Microbiology Commons^™

Conservation Of The Che And Pho Systems In Escherichia Coli, Kimberly B. Zumbrennen, Dr. William R. Mccleary

Journal of Undergraduate Research

Bacteria live in a continuously changing environment. In order to survive, bacteria must monitor nutrients, acidity, temperature, osmolarity, etc. The use of two-component systems to sense and respond to these environmental changes is a common motif observed in a wide variety of organisms. A two-component system consists of two main proteins, a sensor and a response regulator(2). The sensor protein is a trans-membrane protein which monitors environmental fluctuations and activates the response regulator through phosphorylation. The response regulator contains two domains, the receiver module and the output domain. The receiver module is phosphorylated and dephosphorylated by the sensor protein. Communication …

Effect Of Prey Richness On A Consumer’S Intrinsic Growth Rate, Brian J. Darby, Michael A. Herman

School of Biological Sciences: Faculty Publications

The intrinsic growth rate of nonselective microbivores increases asymptotically with increasing prey biomass, but we do not know how intrinsic growth rate is affected by prey richness. The objective of this experiment was to determine the effect of prey richness on the growth kinetics of nematode predators while grazing on mixed bacterial lawns. We found that the intrinsic growth rate of Caenorhabditis elegans in laboratory culture increased asymptotically with prey richness. The mechanism of this pattern was primarily due to the best available prey species in the mixture: the intrinsic growth rate of the consumer feeding on a mixture of …

Remediation Of Tetracycline From Water Sources Using Vetiver Grass (Chrysopogon Zizanioides L. Nash) And Tetracycline-Tolerant Root-Associated Bacteria, Aparupa Sengupta

Dissertations, Master's Theses and Master's Reports - Open

Antibiotics are emerging contaminants worldwide. Due to insufficient policy regulations, public awareness, and the constant exposure of the environment to antibiotic sources has created a major environmental concern. Wastewater treatment plants (WWTP) are not equipped to filter-out these compounds before the discharge of the disinfected effluent into water sources (e.g., lakes and streams) and current available technologies are not equipped to remediate these compounds from environmental sources. Hence, the challenge remains to establish a biological system to remove these antibiotics from wastewater. An invitro hydroponic remediation system was developed using vetiver grass (Chrysopogon zizanioides L. Nash) to remediate tetracycline …

The Incidence Of Antibiotic Resistance In Mesophilic Aeromonas Isolated From The Buffalo River And From A Non-Urban Site Upstream, Amy L. Chapman

Biology Theses

Antibiotics are commonly used in agriculture and industry and their discharge is commonly seen in rivers, like the Buffalo River. This antibiotic discharge may cause a selective environment which favors the growth of antibiotic resistant Aeromonas. To study the effect of urban pollution on the antibiotic resistance in Aeromonas, 229 Aeromonas isolates were collected from fish tissues as well as sediment and water samples collected from the Buffalo River and a non-urban site (Cazenovia Creek). Seven different Aeromonas taxa were identified using biochemical tests. There were 124 (54%) isolates that were classified as atypical, which was the most commonly …

Divergent Mechanisms Of Interaction Of Helicobacter Pylori And Campylobacter Jejuni With Mucus And Mucins, Julie Ann Naughton, Karina Mariño, Brendan Dolan, Colm Reid, Ronan Gough, Mary Gallagher, Michelle Kilcoyne, Jared Gerlachscience,, Lokesh Joshi, Pauline Rudd, Stephen Carrington, Billy Bourke, Marguerite Clyne

Articles

Helicobacter pylori and Campylobacter jejuni colonize the stomach and intestinal mucus, respectively. Using a combination of mucus-secreting cells, purified mucins, and a novel mucin microarray platform, we examined the interactions of these two organisms with mucus and mucins. H. pylori and C. jejuni bound to distinctly different mucins. C. jejuni displayed a striking tropism for chicken gastrointestinal mucins compared to mucins from other animals and preferentially bound mucins from specific avian intestinal sites (in order of descending preference: the large intestine, proximal small intestine, and cecum). H. pylori bound to a number of animal mucins, including porcine stomach mucin, but …

