Environmental Microbiology and Microbial Ecology Commons^™

Using Single-Cell Sorting, Fish And 13c-Labeling To Cultivate And Assess Carbon Substrate Utilization Of ‘Aigarchaeota’ And Other Novel Thermophiles, Damon Kurtis Mosier

Electronic Theses, Projects, and Dissertations

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was …

Fungi In A Hot, Dry, Changing World, Miriam I. Hutchinson

Biology ETDs

My doctoral work focused on understanding the reciprocal relationship between fungi and their environment, namely how fungi respond to environmental flux, as well as how fungi can modify and structure their habitats, especially in the context of climate change. As such, I aimed my research on fungi with distinct adaptations to their environmental niches: endophytic fungi that inhabit plant tissue and thermophilic fungi that are capable of growing at the upper temperature limit for eukaryotic life. My research consisted of three studies. First, I investigated the thermophilic species Myceliophthora heterothallica to demonstrate its use as a model organism for efficient …

Warming Up: Climate Change Related Shifts Of Mycorrhizal Fungal Communities In High Latitude Ecosystems, Megan Rae Devan

Biology ETDs

This dissertation examines how climate change affects mycorrhizal fungal communities in boreal and arctic ecosystems. In chapter one, I revealed that increases in fire severity and related increases in deciduous tree dominance result in greater Ascomycota relative abundance (RA) and subsequent declines in Basidiomycota RA. In chapter two I analyzed the effects of post-fire mycorrhizal fungal communites on host growth. There were trends at the fungal genus level that were largely reflected at the guild level across all hosts; however, there were some fungal genera that had the opposite effect on different host species. In chapter three, I found host …

Genetic Diversity In The Leucoagaricus Cultivar Fungus Of Trachymyrmex Septentrionalis Fungus-Growing Ants, Lee Deininger

MCB Articles

No abstract provided.

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana

Dissertations, Theses, and Capstone Projects

Medicinal plants are one of the biggest sources of natural products with therapeutic importance. There are currently over 28,000 plants with putative medicinal values. Plant-derived compounds have been explored extensively for various biological activities ranging from anti-cancer, immune-boosting to anti-inflammatory and anti-oxidant. Some of the most important therapeutic agents are of plant-origin, such as paclitaxel from Pacific yew (Taxus brevifolia) and artemisinin from qinghao su (a Chinese medicinal herb; a.k.a. Artemisia annua) to name a few.

The study presented in this thesis started out as classical pharmacognosy research, which focused on the identification of immunostimulatory factors in …

Impact Of Industrial Biocides On Bacterial Isolates From Hydraulic Fracturing Produced Water, Waad Ahmed Aljohani

Dissertations, Master's Theses and Master's Reports

Biocides are antimicrobial compounds that are designed to kill diverse groups of microbes in an untargeted fashion. Glutaraldehyde and DBNPA are commonly used to manage microbial growth in different industries. It is possible that biocide use may result in the development of bacterial resistance. However, resistance to DBNPA is believed to be limited under normal use conditions. We isolated a number of bacteria from produced water from a hydraulically fractured site in West Texas. We then tested the ability of these isolates to resist Glutaraldehyde and DBNPA. In this study, we found that these isolates have varying resistance to these …

Detection Of Beta-Lactamase Variants In Municipal Wastewater And Fresh Water, Sunil Pandey

Masters Theses

The occurrence and spread of antibiotic-resistant genes (ARGs) are pressing public health problems worldwide. A key factor contributing to the spread of ARGs is lateral gene transfer. Wastewater treatment plants (WWTPs) are measured hot spots of microbial diversity and resistance because they receive polluted wastewater from diverse sources and contain a variety of different environments with dense bacterial loads. Due to the overuse of antibiotics the genetic capacities of microbes have profited. This helps every source of resistance gene and every means of horizontal gene transmission to develop the multiple mechanism of resistance to each antibiotic used clinically, agriculturally, or …

Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert

LSU Doctoral Dissertations

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …

Harnessing The Anopheles Microbiome To Conditionally Express Anti-Plasmodial Effectors During The Blood Meal, Jackie Shane

Electronic Theses and Dissertations

The control of vector-borne diseases such as malaria has been an extremely important research subject for hundreds of years. Because of the complex lifecycles of the pathogens that cause these diseases, finding a comprehensive treatment or preventative strategy has proven extremely difficult. Malaria alone is responsible for almost half a million deaths annually, most of them children under 5 years old. This disease is caused by parasitic protists in the genus Plasmodium that are transmitted to humans from Anopheles sp. mosquitoes. Most preventative strategies that are in use today revolve around controlling the vectors, including bed nets, insecticides, and larval …

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr.

