Microbiology Commons^™

Geological And Geochemical Controls On Non-Tuberculous Mycobacterium Transmission: Examples From Hawaii, Schuyler Thomas Robinson

Theses and Dissertations

The opportunistic environmental microbes, non-tuberculous Mycobacterium (NTM), pose an increasing risk of disease and death in both immunodeficient and immunocompetent individuals in the USA and across the world. NTM lung disease is particularly prevalent in Hawaii, although the modes of NTM acquisition and transport in Hawaii are not fully understood. This study evaluated 149 soil and 50 water samples across the Hawaiian Islands to determine geochemical factors controlling NTM. Non-metric multidimensional scaling (NMDS) and principal component analyses (PCA) of modern soils show variables such as Total Organic Carbon (TOC), pH, P, mafic silicate minerals, and Pb seem to control NTM …

The Effects Of Constructed Wetlands On Metal Solubilization And Bioavailability In Passive Mine Remediation, Elizabeth Cochran

Electronic Theses and Dissertations

The legacy of coal mining in Appalachia has left many watersheds impacted by abandoned mine drainage. The drainage degrades streams, groundwater and habitats with acidity and toxic heavy metals. The Lowber Passive Remediation System has been in operation since 2004 to remediate high amounts of dissolved Fe, SO₄, Al, and Mn. The site consists of six settling ponds and an extensive wetlands at the finish. This study investigated the resolubilization of Fe and Mn in the wetlands and the role of bacteria in resolubilization. During three seasons, field measurements of water quality and lab analysis of Fe, Mn, …

Beyond Genetics: Addressing Activity In Microbial Ecology, Scott Christopher Thomas

UNLV Theses, Dissertations, Professional Papers, and Capstones

The field of microbial ecology is on the cusp of another revolution, one that uses synergy to address the limitations of previous studies. My dissertation is representative of the new era of research to come, through combining the latest technological advances with established classical methods to provide a more complete understanding of microbial ecosystems. In my first study, I evaluate the conservation of central carbon metabolic pathways and activity along a temperature and diversity gradient (60-95 ℃) through the use of 16S rRNA gene amplicon data, metagenome sequencing, and position-specific 13C-labeled metabolite probing. In my second study, I provide the …

Coupling Metaproteomics With Taxonomy To Determine Responses Of Bacterioplankton To Organic Perturbations In The Western Arctic Ocean, Molly P. Mikan

OES Theses and Dissertations

Understanding how the functionality of marine microbial communities change over time and space, and which taxonomic groups dominate distinct metabolic pathways, are essential to understanding the ecology of these microbiomes and the factors contributing to their regulation of elemental cycles in the oceans. The primary goal of this dissertation was to investigate the community metabolic and taxonomic responses and the degradation potential of two compositionally distinct marine microbiomes within the shallow shelf ecosystem of the Chukchi Sea after rapid fluctuations in algal organic matter availability. Novel bioinformatics tools were collaboratively developed and used together with community proteomics (metaproteomics) to characterize …

Modelling Non-Linear Functional Responses In Competitive Biological Systems., Nickolas Goncharenko

Western Research Forum

One of the most versatile and well understood models in mathematical biology is the Competitive Lotka Volterra (CLV) model, which describes the behaviour of any number of exclusively competitive species (that is each species competes directly with every other species). Despite it's success in describing many phenomenon in biology, chemistry and physics the CLV model cannot describe any non-linear environmental effects (including resource limitation and immune response of a host due to infection). The reason for this is the theory monotone dynamical systems, which was codeveloped with the CLV model, does not apply when this non-linear effect is introduced. For …

Effectiveness Of Windrow Composting Methodology In Killing A Thermo-Tolerant Species Of Salmonella During Mortality Composting, Spencer Gabriel Myers

Master's Theses

In a large agricultural operation, such as the one at Cal Poly San Luis Obispo, disposal of deceased animals is an immense issue. The cost of transporting and rendering every dead animal is inhibitory to the general function of the agricultural operations and their thin budget. Therefore, we propose that composting mortalities could be an economical alternative. Composting is a recognized method for taking animal waste products along with carbon waste and turning it into a pathogen-free, nutrient-rich topsoil. Carcass composting is in fact performed in other countries and states to varying degrees of success. However, the California EPA limits …

Isolation And Identification Of Potential Bioinoculants Based On Phosphate Solubilizing And Plant Growth Promoting Benefits, Rachel Raths

