Environmental Microbiology and Microbial Ecology Commons^™

Optimization Of In-Vessel Food Waste Composting: Enzyme Activity And Microbial Dynamics, Ayawovi Selom Ametepe

Graduate Theses and Dissertations

A series of greenhouse-based, rotary-drum bioreactor experiments was designed to study microbial dynamics and enzyme activity during optimization of food waste composting. This work aims to optimize food waste composting by defining the best food waste-to-bulking agent proportion controlling conditions and by evaluating the food waste composting process when inoculated by a bacterial inoculant product compared to uninoculated compost. Three experiments were run in total. The two first experiments were conducted for 48 days with sampling at each step of composting, while the third experiment last 50 days and included one extra sampling date. In the first experiment, 50:50, 65:35 …

Spatio-Temporal Dynamics Of Fungal Communities And Their Effects On Plants, Kel Cook

Biology ETDs

Fungi perform several critical functions in the environment. Spatiotemporal distributions of fungal communities will mediate when and where these functions happen and how they vary across the landscape. I first explored tropical tree canopy fungal community variation at small spatial scales and documented near total turnover of fungi across sub-meter distances and among adjacent substrates. The second chapter analyzed fungal turnover over the course of three years, where community stability was driven primarily by abundant fungi. In the third chapter, I tested effects of the environment, including host plant and habitat, on canopy fungal communities and found only small effects, …

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …

Isolation Of Plastic-Degrading Fungi From Landfill And Determining The Selected Plastics Biodegradation Capability, Mohan Priya

Student Works (2020-2029)

Polyethylene Terephthalate (PET), Low Density Polyethylene (LDPE) and High Density Polyethylene (HDPE) are the most important polymers used predominantly in present world. Since synthetic polymers hardly undergo degradation and remain in the environment for a very long time, up to 1000 years, these drawbacks increase the percentage of solid wastes in landfill and threaten the environment. To date, Municipal Solid Waste (MSW) landfill is the most favored disposal method especially among the developing countries. The aim of present study is to evaluate the potential of fungus isolated from landfilled plastics to degrade PET, LDPE and HDPE. Besides, effect of different …

Investigation Of An Elevational Gradient Reveals Strong Differences Between Bacterial And Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata, Kadeem J. Gilbert, Leonora S. Bittleston, Mark Arcebal K. Naive, Anthony E. Kiszewski, Perry Archival C. Buenavente, David J. Lohman, Naomi E. Pierce

Publications and Research

Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the …

Microbial Degradation Of Urea Oligomers: Potential Slow Release Nitrogen Fertilizers, Maddy Bygd

Departmental Honors Projects

Urea is the most commonly used nitrogen compound in fertilizers across the world. It provides the most nitrogen at the lowest cost. However, with the size and solubility of this compound, it is easily washed out of the soil. This results in the need to continuously add fertilizer to fields, creating adverse effects on the environment due to nitrogen runoff and leading to increased expenses for farmers. Triuret, a urea oligomer, is a compound with promising potential for use as a nitrogen source, providing a slower release of nitrogen into the soil. It is hypothesized that this compound can be …

Developing Microbial Based Process To Produce High Value Natural Antimicrobial (Glyceollin) In Soybeans And Pullulan From Sucrose, Andrea Zavadil

Electronic Theses and Dissertations

Glyceollin is a secondary metabolite produced under stress conditions by soybean to act as a plant defender to pathogen attack. The antimicrobial nature of glyceollin makes it a promising natural alternative to antibiotics if incorporated into livestock feed. However, production of glyceollin is highly variable, dependent on soybean variety, and fungal elicitor used as inoculum. Our study compares two fungal spore elicitors, Trichoderma reesei and Aspergillus sojae on soybeans of diverse maturity level, and fungal susceptibility to determine highest glyceollin titer. Spore inoculation with T. reesei elicited highest glyceollin titers of 2.42±0.20 mg/g at 120 h, while A. sojae elicited …

Investigating Links Between Soil Microbial Structure And Function In Three Major Plant Communities Across Temporal Scales Of Arctic Alaska, Kaj Lynoe

Electronic Theses and Dissertations

Arctic microbial systems continue to get attention today as our understanding regarding their structure and function in a changing system is paramount to C feedbacks with warming and changes in precipitation. Plant communities and microbial community processes across the Arctic landscape are central to understanding tundra ecosystem processes because environmental conditions and plant community structure drive microbial cycling of soil organic matter. Here, we want to understand how soil microbial respiration, mineralization, biomass, and community composition are linked to three Alaskan tundra plant communities, namely Shrub, Tussock, and Sedge tundra and the seasonal variability in this system. A total of …

Genetic And Biochemical Characterization Of Ergot Alkaloid Synthesizing Fungi And Their Symbionts, Matthew Duane Maust

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ergot alkaloids are fungal tryptophan derived toxins which affect mammalian circulation and neurotransmission. These compounds are biosynthesized by a conserved genetic pathway, known as the ergot alkaloid synthesis (EAS) pathway by fungi belonging to the ascomycete families Trichocomaceae and Clavicipitaceae. Several Ipomoea species and related plants in the morning glory family harbor vertically transmitted symbiotic fungi in the genus Periglandula, also members of Clavicipitaceae, that produce ergot alkaloids. Metabolomic analysis of seeds identified a previously uncharacterized glycoside form of the pharmaceutically important ergot alkaloid, ergonovine. Several species belonging to the fungal genus Metarhizium have recently been shown to have the …

Use Of Uav Imagery And Nutrient Analyses For Estimation Of The Spatial And Temporal Contributions Of Cattle Dung To Nutrient Cycling In Grazed Ecosystems, Amanda E. Shine

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Nutrient inputs from cattle dung are crucial drivers of nutrient cycling processes in grazed ecosystems. These inputs are important both spatially and temporally and are affected by variables such as grazing strategy, water location, and the nutritional profile of forage being grazed. Past research has attempted to map dung deposition patterns in order to more accurately estimate nutrient input, but the large spatial extent of a typical pasture and the tedious nature of identifying and mapping individual dung pats has prohibited the development of a time- and cost-effective methodology. The first objective of this research was to develop and validate …

Coffee Is Not Forever : A Global History Of The Coffee Leaf Rust, Stuart Mccook

Ohio University Press Open Access Books

The global coffee industry, which fuels the livelihoods of farmers, entrepreneurs, and consumers around the world, rests on fragile ecological foundations. In Coffee Is Not Forever, Stuart McCook explores the transnational story of this essential crop through a history of one of its most devastating diseases, the coffee leaf rust. He deftly synthesizes agricultural, social, and economic histories with plant genetics and plant pathology to investigate the increasing interdependence of the world’s coffee-producing zones. In the process, he illuminates the progress and prognosis of the challenges—especially climate change—that pose an existential threat to a crop that global consumers often take …

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 …

Combating Drug Resistance - Comparison Of The Antibiotic Effect Of Hydrastis Canadensis Extract And Pure Berberine Via Minimum Inhibitory Concentration Assay, William Luke Scott, Timothy D. Trott

Research in Biology

Herbal medicines are a melee of complex organic chemicals, making it difficult to ascertain their direct mechanism of action. In contrast to mainstream pharmaceuticals, it is argued that herbal medicines are effective because of multiple constituents working synergistically. The complexity of herbal medicines may give them advantages over simpler pharmaceuticals in combating antibiotic resistant microbes, but these advantages can be difficult to quantitate. Popular literature frequently espouses the healing properties of herbal medicines, but many of these claims are not scientifically supported. Many gains could be realized in public health and medicine if more research was aimed at validating / …

Biogeochemical Response To Vegetation And Hydrologic Change In An Alaskan Boreal Fen Ecosystem, Danielle L. Rupp

Dissertations, Master's Theses and Master's Reports

Boreal peatlands store approximately one third of the earth’s terrestrial carbon, locked away in currently waterlogged and frozen conditions. Peatlands of boreal and arctic ecosystems are affected increasingly by shifting hydrology caused by climate change. The consequences of these relatively rapid ecosystem changes on carbon cycling between the landscape and the atmosphere could provide an amplifying feedback to climate warming. Alternatively, the advancement of terrestrial vegetation into once waterlogged soils could uptake carbon as a sink. Previous work suggests that fens will become an increasingly dominant landscape feature in the boreal. However, studies investigating fens, their response to hydrologic and …

Long-Term Land Management Practices And Their Effect On Soil Health And Crop Productivity, Thomas Joseph Muratore Jr.

Theses and Dissertations--Plant and Soil Sciences

Agricultural intensification reliant on monocrops could change soil health in a way that does not support maximum crop productivity. Twenty-nine-year-old no-till field plots at the University of Kentucky Spindletop research farm showed a significant reduction in corn yields from continuous corn plots compared to those from plots in various types of rotation. The objective of this study was to determine what role soil microbes might play in yield reduction and how management and time effects microbial community structure. Samples were collected from the following treatments: continuous corn (CC), continuous soybean (SS), a 2-year corn/soybean rotation (CCSS), Corn in rotation with …

Context Is Everything: An Investigation Of Spanish River Carbonatite And Its Effects On Soil-Plant-Microorganism Systems, James Mc Jones

Theses and Dissertations (Comprehensive)

With growing concerns about agricultural sustainability and food security, the use of rock fertilizers and agrominerals is receiving renewed interest. A wide variety of geological resources have been proposed as crop nutrient sources, with silicate rocks the predominant focus. Carbonatite rocks are known to weather more readily than silicate rocks; yet, they have received relatively little attention as it is thought their high Ca and Mg contents hinder effective nutrient release. However, there is strong evidence that the nutrients within carbonatite rocks are easily accessible to plants, and that these rocks have noticable effects on crop plant growth. Here I …

Plant And Microbial Responses To Repeated Cu(Oh)2 Nanopesticide Exposures Under Different Fertilization Levels In An Agro-Ecosystem, Marie Simonin, Benjamin P. Colman, Weiyi Tang, Jonathan D. Judy, Steven M. Anderson, Christina M. Bergemann, Jennifer D. Rocca, Jason M. Unrine, Nicolas Cassar, Emily S. Bernhardt

Plant and Soil Sciences Faculty Publications

The environmental fate and potential impacts of nanopesticides on agroecosystems under realistic agricultural conditions are poorly understood. As a result, the benefits and risks of these novel formulations compared to the conventional products are currently unclear. Here, we examined the effects of repeated realistic exposures of the Cu(OH)₂ nanopesticide, Kocide 3000, on simulated agricultural pastureland in an outdoor mesocosm experiment over 1 year. The Kocide applications were performed alongside three different mineral fertilization levels (Ambient, Low, and High) to assess the environmental impacts of this nanopesticide under low-input or conventional farming scenarios. The effects of Kocide over time were …

Isolating And Identifying Fungal Endophytes From Roots Of Rare Orchid Cypripedium Arietinum In Grand Sable Dunes, Michigan, Kari Farkas-Lasich

All NMU Master's Theses

Recently the population of Cypripedium arietinum in Grand Sable Dunes, Michigan was estimated at more than 3.5 million plants, greater than 90% of the world’s known population. There is little research on this species’ root associated fungal endophytes. This new population estimate allows the ethical, destructive sampling required to shed light on root associated symbionts and further successful preservation and restoration of the species. Samples were collected of current year’s roots from 75 C. arietinum orchids at 75 locations within 4 jack pine forests in the Grand Sable Dunes, Pictured Rocks National Lakeshore, Michigan. Fungal endophyte cultures were obtained from …

Cloning And Characterization Of A Pyrethroid Pesticide Decomposing Esterase Gene, Est3385, From Rhodopseudomonas Palustris Psb-S, Xiangwen Luo, Deyong Zhang, Xuguo Zhou, Jiao Du, Songbai Zhang, Yong Liu

Entomology Faculty Publications

Full length open reading frame of pyrethroid detoxification gene, Est3385, contains 963 nucleotides. This gene was identified and cloned based on the genome sequence of Rhodopseudomonas palustris PSB-S available at the GneBank. The predicted amino acid sequence of Est3385 shared moderate identities (30–46%) with the known homologous esterases. Phylogenetic analysis revealed that Est3385 was a member in the esterase family I. Recombinant Est3385 was heterologous expressed in E. coli, purified and characterized for its substrate specificity, kinetics and stability under various conditions. The optimal temperature and pH for Est3385 were 35 °C and 6.0, respectively. This enzyme could …

Phaeophleospora Vochysiae Savi & Glienke Sp. Nov. Isolated From Vochysia Divergens Found In The Pantanal, Brazil, Produces Bioactive Secondary Metabolites, Daiani C. Savi, Khaled A. Shaaban, Francielly M. W. Gos, Larissa V. Ponomareva, Jon S. Thorson, Chirlei Glienke, Jürgen Rohr

Pharmaceutical Sciences Faculty Publications

Microorganisms associated with plants are highly diverse and can produce a large number of secondary metabolites, with antimicrobial, anti-parasitic and cytotoxic activities. We are particularly interested in exploring endophytes from medicinal plants found in the Pantanal, a unique and widely unexplored wetland in Brazil. In a bio-prospecting study, strains LGMF1213 and LGMF1215 were isolated as endophytes from Vochysia divergens, and by morphological and molecular phylogenetic analyses were characterized as Phaeophleospora vochysiae sp. nov. The chemical assessment of this species reveals three major compounds with high biological activity, cercoscosporin (1), isocercosporin (2) and the new compound 3-(sec-butyl)-6-ethyl-4,5-dihydroxy-2-methoxy-6-methylcyclohex-2-enone (3). …

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. …

Range-Wide Prevalence And Impacts Of Pseudocercosporella Inconspicua On Lilium Grayi And An Assessment Of L. Superbum And L. Michauxii As Reservoirs, Cindy L. Barrett

Electronic Theses and Dissertations

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With …

Microbial Interactions In The Phyllosphere Increase Plant Performance Under Herbivore Biotic Stress, Muhammad Saleem, Nicole Meckes, Zahida H. Pervaiz, Milton B. Traw

