Environmental Microbiology and Microbial Ecology Commons^™

The Impacts Of Tilled-In Biodegradable Plastic Mulch On Soil Microbial Communities, Corissa L. Martin

Masters Theses

Plastics mulch films are used in agriculture to help increase crop production by regulating soil water retention and soil temperature while also preventing weed growth. Despite these benefits, plastic mulches have led to higher levels of microplastic pollution as weathering occurs. In response to this issue, biodegradable plastic mulches (BDMs) have been introduced to help reduce plastic pollution as they are designed to be tilled into soil after each growing season to continue degradation. Degradation of these mulch films is dependent on climate and, in some areas, complete degradation can take years. Since some biodegradable plastic mulches are made of …

Ecological Controls On Successional Patterns In Bloom-Forming Cyanobacteria, Kyla L. Hooker

Masters Theses

Harmful algal blooms are widespread in lake ecosystems but the ecological factors underlying their formation and maintenance are poorly understood. We revisit classical ecological theories which characterize and evaluate contrasting bottom-up and top-down influences on the selection of phytoplankton groups, such as Microcystis aeruginosa. We begin with a data compilation and analysis of environmental data from Lake Erie. This data analysis of nutrient concentrations, pigment concentrations, and zooplankton biomasses helps us understand and interpret what is happening in the environment throughout the year. Thus, allowing us to build a mathematical model to test our hypothesis. Our mathematical model asses …

Investigating Microbial Genes Involved In Plant Colonization And The Effects On Plant Microbiome Assembly, David Grant

Masters Theses

The use of chemical fertilizers and pesticides has had negative impacts on ecological systems and alternatives will be needed to both enhance agricultural production and remediate waste that has accumulated via fertilizer use. A promising alternative to tackle both problems utilizes beneficial organisms in microbial communities associated with plants, which are known as bioinoculants. However, the benefits of bioinoculants are inconsistent in field application and require more research in order to harness them in ways to make them a suitable replacement for chemical fertilizers. Here, I investigate characteristics required to enhance bioinoculant efficiency, including mechanisms required to increase microbial colonization …

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. …

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 …

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

Masters Theses

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

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; …

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

Masters Theses

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

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

Masters Theses

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

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

Masters Theses

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

Urea As A Nitrogen Source For Microcystis Aeruginosa, Bernard Shafer Belisle

Masters Theses

Over the last decade, Lake Erie has experienced annual harmful algal blooms events dominated by the toxic cyanobacterium Microcystis aeruginosa. It is still unclear what causes Microcystis blooms to occur, but there is broad agreement that eutrophication of freshwater systems from anthropogenic sources (urban, industrial, etc.), has led to their proliferation. In particular, the organic compound urea has been implicated as an important source of anthropogenic nitrogen, due to its increased use in agricultural practices. Currently, urea constitutes more than 50% of the nitrogen used for agricultural fertilizer globally, and its usage has increased more than a 100-fold over …

The Performance Of Bacterial Phytosensing Transgenic Tobacco Under Field Conditions, Michael Harrison Fethe

Masters Theses

Currently the platforms for wide-area detection of environmental contamination are limited. Therefore, there is interest in developing new platforms, especially for use in crop plants to detect and report the presence of biotic and abiotic stress agents. A biosensor uses a biological organism or substrate to detect the presence of an elicitor (i.e., heavy metal, TNT, or bacteria). The foundational groundwork to create biosensors in transgenic plants exists. The creation of bacterial phytosensing transgenic tobacco containing an orange fluorescent protein (OFP) reporter driven by synthetic pathogen-inducible promoters provides a fluorescent signal when infected with phytopathogens for earlier detection in the …

Environmental Constraints On Cyanomyophage Abundance In The Subtropical Pacific Ocean, Tiana Maria Pimentel

Masters Theses

Viruses are abundant in the world’s oceans and are thought to be important participants in marine biogeochemical cycling. Of these viruses, cyanophages are considered especially important because they infect and lyse cyanobacteria, which are some of the main primary producers in marine environments. Cyanophages are thought to influence the abundance and diversity of cyanobacterial populations and impart significant mortality, thereby affecting primary productivity and microbial community structure. Despite their ecological relevance, little is known about how environmental factors shape cyanophage abundance and diversity over large temporal and spatial scales. To address this gap in knowledge, seawater samples were collected during …

Factors Influencing Diarrheal Pathogen Presence In Tubewells Of Bangladesh, Kati Anne Ayers

Masters Theses

Diarrheal disease pathogens remain a major concern in developing countries as rotavirus is the leading cause of hospitalization of young children worldwide. A recent study has shown shallow groundwater in rural Bangladesh to be contaminated with bacterial and viral pathogens, but found no correlation between rotavirus and any fecal indicator or environmental parameter during the monsoon season of July, 2009. The objectives of this thesis were to examine the non-relationship between pathogens and fecal indicators, as well as to improve the understanding of the seasonal transport of viral pathogens, especially rotavirus, in shallow, sandy aquifers of Bangladesh. This was achieved …

