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 …

Climate Change, Giant Viruses And Their Putative Hosts, Sarah K. Tucker

Masters Theses

Viruses hold our attention for the horrific impact they have on human health and welfare. However, viruses are a critical part of our ecosystem and facilitate the cycling of carbon and other important nutrients. The cycle of virus infection, followed by host resistance and the subsequent evolution of new strains enables adaptation to changing hosts and the environment. Giant viruses, some with particle sizes large enough to be visible in light microscopes and their bewildering array of accessory genes, have captivated scientists and the general public since their discovery two decades ago. Giant viruses are part of the Nucleocytoviricota (NCV) …

Molecular Biodiversity Of Foraminifera, Rabindra Thakur

Masters Theses

Foraminifera are a diverse clade of mostly shell-building single-celled organisms. Estimation of foraminiferal diversity is critical for understanding past and present climatic conditions, as they are highly sensitive to environmental perturbations. Biodiversity estimates of foraminifera began with the counting of test (i.e., shell) microfossils composed of calcium carbonate, as they are well preserved in sediment samples. However, this view has changed with molecular biodiversity estimates, which suggest that early-diverging single-chamber (i.e., "monothalamid") species that lack preservation ability are more diverse than anticipated. Although biodiversity estimates of foraminifera at the molecular level have changed our perceptions, they possess various challenges, especially …

The Application Of Microbial Source Tracking To Aid In Site Prioritization For Remediation In Lower Michigan, John J. Hart

Masters Theses

Non-point source fecal pollution is a threat to both the environment and public health. Climate change, aging infrastructure, and intensified agricultural practices are predicted to accentuate this issue. In Michigan, due to the high instance of aging infrastructure and intensified agriculture, non-point source fecal pollution has caused many waterbodies to exceed the state standards posing a risk to recreational activities and source water. Due to this threat, there is an increased effort to identify and remediate these sources. My study focused on improving the identification of non-point source fecal pollution through a combination of culture-based and molecular fecal indicator bacteria …

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 …

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has been widely …

Effects Of Traditional And Microbially-Focused Restoration Techniques On Soil Communities In Tallgrass Prairies, Zachary J. Whitacre

Masters Theses

Tallgrass prairies have virtually disappeared in many parts of their former range due to the conversion of this ecosystem to farmland. In more recent years there have been efforts to restore these prairies on reclaimed agricultural land. However, these restored prairies do not resemble their remnant counterparts in many ways, such as in soil microbial community composition and metrics related to carbon storage. In Chapter 1, I show that bacterial communities in a restored prairie and an adjacent remnant prairie in southwest Michigan differ in their immediate and longer-term responses to prescribed fire, a commonly used prairie restoration and maintenance …

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. …

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 …

Characterization Of Pinitol Catabolism In Sinorhizobium Meliloti And Its Role In Nodule Occupancy, Angela Irene Kennedy-Mendez

Masters Theses

Sinorhizobium meliloti, which is the nitrogen fixing symbiont of Medicago sativa (alfalfa), was used to test the hypothesis that D-chiro-inositol is an intermediate of pinitol catabolism and that pinitol catabolism plays a role in S. melilot s ability to compete for nodule occupancy. An analytical method, involving gas chromatography and mass spectrometry (GCMS), was developed to detect and separate pinitol and D-chiro-inositol. The S. meliloti wild type, and three isogenic mutant strains (idhA, mocD, and mocE) were grown in minimal medium with pinitol and pinitol plus glycerol. The S. meliloti wild type can utilize pinitol as a sole carbon source, …

Investigation Of Cytochrome P450 Monooxygenases In S. Homoeocarpa For Chlorothalonil Biotransformation, Robert Green

Masters Theses

Sclerotinia homoeocarpa (F.T. Bennett) is one of the most economically important pathogens on high amenity cool-season turfgrasses where it causes dollar spot. Due to decades of over-reliance and repeated chemical treatments, S. homoeocarpa has developed resistance and insensitivity to multiple classes of fungicides. To understand the genetic mechanisms of fungicide resistance, the whole genomes of two strains with varying resistance levels to fungicides, were sequenced. In unpublished data (Sang et al.), a RNA-sequencing analysis revealed three CYP450s that were validated to play a functional role in S. homoeocarpa’s resistance against different fungicide classes. We also identified CYP450 metabolic action …

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 …

Media Optimization, Scale-Up And Repeated Fed-Batch Operations For The Production Of 1,3-Propanediol From Glycerol By Halanaerobium Hydrogeniformans, Shivani Kalia

Masters Theses

"The development of renewable energy sources, such as biofuels, is of great interest in today's world due to depletion of fossil fuels and concerns about climate change. The production of the main by-product, crude glycerol, in biodiesel production presents an opportunity for the production of industrially relevant commodities. Crude glycerol in biodiesel waste is highly impure and possesses high salt concentrations and alkalinity, making it infeasible for direct industrial utilization. Moreover, current glycerol purification methods are highly cost-intensive, necessitating a search for cost-effective approaches that are feasible to employ. Genome data analysis of Halanaerobium hydrogeniformans, revealed the metabolic capability …

Distribution Of Enterotoxigenic Clostridium Perfringens Spores In U.S. Retail Spices, Chi-An Lee

Masters Theses

246 samples of bulk and packaged spices from retail stores in the western, southeastern, southern, midwestern, and northeastern areas of the U.S. were examined for the presence of Clostridium -perfringens. Isolates were checked for the presence of the lecithinase gene (cpa) and enterotoxin genes (cpe) by PCR. Enterotoxin formation during sporulation was investigated using the Oxoid Toxin Detection Kit. Forty-three confirmed isolates (from 17% of total samples) were cpa-positive. Of those, 27 were cpe-positive. Together, levels of C. perfringens spores ranged from 3.6-2400/gm. The amount of enterotoxin in cell extracts ranged from …

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 …

Effects Of Treated Wastewater Effluent On Microbial Community Structure In A Natural Receiving Aquatic System, Matthew D. Hladilek

Masters Theses

Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of these lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at fourteen sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated …

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 …

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 …

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 …

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 …