Ecology and Evolutionary Biology Commons^™

Making Sense Of Soil Microbiome Complexity For Plant And Ecosystem Function In A Changing World, Kendall K. Beals

Doctoral Dissertations

Soils contain the highest biodiversity on Earth. While the importance of the soil microbiome for larger-scale ecological phenomena such as nutrient and carbon cycling, plant growth and plant community dynamics is well-established, the fundamental question of the ecological and evolutionary function of this immense belowground microbial diversity for plant and ecosystem function still remains a great challenge in microbial ecology research. The objective of this dissertation is to understand how the importance of soil microbial community composition for plant and ecosystem function and how changes to soil microbial community composition from climate change-induced disturbance events, specifically fire, influence plant and …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

A Novel Approach For Characterizing The Ultra-Micro Size-Fraction Community, Abdullah Ahmed Salim, Priscilla Nicole Pineda, Isabella Alamilla, Andrew Dean Putt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

A Novel Approach for Characterizing the Ultra-Micro Size-Fraction Community

Students: Abdullah Salim, Priscilla Pineda, Isabella Alamilla

Mentors/Supervisors: Andrew Putt, Terry C. Hazen

ABSTRACT

The ultra-micro size-fraction (UMSF) are bacteria that can pass through the 0.2 µm pore membrane filters employed in environmental surveys. Despite being ubiquitous and having high metabolic activity, UMSF remain elusive and largely uncultured. Investigations of UMSF are skewed by difficulties in culturing and a lack of techniques for measuring UMSF biogeochemical signatures. This study measures surface stream UMSF community diversity, and community response to the addition of the synthetic pharmaceutical and cosmetic carbon product cyclodextrin which …

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

Doctoral Dissertations

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

Carbon Metabolism In Cave Subaerial Biofilms, Victoria E. Frazier

Masters Theses

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

Root Phosphomonoesterase As A Vital Component Of Increasing Phosphorus Availability In Tropical Forests, Kristine Grace Manno Cabugao

Doctoral Dissertations

Tropical forests, relative to other terrestrial ecosystems, exchange the largest amount of carbon with the atmosphere and also constitute a significant carbon sink. However, nutrient limitation, particularly of phosphorus (P), could limit growth of tropical forests and their function with the global carbon cycle. Thus, understanding root mechanisms to acquire P is necessary to representing the P cycle and corresponding interactions with plant growth. A large portion of total soil P in tropical forests occurs in organic forms, only accessible through root and microbial production of phosphatase enzymes. These phosphatase enzymes mineralize organic P into orthophosphate, the form of P …

From Genes To Ecosystems: Resource Availability And Dna Methylation Drive The Diversity And Abundance Of Restriction Modification Systems In Prokaryotes, Spiridon E. Papoulis

Doctoral Dissertations

Together, prokaryotic hosts and their viruses numerically dominate the planet and are engaged in an eternal struggle of hosts evading viral predation and viruses overcoming defensive mechanisms employed by their hosts. Prokaryotic hosts have been found to carry several viral defense systems in recent years with Restriction Modification systems (RMs) were the first discovered in the 1950s. While we have biochemically elucidated many of these systems in the last 70 years, we still struggle to understand what drives their gain and loss in prokaryotic genomes. In this work, we take a computational approach to understand the underlying evolutionary drivers of …

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) and …

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. Biogeographic analysis …

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.

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 …

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 tetrameric …

Improving Aedes Mosquito Surveillance And La Crosse Virus Screening In Eastern Tennessee, Cassandra Urquhart

Masters Theses

La Crosse virus (LACV), transmitted by infected Aedes triseriatus, Ae. albopictus, and Ae. japonicus mosquitoes is the leading cause of pediatric arboviral encephalitis. Severe cases of LAC encephalitis occur in individuals 16-years-old or younger and may cause permanent neurological damage or fatality. No vaccines exist making mosquito control and disease prevention crucial to public health. Effective screening and surveillance practices are key components to these goals. While a number of standard mosquito surveillance methods exist, continuous testing and improved understanding of vector biology to determine the best ways to implement these methods is important. Additionally, the current standard …

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; …

Quantitative Characterization Of Proteins And Post-Translational Modifications In Complex Proteomes Using High-Resolution Mass Spectrometry-Based Proteomics, Zhou Li

Doctoral Dissertations

Mass spectrometry-based proteomics is focused on identifying the entire suite of proteins and their post-translational modifications (PTMs) in a cell, organism, or community. In particular, quantitative proteomics measures abundance changes of thousands of proteins among multiple samples and provides network-level insight into how biological systems respond to environmental perturbations. Various quantitative proteomics methods have been developed, including label-free, metabolic labeling, and isobaric chemical labeling. This dissertation starts with systematic comparison of these three methods, and shows that isobaric chemical labeling provides accurate, precise, and reproducible quantification for thousands of proteins. Based on these results, we applied this approach to characterizing …

Wood Decomposition In A Warmer World, Emily Elizabeth Austin

Doctoral Dissertations

Climatic warming is altering species distributions and ecosystem functions across the globe. Wood is an important carbon pool and the fungal communities in wood are relatively simple compared to those in soil. These factors make decomposing wood an ideal system for exploring the influence of decomposer community on the response of decomposition to warming. My research has focused on the effects of warming wood decomposition rates and wood decomposing communities. Using field and lab- based manipulative experiments and field observations I explore the influence of tree species, wood decomposition stage, geography and warming on fungal community structure and activity. In …

Soil Microbial Community Succession During Cadaver Decomposition, Kelly Lynn Cobaugh

Masters Theses

Microbes play critical roles in nutrient cycling in terrestrial ecosystems. In particular, microbial decomposition of organic matter is a key step in carbon and nutrient cycling, linking above-ground and below-ground pools. It is well known that the microbial community changes in structure and function following the introduction of organic matter into a terrestrial system. The decomposition of plant litter has been extensively investigated but the decomposition of animal-derived organic matter has often been overlooked. The unique characteristics of animal input are hypothesized to dictate a distinct decomposition process. This study examined the microbial community responsible for decomposition of animal-derived organic …

Diversity And Activity Of Roseobacters And Roseophage, Charles Ryan Budinoff

Doctoral Dissertations

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

The Effects Of Nutrient Limitation And Cyanophage On Heterotrophic Microbial Diversity, Claire Elyse Campbell

Masters Theses

Marine viruses are critically important in the regulation of biogeochemical cycles and host microbial communities. In this study, we tested whether the indirect effects of virus predation on a phototroph (i.e., Synechococcus) affected the composition of co-occurring heterotrophic bacteria under nitrogen and phosphorus limitation in long-term chemostat experiments. Using 454 Titanium barcoded pyrosequencing of the 16S rRNA gene, microbial diversity and technical (i.e., sequencing) reproducibility were assessed for nine individual chemostats across five different time points. A total of 325,142 reads were obtained; 194,778 high-quality, non-cyanobacterial sequences were assigned to 110 OTUs. Our results show high reproducibility …