Electronic Theses and Dissertations

Conservative models have shown that as populations rise, food production needs to double by 2050. Population increase and the green revolution have caused fertilizer inputs to increase since the 1960’s, increasing environmental issues and production costs. These intensive practices have led to degraded arable land and there has been an increase in urbanization meaning we need to make best use of the farming land that is available and ensure it is sustainable for future food production. Due to this, there has been a higher demand for research on more environmentally and economically friendly approaches to food production. Plant growth promoting …

A Full-Ocean-Depth Rated Modular Lander And Pressure-Retaining Sampler Capable Of Collecting Hadal-Endemic Microbes Under In Situ Conditions, Logan M. Peoples, Matthew Norenberg, David Price, Madeline Mcgoldrick, Mark Novotny, Alexander Bochdansky, Douglas H. Bartlett

OES Faculty Publications

The hadal zone remains one of the least studied environments because of its inaccessibility, in part because of hydrostatic pressures extending to 110 MPa. Few instruments are capable of sampling from such great depths. We have developed a full-ocean-depth-capable lander that can be fit with sampling packages for the collection of still images, video, motile megafauna, and hadal seawater. One payload includes a pressure-retaining sampler (PRS) able to maintain seawater samples under in situ pressure during recovery. We describe the technical specifications of the lander and the PRS and preliminary results from three deployments at depths in excess of 10,700 …

Metaproteomics Reveal That Rapid Perturbations In Organic Matter Prioritize Functional Restructuring Over Taxonomy In Western Arctic Ocean Microbiomes, Molly P. Mikan, H. Rodger Harvey, Emma Timmins-Schiffman, Michael Riffle, Damon H. May, Ian Salter, William S. Noble, Brook L. Nunn

OES Faculty Publications

We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value < 0.01) in biological and molecular functions associated with carbon and nitrogen recycling were observed. Within the first day under both organic matter conditions, Bering Strait surface microbiomes increased protein synthesis, carbohydrate degradation, and cellular redox processes while decreasing C1 metabolism. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level. The dynamic responses of these two oceanic microbial communities have important implications for timing and magnitude of responses to organic perturbations within the Arctic Ocean and how community-level functions may forecast biogeochemical gradients in oceans.

Nitrogen Assimilation In Picocyanobacteria Inhabiting The Oxygen-Deficient Waters Of The Eastern Tropical North And South Pacific, Montserrat Aldunate, Carlos Henriquez-Castillo, Qixing Ji, Jessica Lueders-Dumont, Margaret R. Mulholland, Bess B. Ward, Peter Von Dassow, Osvaldo Ulloa

OES Faculty Publications

Prochlorococcus and Synechococcus are the most abundant free-living photosynthetic microorganisms in the ocean. Uncultivated lineages of these picocyanobacteria also thrive in the dimly illuminated upper part of oxygen-deficient zones (ODZs), where an important portion of ocean nitrogen (N) loss takes place via denitrification and anaerobic ammonium oxidation. Recent metagenomic studies revealed that ODZ Prochlorococcus have the genetic potential for using different N forms, including nitrate and nitrite, uncommon N sources for Prochlorococcus, but common for Synechococcus. To determine which N sources ODZ picocyanobacteria are actually using in nature, the cellular 15N natural abundance (δ15N) and assimilation rates of …

Linking Microbial Community Structure And Ecosystem Functions In Acidic Soil From Pennsylvania, Usa, Madison T. James, Sophia T. Farrisi, Shreya Shah, Vishal Shah

Sustainability Research & Creative Activities Grants Reports

Microorganisms play a critical role in the structure and functioning of soil ecosystems. Within acidic soil across the northeastern United States and Canada, we have little understanding of the microbial diversity present and its relationship to the biochemical cycles. The current study is aimed at understanding the taxonomical and functional diversities in the acidic soil obtained from near various types of trees, how the diversities change as a function of depth, and the linkage between taxonomical and functional diversities. From eight sampling locations, soil samples were collected from three horizons (depths). The three depths were 0-10 cm (A), 11-25 cm …

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 …

Microbiome And Metagenome Of An Anthropogenic Hyperalkaline Slag-Fill Waterway In South Chicago, Illinois, Usa, Jan Ingemar Ohlsson

Graduate Research Theses & Dissertations

The aquifers and waterways around the Lake Calumet area of south Chicago, IL, USA have been affected by a century of intensive industrial waste dumping. Steel slag in particular was used as infilling to claim most of the Calumet Wetlands for industrial and residential development. Since the prohibition and cessation of these disposal activities, a growing body of research has recorded the environmental and health effects of the infill, particularly where interactions between slag minerals and rainwater produces extremely alkaline groundwater (pH ≥13). Atmospheric carbon dioxide interacting with these calcium hydroxide-rich slag fluids produces massive precipitation of a loose, white …