Plant and Soil Sciences Faculty Publications

The phyllosphere supports a tremendous diversity of microbes and other organisms. However, little is known about the colonization and survival of pathogenic and beneficial bacteria alone or together in the phyllosphere across the whole plant life-cycle under herbivory, which hinders our ability to understand the role of phyllosphere bacteria on plant performance. We addressed these questions in experiments using four genetically and biogeographically diverse accessions of Arabidopsis thaliana, three ecologically important bacterial strains (Pseudomonas syringae DC3000, Xanthomonas campestris, both pathogens, and Bacillus cereus, plant beneficial) under common garden conditions that included fungus gnats (Bradysia spp.). …

Molecular Diversity Of Foliar Fungal Endophytes In Relation To Defense Strategies And Disease In Whitebark Pine, Lorinda Bullington

Graduate Student Theses, Dissertations, & Professional Papers

An invasive fungal pathogen, Cronartium ribicola (the causative agent of white pine blister rust) infects and kills whitebark pine (Pinus albicaulis) throughout the western US. Blister rust has decreased whitebark pine populations by over 90% in some areas. Whitebark pine, a keystone species, has been proposed for listing under the Endangered Species Act in the U.S., and the loss of this conifer is predicted to have severe impacts on forest composition and function in high elevations. Hundreds of asymptomatic fungal species live inside whitebark pine tissue, and recent studies suggest that these fungi can influence the frequency and …

Effects Of Fertilizer And Shade Management On Nitrogen Mineralization, Nitrifying Microbial Abundance And Nitrogen-Fixing Capacity Of Erythrina Poeppigiana In Coffee (Coffea Arabica) Agroforestry Systems In Costa Rica, Stuart E. Barker Iii

College of Graduate Studies: Theses & Dissertations

Worldwide chemical fertilizer use has increased by four times during the last 50 years. Conventional agricultural systems have a high nitrifying nature, resulting in a loss of nearly 70% of overall nitrogen (N) fertilizer inputs, an estimated economic loss of $81 billion. Over application of fertilizer is rampant in tropical developing nations in Central America, where coffee is major crop. Agroforestry offers ecologically sustainable land management strategies that promote the provision of ecosystem services such as, protection of biodiversity, climate change mitigation, and water and soil regulation. When legume trees are incorporated as the shade tree in coffee production, direct …

Do Novel Weapons That Degrade Mycorrhizal Mutualisms Explain Invasive Species Success?, Philip L. Pinzone Mr.

Biology Theses

Invasive plants often dominate novel habitats where they did not co-evolve with local species. Several hypotheses suggest mechanisms that explain increased exotic plant success, including 'novel weapons' and 'degraded mutualisms'. Japanese knotweed (Fallopia japonica) and European buckthorn (Rhamnus cathartica) are widespread plant invaders in North America that can dominate ecosystems. The goal of this study is to test whether these impacts are more consistent with novel weapons or degraded mutualism hypotheses. I examine tree seedling recruitment, (germination and initial survival) growth, (biomass) and mycorrhizal invasion (AMF content) as a function of F. japonica and R. cathartica …

Regulation Of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity In The Model Rhizosphere-Dwelling Bacterium Pseudomonas Putida Kt2440, Ran An, Luke Moe

Plant and Soil Sciences Faculty Publications

Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts …

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 …

From Milpas To The Market: A Study On The Use Of Metal Silos For Safer And Better Storage Of Guatemalan Maize, José Rodrigo Mendoza

Department of Food Science and Technology: Dissertations, Theses, and Student Research

This project aimed to implement the use of metal silos to improve quality and safety of maize consumed by inhabitants of the highlands of Guatemala. This manuscript includes a literature review of the maize production chain in Guatemala, a survey about agricultural practices used in the region of study, as well as a characterization of the analyzed maize regarding its mycoflora, nutritional composition, and insect infestation. To better understand the current situation regarding agricultural practices and maize consumption, a survey was carried out. Sample consisted of 280 families representing 14 rural communities distributed in the townships of Todos Santos and …

"Patterns In The Abundance Of Benthic Algae In Streams", Courtney Wright

Honors Theses

Benthic, microscopic algae are the main drivers of primary productivity in streams. The relationship between the abundance and productivity of benthic algae in streams and lakes and the availability of limiting nutrients, especially soluble reactive phosphorus (SRP), has been extensively studied (reviewed in Allan and Castillo 2007, Larned 2010). However, nearly all of this research has been conducted on the periphyton assemblage found on hard substrates (e.g., stones, wood), while very little work has addressed the factors affecting the abundance of epipelic algae (i.e., the algae associated with depositional (soft) sediments such as sands and silts). One of the few …