Georgia Journal of Science

Pueraria montana, better known as kudzu, is an invasive species rapidly spreading throughout the southeastern United States. This plant can form root nodules which house nitrogen-fixing bacteria, allowing atmospheric nitrogen to be converted into biologically available forms of nitrogen for use by the plant host. Given the centrality of these bacteria to the spread of kudzu, isolates from nodules were characterized after collection from seven different locations across the metropolitan Atlanta area. Twenty-five isolates were grown on two different variants of nitrogen free media. Four different carbon sources were evaluated as well. Finally, growth under both aerobic and anaerobic …

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

Isolation, Sequencing, And Characterization Of Four Transmissible Antibiotic Resistance Plasmids Captured From Bacteria In Stream Sediments, Curtis J. Kapsak

Masters Theses, 2010-2019

Self-transmissible plasmids are key vectors in the transfer of resistance, catabolic, and other genes among bacteria native to environments such as streams and wetlands. The evolution of antibiotic resistance in particular is known to be powerfully affected by conjugative plasmid transfer due to the ease in which some plasmids can be horizontally transferred into a broad range of host bacteria and their ability to exchange mobile genetic elements that often contain antibiotic resistance genes.

In this study, we captured tetracycline resistance plasmids from stream sediments impacted by agricultural runoff. We selected for resistance plasmids using tetracycline, an antibiotic commonly used …

Changes In The Microbial Community Of Lubomirskia Baicalensis Affected By Red Sponge Disease, Colin Rorex

Electronic Theses and Dissertations

Lake Baikal is the oldest known lake and a unique ecosystem, home to several species of fresh water sponge. A disease outbreak affecting the dominant species, Lubormirskia baialensis, was recently reported. The cause of the disease has not been determined but one of the current hypothesis is that the increase in methane concentration is correlated to the disease outbreak. This pilot study characterized the microbiomes of sick and healthy sponges through the use of 16S rRNA sequencing. Sick sponge microbiomes shared a conserved group of taxa while the healthy sponge microbiomes had greater diversity. Indicator species analysis identified two significant …

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

A New Toolset For Protein Expression And Subcellular Localization Studies In Citrus And Its Application To Citrus Tristeza Virus Proteins, Amit Levy, Choaa El-Mochtar, Chunxia Wang, Michael M. Goodin, Vladimir Orbovic

Plant Pathology Faculty Publications

Background

Transient gene expression is a powerful tool to study gene function in plants. In citrus, Agrobacterium transformation is the method of choice for transient expression studies, but this method does not work efficiently with many gene constructs, and there is a need for a more robust transient expression system in citrus leaves. Biolistic particle delivery is an alternative to Agrobacterium transformation, and in some plants, such as Arabidopsis, gives higher transformation rates in leaf tissues than Agrobacterium.

Results

Here we describe an improved method for gene expression in epidermal cells of citrus leaves, using the Bio-Rad Helios gene-gun. …

Metatranscriptome Of Human Faecal Microbial Communities In A Cohort Of Adult Men, Galeb S. Abu-Ali, Raaj S. Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L. Ivey, David A. Drew, Casey Dulong, Eric Rimm, Jacques Izard, Andrew T. Chan, Curtis Huttenhower

Department of Food Science and Technology: Faculty Publications

The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human fecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms. Finally, longitudinal metagenomic profiles allowed ecological …

Molecular And Evolutionary Analysis Of Cyanobacterial Taxonomic Methods, Chelsea Denise Villanueva

UNF Graduate Theses and Dissertations

Cyanobacteria are a group of photo-oxygenic bacteria found in nearly every ecosystem, but much cyanobacterial diversity, in various habitats, has yet to be explored. Cyanobacteria are often conspicuous components of photosynthetic flora, providing significant carbon and nitrogen inputs to surrounding systems. As possible primary colonizers of stone substrates not native to this region, cyanobacteria isolated from headstones may provide biogeographically informative data. An exploratory study of lichen-dominated microbial consortia, growing on headstones, was conducted to isolate and identify novel microaerophytic cyanobacteria, and resulted in the establishment of four novel cyanobacterial taxa. Phylogenetic analyses of photobionts in one tripartite lichen revealed …

Functional Characteristics And Genomic Sequencing Of Antarctic Environmental Isolates, Amanda Kemper, Christina Aigner, Michelle Tigges, Sara Anderson

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Bacterial Communities Associated With Healthy And Diseased Acropora Cervicornis (Staghorn Coral) Using High-Throughput Sequencing, Charles Walton

HCNSO Student Theses and Dissertations

Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive.