Hypersaline Lake Environments Exhibit Reduced Microbial Dormancy, Joshua Christopher Vert

Theses and Dissertations

From acid seeps and deep-sea thermal vents to glacial ice and hypersaline lakes, extreme environments contain relatively simplified communities consisting of extremophiles that have evolved to survive and thrive under adverse abiotic conditions. In more neutral environments, microorganisms use dormancy as a common life history strategy to weather temporal fluctuations of resources or stresses until more 'optimal' conditions are present. It is unclear if dormancy is an essential survival mechanism for microorganisms in extreme environments; however, recent studies suggest that extreme environments may create stable conditions for extremophiles to the extent that dormancy is of less ecological importance. Using lake …

Identifying Pathogenic Salmonella Serotypes Isolated From South Central Va Waterways Via Sequential Pcr Analysis, Timothy M. Smith, Jr.

Theses & Honors Papers

Researchers often debate whether all serovars of Salmonella enterica are pathogenic to humans. Broiler houses containing chickens are a major source of Salmonella and serve as potential reservoirs. Therefore, farmers must take substantial measures in order to avoid contamination with their products. The primary objective of the study was to determine whether the four most clinically relevant Salmonella spp. serovars from poultry houses could be isolated from the environmental waterways in Prince Edward and Cumberland Counties of Virginia. The study adapted a serotyping method designed for typing Salmonella to gain a perspective of possible serovars that may be found in …

Assessing The Effects Of Titanium Dioxide Nanoparticles On Microbial Communities In Stream Sediment Using Artificial Streams And High Throughput Screening, Alexandra Ozaki

Master's Theses

Nano-titanium dioxide (nano-TiO2) is an engineered nanomaterial used in a wide array of commercial products. The production and use of large amounts of nano-TiO2 is resulting in the unintended release to the environment. Nano-TiO2 is known to be cytotoxic due primarily to its ability to generate reactive oxygen species, and negative impacts on a variety of organisms have been demonstrated, but the effects of nano-TiO2 on complex microbial communities under ecologically relevant conditions have rarely been tested. We conducted a controlled manipulative experiment using recirculating model streams dosed with a one-time amendment of 1mg L-1 nano-TiO2 (specifically P25). Within one …

Plant-Mediated Effects On Microbial Diversity In Mesocosms Of An Oligotrophic Bog, Karl J. Romanowicz Iv

Dissertations, Master's Theses and Master's Reports - Open

Globally, peatlands occupy a small portion of terrestrial land area but contain up to one-third of all soil organic carbon. This carbon pool is vulnerable to increased decomposition under projected climate change scenarios but little is known about how plant functional groups will influence microbial communities responsible for regulating carbon cycling processes. Here we examined initial shifts in microbial community structure within two sampling depths under plant functional group manipulations in mesocosms of an oligotrophic bog. Microbial community composition for bacteria and archaea was characterized using targeted 16S rRNA Illumina gene sequencing. We found statistically distinct spatial patterns between the …

Natural And Lignocellulose-Enriched Microbial Communities In Great Boiling Spring, Nv, Jessica Cole

UNLV Theses, Dissertations, Professional Papers, and Capstones

The natural microbial communities present in Great Boiling Spring were investigated and contrasted against those present after in situ enrichment with lignocellulose. High-throughput cultivation-independent DNA sequencing of the V8 region of the small subunit (SSU) rRNA gene generated a total of 274,119 quality-filtered pyrosequencing fragments. Twelve natural spring samples were analyzed, including four high-temperature water samples and eight sediment samples ranging from 87 - 62 °C. Eight lignocellulosic enrichments incubated in the spring sediment and water at two high-temperature sites were analyzed. The natural water communities were found to be extremely uneven but relatively constant throughout time. The natural sediment …