Impacts Of Plant-Microbe Interactions On Seedling Performance In A Riparian Forest Invaded By Lonicera Maackii, Taylor E. K. Strehl

Masters Theses

Soil microbes have profound impacts on plant growth and survival and can either promote or inhibit plant dominance. Exotic plants are often strongly invasive because they have escaped their natural enemies, potentially including antagonistic soil microbes. I examined how the invasive shrub Lonicera maackii and a common native tree, Acer negundo, responded to soil microbial communities to determine the role of soil microbes in regulating invasion success. This was done by growing both species with microbes from invaded (L. maackii) and uninvaded (A. negundo) soils collected from three locations within a riparian forest. Seedlings were …

Prokaryotic Diversity And Aqueous Geochemistry Of Subsurface Environments Of The Death Valley Regional Flow System, Joshua David Sackett

UNLV Theses, Dissertations, Professional Papers, and Capstones

This dissertation summarizes over four years of effort towards the completion of a Ph.D. in Biological Sciences. The work presented in this document covers a broad range of topics, but a central unifying theme is prokaryotic life in the continental subsurface. The work presented in each chapter relied heavily on cultivation-independent methods for assessing prokaryotic communities, including prokaryotic community structure reconstruction from high-throughput sequencing of 16S rRNA gene libraries and single-cell genome analysis of novel uncultivated bacteria.

Chapter 2 examines the aqueous geochemistry and prokaryotic diversity of Devils Hole, a cavernous limnocrene and sole natural habitat for the critically endangered …

Pengaruh Pupuk Hayati Majemuk Dan Pupuk Fosfor Terhadap Pertumbuhan Dan Hasil Kedelai Di Inceptisol Jatinangor, Aep Wawan Irwan, Tati Nurmala

Jurnal Kultivasi

Kedelai merupakan salah satu tanaman yang membutuhkan fosfor dalam jumlah besar. Ketersediaan P merupakan faktor pembatas utama pada pertumbuhan dan produksinya. Fosfor tidak banyak tersedia untuk tanaman, sehingga dibutuhkan pupuk hayati yang mengandung mikroorganisme untuk dapat melarutkan fosfor. Penelitian ini bertujuan untuk memperoleh dosis pupuk hayati majemuk dan pupuk P yang efektif dan dapat memberikan pengaruh terbaik terhadap pertumbuhan, komponen hasil, dan hasil tanaman kedelai kultivar Anjasmoro. Penelitian dilakukan pada bulan Maret sampai Juni 2017 di Kebun Percobaan Ciparanje, Fakultas Pertanian Universitas Padjadjaran, dengan ketinggian tempat yaitu ± 780 mdpl. Percobaan dilakukan dengan menggunakan Rancangan Acak Kelompok terdiri dari 9 …

Methanogens, Plausible Extraterrestrial Life Forms On Mars, And Their Tolerance To Increasing Concentrations Of Illite Clay, Chandler Kern

Biological Sciences Undergraduate Honors Theses

Methanogens, some of Earth’s most primitive prokaryotic organisms, are candidates for possible life forms capable of inhabiting Mars. Specifically, four different species (Methanobacterium formicicum, Methanococcus maripaludis, Methanosarcina barkeri, Methanothermobacter wolfeii) were analyzed for their tolerance to the presence of illite clay. Illite is a crystalline mineral that has been identified from regions of Mars’s surface. Results indicated that all four species grew with some success in the illite at different concentrations. This experimentation with methanogens’ abilities to survive and reproduce in the presence of illite allows for a more accurate understanding of the potential capability of microbial …

Microbial Diversity In Urban Environments: Concern For Antibiotic Resistance, Ality Aghedo, Mangala Tawde, Nazrul I. Khandaker

Publications and Research

We are almost oblivious to the presence of microorganisms in our daily lives, but they exist and come into contact with us all the time. While some bacteria are harmless, and even beneficial, other bacteria can cause infections. A common treatment to bacterial infections is antibiotics and the success of an antibiotic depends on the resistance of the bacteria to the antibiotic. We conducted experiments to identify the types of bacteria that can be found on surfaces or within soil environments that come into contact with a vast number of people on a daily basis and how this can affect …