Coral diseases have been characterized by shifts in their …

Study Of Rickettsia Parkeri Colonization And Proliferation In The Tick Host Amblyomma Maculatum (Acari: Ixodidae), Khemraj Budachetri

Dissertations

Amblyomma maculatum (Gulf coast tick) ticks are prevalent across the Atlantic to Gulf Coast region of United States. These ticks are recognized vectors of Rickettsia parkeri, a spotted fever group of Rickettsia (SFGR) known to cause American boutonneuse fever associated with fever and eschar rashes localized to the site of bites. We hypothesized that Rickettsia parkeri colonization and proliferation in the tick vector involve pathogen-symbiont dynamics and tick-pathogen interactions, which influence rickettsial transmission to the victims after tick bites. The rickettsial infection is maintained across the tick life cycle for many generations due to transovarial and transstadial transmission of …

Phytohormone Signaling In Chlorella Sorokiniana: Perspectives On The Evolution Of Plant Cell-To-Cell Signaling, Maya Khasin

School of Biological Sciences: Dissertations, Theses, and Student Research

Cell-to-cell communication is a key aspect of microbial physiology and population dynamics, and a cornerstone in understanding the evolution of multicellularity. Quorum sensing in bacteria is a canonical example of microbial cell-to-cell signaling, in which bacteria use small molecule signals in order to monitor their population size and modulate their physiology accordingly. We propose that the evolution of plant hormone signaling arose in unicellular green algae, analogously to quorum sensing in bacteria, and that the complexity of these pathways required the recruitment of increasingly specific enzymes to increasingly sophisticated gene networks throughout the course of phytohormone signaling evolution. Using Chlorella …

An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon

Master's Theses

The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as …

Review Of The Algal Biology Program Within The National Alliance For Advanced Biofuels And Bioproducts, Clifford J. Unkefer, Richard T. Sayre, Jon K. Magnuson, Daniel B. Anderson, Ivan Baxter, Ian K. Balby, Judith K. Brown, Michael Carleton, Rose Ann Cattolico, Taraka Dale, Timothy P. Devarenne, C. Meghan Downes, Susan K. Dutcher, David T. Fox, Ursula Goodenough, Jan Jaworski, Jonathan E. Holladay, David M. Kramer, Andrew T. Koppisch, Mary S. Lipton, Babetta L. Marrone, Margaret Mccormick, István Molnár, John B. Mott, Kimberly L. Ogden, Ellen A. Panisko, Matteo Pellegrini, Juergen Polle, James W. Richardson, Martin Sabarsky, Shawn R. Starkenburg, Gary D. Stormo, Munehiro Teshima, Scott N. Twary, Pat J. Unkefer, Joshua S. Yuan, José A. Olivares

Publications and Research

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genome …

Contributions Of Gene Copy Number Variation To Genome Evolution And Local Adaptation Of The Cyanobacterium Acaryochloris, Amy L. Gallagher

Graduate Student Theses, Dissertations, & Professional Papers

Acaryochloris is a recently discovered genus of cyanobacteria, unique in its use of an uncommon chlorophyll as its major photosynthetic pigment, and in its peculiar genome dynamics. Members of this genus exhibit increased genic copy number variation (CNV), which is thought to be primarily derived from gene duplications and horizontal gene transfer (HGT). Acaryochloris provides an ideal system to explore mechanisms behind maintenance of gene duplicates and the influence of CNV in local adaptation. Here, I propose a mechanism for retention of gene duplicates of the bacterial recombinase, RecA, in Acaryochloris genomes and provide preliminary evidence that these paralogs are …

Analysis Of Microbial Diversity In Disturbed Soil, Tyler G. Sanda

Williams Honors College, Honors Research Projects

This paper uses the composition and abundance of microbial species to analyze soil recovery in disturbed land. Surface mining disturbs ecological communities throughout the world. As organizations seek to reclaim these disturbed lands, a proper analysis of recovery is needed. In previous studies, recovery of disturbed land was limited to surface examinations, which do not characterize the possible unseen devastating effects of the subsoil. Soil microorganisms are extremely sensitive to environmental changes such as strip mining. It is proposed that these microorganisms may serve as better indicators of recovery post disturbance. Our analysis indicates microbial recovery, however it may not …

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …