Environmental Microbiology and Microbial Ecology Commons^™

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 …

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 …

Occurrence, Antibiotic Resistance, And Survival Of Fecal Enterococci In Turkey Litter, Steven Glynn Mcbride Ii

Masters Theses, 2010-2019

The United States Environmental Protection Agency’s National Water Quality Inventory and the Commonwealth of Virginia’s 305(b)/303(d) Water Quality Assessment Integrated Report show fecal bacteria to be the most common cause of impairment for both streams and estuaries. Human and animal sources have both been identified as significant contributors of pathogenic bacteria to surface waters. In this study, turkey litter from a farm in Shenandoah County, VA was surveyed for total culturable bacteria and total culturable enterococci before and after a transition to organic rearing practices. The enterococci were identified to species phenotypically using the Biolog Microbial Identification System and resistance …

The Influence Of The Invasive Chinese Tallow (Triadica Sebifera) Leaf Litter On Aquatic Chemistry And Microbial Community Composition, Raymond D. Montez

Electronic Theses and Dissertations

Global climate change and anthropogenic activity have facilitated the movement and invasive potential of nonnative plants in native environments. These invasions can have negative effects on ecosystem diversity and function. The nonnative and invasive plant, Chinese Tallow (Triadica sebifera), has already invaded much of the south eastern US where it is outcompeting native tree species and changing ecosystem diversity in a variety of habitats. Leaf litter from the Chinese tallow has been shown cause changes in dissolved oxygen and pH in the aquatic environment. Turbidity is also affected when Chinese tallow litter is present in water. A series of …

Review Of The Cultivation Program Within The National Alliance For Advanced Biofuels And Bioproducts, Peter J. Lammers, Michael Huesemann, Wiebke Boeing, Daniel B. Anderson, Robert G. Arnold, Xuemei Bai, Manish Bhole, Yalini Brhanavan, Louis Brown, Jola Brown, Judith K. Brown, Stephen Chisholm, C. Meghan Downes, Scott Fulbright, Yufeng Ge, Jonathan E. Holladay, Balachandran Ketheesan, Avinash Khopkar, Ambica Koushik, Paul Laur, Babetta L. Marrone, John B. Mott, Nagamany Nirmalakhandan, Kimberly L. Ogden, Ronald L. Parsons, Juergen Polle, Randy D. Ryan, Tzachi Samocha, Richard T. Sayre, Mark Seger, Thinesh Selvaratnam, Ruixiu Sui, Alex Thomasson, Adrian Unc, Wayne Van Vorrhies, Peter Waller, Yao Yao, José A. Olivares

Publications and Research

The cultivation efforts within the National Alliance for Advanced Biofuels and Bioproducts (NAABB)were developed to provide four major goals for the consortium, which included biomass production for downstream experimentation, development of new assessment tools for cultivation, development of new cultivation reactor technologies, and development of methods for robust cultivation. The NAABB consortium test beds produced over 1500 kg of biomass for downstream processing. The biomass production included a number of model production strains, but also took into production some of the more promising strains found through the prospecting efforts of the consortium. Cultivation efforts at large scale are intensive and …

Fecal Bacterial Communities As An Indicator Of Trophic Interactions Among Anuran Larvae, Steven Jacob Everman

Master's Theses

Anurans are mass spawners, often with multiple females spawning together, resulting in thousands of tadpoles sharing a habitat. Such large numbers of tadpoles with limited dispersal can lead to intense competition for resources. Inter and intra-specific competition for food could have negative impacts on the growth and survival of smaller tadpoles. Fecal bacterial communities have the potential to be used as indicators of changes in diet making it possible to determine if tadpoles in the wild are eating the same food or not. After feeding on two prepared diets that differed in the percentage of complex carbohydrates, the fecal bacterial …

Plant-Biocrust Interactions Mediated By The Fungal Loop, Eva Dettweiler-Robinson

Biology ETDs

Plant-microbial interactions influence biogeochemical cycles. Plants and biological soil crusts are primary producers in drylands. Biocrusts include cyanobacteria, lichens, mosses, algae, fungi, bacteria, and archaea on the soil surface, some of which fix atmospheric nitrogen. I investigated controls on biocrust carbon fluxes and their contribution to ecosystem fluxes, the incorporation of plant-derived carbon into biocrusts, and the role of soil fungi in promoting performance of plants and biocrusts. Biocrusts responded to temperature and moisture differently by biome. Biocrusts in grasslands/shrublands contributed >25% of total summertime ecosystem respiration, but biocrusts in savannas/woodlands contributed < 1%. Biocrusts contributed < 2% to GPP in any biome. To augment their native photosynthesis, biocrusts may include 16% plant-derived carbon. Fungal connections improved plant and biocrust performance and reduced differences in the CN ratio between organisms compared to when connections were impeded. Investigation of interactions among biocrusts, plants, and fungi has improved understanding of resource cycling in drylands.

Characterization Of Antimicrobial Activity Of Culturable Bacteria Isolated From Krubera-Voronja Cave, Aiste Klusaite, Vida Vickackaite, Birute Vaitkeviciene, Rasa Karnickaite, Dominykas Bukelskis, Ieva Kieraite-Aleksandrova, Nomeda Kuisiene

International Journal of Speleology

In the present study we aimed to perform the first analysis of antimicrobial activity of bacteria isolated from Krubera-Voronja Cave, with the main focus on their activity against Grampositive bacteria, including Gram-positive pathogens. Using five different media, in total 874 heterotrophic cultures were isolated from water and sediment samples collected in Krubera-Voronja Cave at a depth from 220 m to 1640 m. 14.0% of all isolates demonstrated antibacterial activity against Gram-positive and Gram-negative test microorganisms. Our results show that this percentage was not uniform; it increased with the sampling depth and was the highest in the lower part of the …

Fungi In The Healthy Human Gastrointestinal Tract, Heather E. Hallen-Adams, Mallory J. Suhr

Department of Food Science and Technology: Faculty Publications

Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are …

A Global Edna Comparison Of Freshwater Bacterioplankton Assemblages Focusing On Large-River Floodplain Lakes Of Brazil, Michael Tessler, Mercer R. Brugler, Rob Desalle, Rebecca Hersch, Luiz Felipe M. Velho, Bianca T. Segovia, Fabio A. Lansac-Toha, Michael J. Lemke

Publications and Research

With its network of lotic and lentic habitats that shift during changes in seasonal connection, the tropical and subtropical large-river systems represent possibly the most dynamic of all aquatic environments. Pelagic water samples were collected from Brazilian floodplain lakes (total n = 58) in four floodpulsed systems (Amazon [n = 21], Araguaia [n = 14], Paraná [n = 15], and Pantanal [n = 8]) in 2011–2012 and sequenced via 454 for bacterial environmental DNA using 16S amplicons; additional abiotic field and laboratory measurements were collected for the assayed lakes.We report here a global comparison of the bacterioplankton makeup of freshwater …

Presence Of The Cyanotoxin Microcystin In Arctic Lakes Of Southwestern Greenland, Jessica Trout-Haney, Zachary Wood, Kathryn Cottingham

Dartmouth Scholarship

Cyanobacteria and their toxins have received significant attention in eutrophic temperate and tropical systems where conspicuous blooms of certain planktonic taxa release toxins into fresh water, threatening its potability and safe use for recreation. Although toxigenic cyanobacteria are not confined to high nutrient environments, bloom-forming species, or planktonic taxa, these other situations are studied les often studied. For example, toxin production in picoplankton and benthic cyanobacteria—the predominant photoautotrophs found in polar lakes—is poorly understood. We quantified the occurrence of microcystin (MC, a hepatotoxic cyanotoxin) across 18 Arctic lakes in southwestern Greenland. All of the focal lakes contained detectable levels of …

Atp Luminescence Assay As A Bioburden Estimator Of Biomass Accumulation In Caves, Janez Mulec, Andreea Oarga-Mulec

International Journal of Speleology

A commercially available adenosine triphosphate (ATP) detection system (Hygiena, USA), supported by cultivable microbial indicators, was used to estimate bioburden in different habitats in and outside show caves: air, water and solid surfaces. A strong positive correlation between ATP concentration expressed as Relative Light Units (RLU) and Colony-Forming-Units (CFU) was observed for swab samples from cave surfaces. In terms of ATP units, surfaces in a single cave system (Postojna Cave) varied considerably (240-1,258,800 RLU/ 20 cm²) and commonly exceeded the bioburden level of analogues on the surface (0-114,390 RLU/ 20 cm²). Cave sub-habitats were colonized by …

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 …

Shifts In Myxomycete Community Structure In Selected Microhabitats Across Nutrient Treatments In A Lowland Tropical Forest Of Panama, Laura M. Walker

Graduate Theses and Dissertations

Myxomycetes (plasmodial slime molds) are abundant amoeboid predators of bacteria and other microorganisms. They are found worldwide, largely in association with decaying plant material in terrestrial habitats. Their consumption of bacterial prey puts microbial predators such as myxomycetes in a key position in various ecosystem processes wherein they help regulate the flow of nutrients (e.g., N and C) through the ecosystem. The importance of microbial predators in nutrient cycling and plant productivity is well established. Given the extent to which tropical ecosystems influence global nutrient fluxes, along with the ecologically significant role that myxomycetes play in these processes, there is …

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 …

Bioaugmentation And Correlating Anaerobic Digester Microbial Community To Process Function, Kaushik Venkiteshwaran

Dissertations (1934 -)

This dissertation describes two research projects on anaerobic digestion (AD) that investigated the relationship between microbial community structure and digester function. Both archaeal and bacterial communities were characterized using high-throughput (Illumina) sequencing technology with universal 16S rRNA gene primers. In the first project, bioaugmentation using a methanogenic, aerotolerant propionate enrichment culture was investigated as a possible method to increase digester methane production. Nine anaerobic digesters, seeded with different biomass, were operated identically and their quasi steady state function was compared. Before bioaugmentation, different seed biomass resulted in different quasi steady state function, with digesters clustering into high, medium or low …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Handwashing: A Study Of The History, Methods, And Psychology Surrounding Hand Hygiene, Daniel J. Remillard

Senior Honors Theses

This paper covers three different areas concerning handwashing. First a review of the history of handwashing is done, going from ancient times to its introduction into modern medicine via Dr. Ignaz Semmelweis. This section gives a sobering reminder not to instantly reject data that comes in conflict with prevalent thought.

Then current medical knowledge about handwashing is examined, and the conclusion reached states that handwashing is best done with non-antibacterial soap.

Finally, a review of the psychology of handwashing shows that medical professionals often tend toward neglect if unwatched and unmotivated by an outside source. However, those suffering from obsessive …