Spatial And Temporal Immune Response In House Flies In Response To Ingestion Of Bacillus Cereus And Eschericha Coli 0157-H7, Adam Fleming

College of Graduate Studies: Theses & Dissertations

House flies (Musca domestica L.) feed and breed on septic substrates, putting them in direct contact with a multitude of disease causing agents and can act as a bridge for those agents to humans. The house fly has previously been shown to carry many different species of bacteria that are pathogenic. Escherichia coli O157:H7 is a pathogenic enterohemorrhagic serotype of E. coli that can be vectored by the house fly. Bacillus cereus is a foodborne pathogen that has also been isolated from the house fly in previous studies. To examine vector potential for these pathogens, house flies were fed green …

Characterization Of Xylan Utilization And Discovery Of A New Endoxylanase In Thermoanaerobacterium Saccharolyticum Through Targeted Gene Deletions, Kara K. Podkaminer, Adam M. Guss, Heather L. Trajano, David A. Hogsett, Lee R. Lynd

Dartmouth Scholarship

The economical production of fuels and commodity chemicals from lignocellulose requires the utilization of both the cellulose and hemicellulose fractions. Xylanase enzymes allow greater utilization of hemicellulose while also increasing cellulose hydrolysis. Recent metabolic engineering efforts have resulted in a strain of Thermoanaerobacterium saccharolyticum that can convert C5 and C6 sugars, as well as insoluble xylan, into ethanol at high yield. To better understand the process of xylan solubilization in this organism, a series of targeted deletions were constructed in the homoethanologenic T. saccharolyticum strain M0355 to characterize xylan hydrolysis and xylose utilization in this organism. While the deletion of …

The Crispr/Cas Adaptive Immune System Of Pseudomonas Aeruginosa Mediates Resistance To Naturally Occurring And Engineered Phages, Kyle C. Cady, Joe Bondy-Denomy, Gary E. Heussler, Alan R. Davidson, George A. O'Toole

Dartmouth Scholarship

Here we report the isolation of 6 temperate bacteriophages (phages) that are prevented from replicating within the laboratory strain Pseudomonas aeruginosa PA14 by the endogenous CRISPR/Cas system of this microbe. These phages are only the second identified group of naturally occurring phages demonstrated to be blocked for replication by a nonengineered CRISPR/Cas system, and our results provide the first evidence that the P. aeruginosa type I-F CRISPR/Cas system can function in phage resistance. Previous studies have highlighted the importance of the protospacer adjacent motif (PAM) and a proximal 8-nucleotide seed sequence in mediating CRISPR/Cas-based immunity. Through engineering of a protospacer …

Lapg, Required For Modulating Biofilm Formation By Pseudomonas Fluorescens Pf0-1, Is A Calcium-Dependent Protease, Chelsea D. Boyd, Debashree Chatterjee, Holger Sondermann, George A. O'Toole

Dartmouth Scholarship

Biofilm formation by Pseudomonas fluorescens Pf0-1 requires the cell surface adhesin LapA. We previously reported that LapG, a periplasmic cysteine protease of P. fluorescens, cleaves the N terminus of LapA, thus releasing this adhesin from the cell surface and resulting in loss of the ability to make a biofilm. The activity of LapG is regulated by the inner membrane-localized cyclic-di-GMP receptor LapD via direct protein-protein interactions. Here we present chelation and metal add-back studies demonstrating that calcium availability regulates biofilm formation by P. fluorescens Pf0-1. The determination that LapG is a calcium-dependent protease, based on in vivo and in vitro …

Host Pathogen Interactions: Is Arabidopsis Thaliana Remembered By Its Nemesis Pseudomonas Syringae?, Daniel Z. Kreiser

