplified Communities Of Estuarine Bacteria, Abigail Amina Edwards May 2017

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

Chancellor’s Honors Program Projects

No abstract provided.


Characterization Of The Chea2 Chemotaxis Operon In Azospirillum Brasilense, Erin Lutz May 2017

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

Chancellor’s Honors Program Projects

No abstract provided.


Heat Inactivation Kinetics Of Tulane Virus And Aichi Virus, Sukriti Ailavadi May 2017

Heat Inactivation Kinetics Of Tulane Virus And Aichi Virus, Sukriti Ailavadi

Masters Theses

Human noroviruses (HNoVs) and Aichi virus (AiV) causes significant number of gastrointestinal diseases worldwide. Tulane virus (TV), a cultivable HNoV surrogate, is used to determine control measures against HNoV. The objectives of this study were to determine the heat inactivation kinetics of TV and AiV in cell-culture media and TV in spinach using the first-order and Weibull models. TV and AiV in cell-culture media at ~7 log PFU/ml in 2-ml glass vials were heated at 50-58°C [degree Celsius] up to 10 min in a circulating water-bath. Surviving infectious viruses were enumerated by standard plaque assays using confluent host ...


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 May 2017

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 ...


The Microbial Ecology Of Bacterial Lignocellulosic Degradation In The Ocean, Hannah Laing Yee Woo May 2017

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 ...


Ecological And Evolutionary Dynamics Of Plant-Soil Feedbacks: Influences On Evolution And Range Dynamics, Michael E. Van Nuland May 2017

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 ...


Exploring Enrichment Cultures Of Denitrifying Microorganisms From El Yunque National Forest, Samiha Ahsan, Jenny Onley, Frank Loeffler Dec 2016

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.


Switchgrass Extractives Have Potential As A Value-Added Antimicrobial Against Plant Pathogens And Foodborne Pathogens, Alexander Ian Bruce Dec 2016

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 ...


Molecular And Ecological Aspects Of The Interactions Between Aureococcus Anophagefferens And Its Giant Virus, Mohammad Moniruzzaman Dec 2016

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 ...


Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li Dec 2016

Tetrameric Photosystem I: From Initial Discovery And Characterization In Chroococcidiopsis Sp. Ts-821 To Exploration Of Its Distribution And Understanding Of Its Significance In Cyanobacteria, Meng Li

Doctoral Dissertations

Photosystem I (PSI) forms trimeric complexes in most characterized cyanobacteria. We had reported the tetrameric form of PSI in the unicellular cyanobacterium, Chroococcidiopsis sp. TS-821 (TS-821). Using Cryo-EM, a 3D model of the PSI tetramer structure at 11.5 [Angstrom] resolution was obtained and a 2D map within the membrane plane of at 6.1 [Angstrom]. In contrast to the three-fold symmetry in trimeric PSI crystal structure from T. elongatus, two different inter-monomer interactions involving PsaLs are found in the PSI tetramer. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria. Additionally, this ...