Revealing The Ecological Role Of Gemmatimonadetes Through Cultivation And Molecular Analysis Of Agricultural Soils, Mariam Naomi Fawaz

Masters Theses

Bacteria belonging to phylum Gemmatimonadetes are frequently detected in a variety of environments using culture-independent methods. Despite their ubiquity and prevalence, almost nothing is known about their physiology or ecology because so few strains have been isolated. The first objective of this study was to determine the distribution of Gemmatimonadetes within soil aggregates and the response of the relative abundance of Gemmatimonadetes to dry/wet cycling and soil management. The second objective was to analyze the effects of soil management, aggregate size, and atmospheric conditions on cultivability of Gemmatimonadetes. Universal and Gemmatimonadetes-specific 16S rRNA gene primers were used to …

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 …

Long Term Impacts Of A Genetically Engineered Microorganism (Gem) And Polycyclic Aromatic Hydrocarbons (Pahs) On Soil Bacterial Communities, Xiaoci Ji

Masters Theses

Microbes capable of polyaromatic hydrocarbon (PAH) biodegradation can be used to remediate soils contaminated with these persistent pollutants. To monitor in situ PAH-biodegradation, the bioluminescent bio-reporter Pseudomonas fluorescens HK44, containing a lux luminescent gene cassette inserted into its naphthalene degradation operon, was released into PAH-contaminated soil in lysimeters in 1996. Three treatments were imposed: strain HK44 mixed with PAH-contaminated soil (PAH+, HK44+; n=3); strain HK44 mixed with uncontaminated soil (PAH–, HK44+; n=2) and PAH-contaminated soil alone (PAH+, HK44–; n=1). The objective of this study was to assess the long term impacts of these treatments on the indigenous soil bacterial community …

Exploring Anaerobic Reductive Dechlorination At Low Ph Environments, Yi Yang

Masters Theses

Chlorinated aliphatic hydrocarbons (CAHs), such as tetrachloroethene (PCE) and trichloroethene (TCE), are ubiquitously pollutants in aquifer sediments and groundwater due to their heavy usage in industry and inappropriate disposal in the last century. Among about 1300 NPL (National Priorities List) sites, PCE and TCE are the two most frequently detected hazardous contaminants.

Engineered bioremediation, including biostimulation and bioaugmentation, is a promising technology to clean those PCE and/or TCE contaminated sites. However, in many contaminated groundwater systems and hazardous waste sites, pH can be lower than 5 to 6. And release of HCl (strong acid) from anaerobic reductive dechlorination may lower …

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 …

Functional Cloning And Characterization Of Antibiotic Resistance Genes From The Chicken Gut Microflora, Wei Zhou

Masters Theses

A recent study using human fecal samples in conjunction with a culture-independent approach revealed immense diversity of antibiotic resistance (AR) genes in the human gut microflora. We hypothesize that food animal gut microflora also contain diverse and novel AR genes which could contribute to the emergence and transmission of AR in pathogens important in animal and human health. To test this, we examined AR reservoir in chicken gut microflora using a metagenomic, functional cloning method. Total genomic DNA was extracted from individual cecal contents of two free range chickens and two conventionally raised chickens. The DNAs were physically sheered into …

Cattle Access Affects Periphyton Community Structure In Tennessee Farm Ponds., Robert Gerald Middleton

Masters Theses

Cattle farming is vital to the economy of the United States. Frequently, cattle are given access to ponds and streams for water. The relative impacts of cattle access in natural water sources on the periphyton community have been rarely investigated. Periphyton is the basis of the aquatic food web, and community composition can serve as a bioindicator of pollution. Thus, my objectives were to quantify the effects of cattle access in aquatic lentic systems on periphyton community structure and biovolume, identify taxa that were associated with cattle access, and identify abiotic mechanisms that might be driving assemblage changes. I conducted …

Agricultural Soil Bacteria; A Study Of Collection, Cultivation, And Lysogeny, Katherine Elizabeth Sides

Masters Theses

The aim of this research project was to test new collection and cultivation techniques that may increase the range of cultivable diversity of soil bacteria. Fortified BioSep beads were employed in situ to capture soil bacteria, and the success of the beads was analyzed using Phylochip microarray analysis. In the cultivation phase, three different media substrates and increased incubation period were evaluated for the ability to select novel or rare bacteria. Over 700 agricultural soil bacterial isolates were classified, including a rare Gemmatimonadetes sp., a rare Verrucomicrobia sp., several Acidobacteria sp., and many novel isolates. Land management, media, and incubation …