Lawrence University Honors Projects

Plants contain innate immune systems that deter pathogen infection. Pattern recognition receptors bind microbe-associated molecular patterns (MAMPs), triggering immunity. MAMPs are proteins exclusive to pathogens that are typically indispensable for their survival. For this reason, MAMPs cannot be mutated or removed without causing pathogen death. However, this does not necessitate constitutive expression of MAMPs. In this study, the MAMP response of Arabidopsis thaliana was utilized to determine differential detection of MAMPs expressed by Pseudomonas syringe pv. tomato DC3000 when pretreated with A. thaliana. Results demonstrated that more MAMPs are detected when P. syringae had previously encountered A. thaliana, …

Bacterial Community Structure Of Contrasting Soils Underlying Bornean Rain Forests: Inferences From Microarray And Next-Generation Sequencing Methods, Sabrina E. Russo, Ryan Legge, Karrie A. Weber, Eoin L. Brodie, Katherine C. Goldfarb, Andrew K. Benson, Sylvester Tan

School of Biological Sciences: Faculty Publications

Soil microbial diversity is vast, and we lack even basic understanding of how this diversity is distributed ecologically. Using pyrosequencing and microarray methods, we quantified the structure of bacterial communities in two contrasting soils underlying Bornean rain forest (clay and sandy loam) that differ markedly in soil properties, aboveground tree flora, and leaf litter decomposition rates. We found significant soil-related taxonomic and phylogenetic differences between communities that, due to their proximity, are independent of climate. Bacterial communities showed distinct compositional and taxon-abundance distributions that were significantly correlated with the structure of the overlying tree community. Richness of bacteria was greater …

Structural Characterization Of A Conserved, Calcium-Dependent Periplasmic Protease From Legionella Pneumophila, Debashree Chatterjee, Chelsea D. Boyd, George A. O'Toole, Holger Sondermann

Dartmouth Scholarship

The bacterial dinucleotide second messenger c-di-GMP has emerged as a central molecule in regulating bacterial behavior, including motility and biofilm formation. Proteins for the synthesis and degradation of c-di-GMP and effectors for its signal transmission are widely used in the bacterial domain. Previous work established the GGDEF-EAL domain-containing receptor LapD as a central switch in Pseudomonas fluorescens cell adhesion. LapD senses c-di-GMP inside the cytosol and relays this signal to the outside by the differential recruitment of the periplasmic protease LapG. Here we identify the core components of an orthologous system in Legionella pneumophila. Despite only moderate sequence conservation at …

Toxin-Antitoxic Loci Vapbc-1 And Vapxd Contribute To Survival And Virulence In Nontypeable Haemophilus Influenzae, Dabin Ren, Anna N. Walker, Dayle A. Daines

Biological Sciences Faculty Publications

Background: Nontypeable Haemophilus influenzae (NTHi) is a significant human pathogen responsible for respiratory tract infections and the most common cause of recurrent otitis media. Type II toxin-antitoxin (TA) systems are genetic elements that code for a stable protein toxin and a labile antitoxin that are thought to be involved in metabolic regulation of bacteria by enabling a switch to a dormant state under stress conditions. The contribution to infection persistence of the NTHi TA loci vapBC-1 and vapXD was examined in this study.

Results: Deletions in vapBC-1, vapXD and vapBC-1 vapXD significantly decreased the survival of NTHi co-cultured with …

2-Heptyl-4-Quinolone, A Precursor Of The Pseudomonas Quinolone Signal Molecule, Modulates Swarming Motility In Pseudomonas Aeruginosa, Dae-Gon Ha, Judith H. Merritt, Thomas H. Hampton, James T. Hodgkinson, Matej Janecek, David R. Spring, Martin Welch, George A. O'Toole

Dartmouth Scholarship

Pseudomonas aeruginosa is an opportunistic pathogen capable of group behaviors, including biofilm formation and swarming motility. These group behaviors are regulated by both the intracellular signaling molecule c-di-GMP and acylhomoserine lactone quorum-sensing systems. Here, we show that the Pseudomonas quinolone signal (PQS) system also contributes to the regulation of swarming motility. Specifically, our data indicate that 2-heptyl-4-quinolone (HHQ), a precursor of PQS, likely induces the production of the phenazine-1-carboxylic acid (PCA), which in turn acts via an as-yet-unknown downstream mechanism to repress swarming motility. We show that this HHQ- and PCA-dependent swarming repression is apparently independent of changes in global …

High Ethanol Titers From Cellulose By Using Metabolically Engineered Thermophilic, Anaerobic Microbes, D. Aaron Argyros, Shital A. Tripathi, Trisha F. Barrett, Stephen R. Rogers, Lawrence F. Feinberg, Daniel G. Olson, Justin M. Foden, Bethany B. Miller, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

This work describes novel genetic tools for use in Clostridium thermocellum that allow creation of unmarked mutations while using a replicating plasmid. The strategy employed counter-selections developed from the native C. thermocellum hpt gene and the Thermoanaerobacterium saccharolyticum tdk gene and was used to delete the genes for both lactate dehydrogenase (Ldh) and phosphotransacetylase (Pta). The Δldh Δpta mutant was evolved for 2,000 h, resulting in a stable strain with 40:1 ethanol selectivity and a 4.2-fold increase in ethanol yield over the wild-type strain. Ethanol production from cellulose was investigated with an engineered coculture of organic acid-deficient engineered strains of …

Influence Of Environmental Conditions On Biofilm Formation Of Listeria Monocytogenes, Jing Li

All Theses

L. monocytogenes is a Gram-positive bacterium, ubiquitously distributed in the environment. It is the etiologic agent of listeriosis, a food-borne disease affecting humans and a variety of vertebrates. L. monocytogenes can form biofilm which is a multi-cellular layer of adherent bacteria surrounded by an extracellular polysaccharide matrix. Biofilm bacteria are extremely resistant to sanitizers and are difficult to be eradicated, therefore posing a big challenge to food processing industry and food service department.
In this work, we tested the biofilm formation in a number of L. monocytogenes serotypes under different environmental conditions, such as temperatures, pH and media (BHI, LB, …

Iron Limitation Of A Springtime Bacterial And Phytoplankton Community In The Ross Sea: Implications For Vitamin B12 Nutrition, Erin M. Bertrand, Mak A. Saito, Peter A. Lee, Robert B. Dunbar, Peter N. Sedwick, Giacomo R. Ditullio

OES Faculty Publications

The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B-12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B-12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B-12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early …

Protection And Attachment Of Vibrio Cholerae Mediated By The Toxin-Coregulated Pilus In The Infant Mouse Model, Shelly J. Krebs, Ronald K. Taylor

Dartmouth Scholarship

Colonization of the human small intestine by Vibrio cholerae is an essential step in pathogenesis that requires the type IV toxin-coregulated pilus (TCP). To date, three functions of TCP have been characterized: it serves as the CTXΦ receptor, secretes the colonization factor TcpF, and functions in microcolony formation by mediating bacterium-bacterium interactions. Although type IV pili in other pathogenic bacteria have been characterized as playing a major role in attachment to epithelial cells, there are very few studies to suggest that TCP acts as an attachment factor. Taking this into consideration, we investigated the function of TCP in attachment to …

Novel Model For Multispecies Biofilms That Uses Rigid Gas-Permeable Lenses, Rebecca Peyyala, Sreenatha S. Kirakodu, Jeffrey L. Ebersole, Karen F. Novak

Center for Oral Health Research Faculty Publications

Oral biofilms comprise complex multispecies consortia aided by specific inter- and intraspecies interactions occurring among commensals and pathogenic bacterial species. Oral biofilms are primary initiating factors of periodontal disease, although complex multifactorial biological influences, including host cell responses, contribute to the individual outcome of the disease. To provide a system to study initial stages of interaction between oral biofilms and the host cells that contribute to the disease process, we developed a novel in vitro model system to grow biofilms on rigid gas-permeable contact lenses (RGPLs), which enable oxygen to permeate through the lens material. Bacterial species belonging to early- …

Roles Of Three Transporters, Cbcxwv, Bett1, And Bett3, In Pseudomonas Aeruginosa Choline Uptake For Catabolism, Adel A. Malek, Chiliang Chen, Matthew J. Wargo, Gwyn A. Beattie, Deborah A. Hogan

Dartmouth Scholarship

Pseudomonas aeruginosa uses the quaternary amine choline as a carbon source, osmoprotectant, and macromolecular precursor. The importance of choline in P. aeruginosa physiology is highlighted by the presence of multiple known and putative choline transporters encoded within its genome. This report describes the relative roles of three choline transporters, the ABC transporter CbcXWV and two symporters, BetT1 and BetT3, in P. aeruginosa growth on choline under osmotic conditions that are physiologically relevant to eukaryotic hosts. The increased lag phases exhibited by the ΔbetT1 and ΔbetT1 ΔbetT3 mutants relative to the wild type upon transfer to medium with …

Whole-Genome Sequencing Of Staphylococcus Aureus Strain Rn4220, A Key Laboratory Strain Used In Virulence Research, Identifies Mutations That Affect Not Only Virulence Factors But Also The Fitness Of The Strain, Dhanalakshmi Nair, Guido Memmi, David Hernandez, Jonathan Bard, Marie Beaume, Steven Gill, Patrice Francois, Ambrose L. Cheung

Dartmouth Scholarship

Staphylococcus aureus RN4220, a cloning intermediate, is sometimes used in virulence, resistance, and metabolic studies. Using whole-genome sequencing, we showed that RN4220 differs from NCTC8325 and contains a number of genetic polymorphisms that affect both virulence and general fitness, implying a need for caution in using this strain for such studies.

Pcr Primers For The Detection Of Propane And Butane-Oxidizing Microorganisms, Brian Jeremy Chan

Master's Theses

In an increasingly energy-hungry world, our capacity to meet the heightened energy demands of the future has become a pressing matter. The most urgent of these concerns are tied to the accessibility of petroleum. Various experts have proselytized both the imminent arrival of peak oil production rates and the ensuing decline of those rates thereafter. And to that end, the development of novel and advanced oil exploration methodologies has become almost as important as finding the sources of oil themselves.

The soils above petroleum reservoirs play host to various communities of alkane- oxidizing bacteria that can utilize the natural gas …

Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd

Dartmouth Scholarship

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …

Laser-Induced Breakdown Spectroscopy (Libs): An Innovative Tool For Studying Bacteria, Qassem I. Mohaidat

Wayne State University Dissertations

Laser-induced breakdown spectroscopy (LIBS) has gained a reputation as a flexible and convenient technique for rapidly determining the elemental composition of samples with minimal or no sample preparation. In this dissertation, I will describe the benefits of using LIBS for the rapid discrimination and identification of bacteria (both pathogenic and non-pathogenic) based on the relative concentration of trace inorganic elements such as Mg, P, Ca, and Na. The speed, portability, and robustness of the technique suggest that LIBS may be applicable as a rapid point-of-care medical diagnostic technology.

LIBS spectra of multiple genera of bacteria such as Escherichia, Streptococcus, Mycobacterium, …

Microbial Landscapes Of Corals And Ctenophores, Camille Arian Daniels

USF Tampa Graduate Theses and Dissertations

As technology and engineering allow mankind to survey nature at finer scales, the importance of bacteria has been elucidated in their metabolic diversity, ability to transfer genetic information, involvement in biogeochemical cycling, and sheer abundance. With an individual domain of life unto themselves, this diverse group of microorganisms plays an integral role in facilitating life on land and in the oceans, and is second only to viruses in abundance on Earth. They carve niches in a wide range of environments, including those inhospitable to other life forms, and reside in concert or to the detriment of other microbes and/or hosts …