Effects Of Red Clover Isoflavones On Tall Fescue Seed Fermentation And Microbial Populations In Vitro, Emily A. Melchior, Jason K. Smith, Liesel G. Schneider, J. Travis Mulliniks, Gary E. Bates, Zachary D. Mcfarlane, Michael D. Flythe, James L. Klotz, Jack P. Goodman, Huihua Ji, Phillip R. Myer

Plant and Soil Sciences Faculty Publications

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L …

Theory On Thermodynamic Constraints To Biogeochemical And Metabolic Diversity, Jordan Okie, Everett Shock

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Adapting Cell-Free Protein Synthesis As A Platform Technology For Education, Grace W. Chu, Max Z. Levine, Nicole E. Gregorio, Javin P. Oza

STAR Program Research Presentations

Cell-free protein synthesis (CFPS) has emerged as an enabling biotechnology for research and biomanufacturing as it allows for the production of protein without the need for a living cell. Applications of CFPS include the construction of libraries for functional genomics and structural biology, the production of personalized medicine, and the expression of virus-like particles. The absence of a cell wall provides an open platform for direct manipulation of the reaction conditions and biological machinery. This project focuses on adapting the CFPS biotechnology to the classroom, making a hands-on bioengineering approach to learning protein synthesis accessible to students grades K-16 through …

Iac Gene Expression In The Indole-3-Acetic Acid-Degrading Soil Bacterium Enterobacter Soli Lf7, Isaac V. Greenhut, Beryl L. Slezak, Johan H. J. Leveau

Plant and Soil Sciences Faculty Publications

We show for soil bacterium Enterobacter soli LF7 that the possession of an indole-3-acetic acid catabolic (iac) gene cluster is causatively linked to the ability to utilize the plant hormone indole-3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes, chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (iac cluster were genes for a major facilitator superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels …

Investigation Of Biogeochemical Mechanisms Of Greenhouse Gas Production In The Urban Hudson River Estuary, Brian Alan Brigham

Dissertations, Theses, and Capstone Projects

Coastal megacities deposit significant amounts of carbon (C), nitrogen (N) and other pollutants into surrounding waters. These inputs, including wastewater and surface water runoff, may affect estuarine and adjacent wetland biogeochemical cycles, microbial production and ultimately greenhouse gas (GHG) efflux. In many megacities pollutant loading is typically greatest after periods of precipitation when the volume of wastewater and storm water runoff exceeds local sanitation capacity, resulting in the discharge of raw sewage into adjacent waters. These combined sewage overflow (CSO) events have received considerable attention primarily due to their potential impact on human health and eutrophication. However, whether these events …

Pengaruh Pupuk Hayati Dan Pengapuran Terhadap Produktivitas Kedelai Di Tanah Inceptisol Jatinangor, Aep Wawan Irwan, Tati Nurmala

Jurnal Kultivasi

Kedelai merupakan tanaman pangan dengan kandungan protein tinggi sebagai bahan baku utama berbagai makanan, sehingga kebutuhan kedelai di Indonesia selalu tinggi. Hasil kedelai dapat ditingkatkan melalui aplikasi pupuk hayati dan pengapuran. Penelitian ini dilaksanakan di Kebun Percobaan Fakultas Pertanian Universitas Padjadjaran, Jatinangor, Sumedang pada ordo tanah Inseptisol. Penelitian dilakukan dari Maret 2017 sampai Juni 2017. Rancangan percobaannya adalah Rancangan Acak Kelompok, terdiri dari sembilan perlakuan, yaitu tanpa pupuk hayati dan tanpa pengapuran (kontrol); pupuk hayati 5 liter/ha + tanpa pengapuran; pupuk hayati 8 liter/ha + tanpa pengapuran; tanpa pupuk hayati + pengapuran 140 kg/ha; pupuk hayati 5 liter/ha + pengapuran …

Next Generation Sequencing Methods For Coastal Zone Water Quality Monitoring, Catherine Iskrenko

HCNSO Student Capstones

When analyzing the water quality of the coastal zone, culture-based techniques have been utilized most often to identify Fecal Indicator Bacteria in samples. Since the advent of the Sanger Method for DNA sequencing, other techniques have arisen that provide significantly more information on the microorganisms in sample, but they are still not the mainstream for water quality analysis. This capstone reviews and compares culture-based techniques, DNA sequencing, RNA sequencing, qPCR for biomarker, and 16S rDNA sequencing to highlight their merits and shortcomings for analyzing environmental water samples. The technique presented that provides the broadest range of information (including the identification …

Tof-Sims Analysis Of Plant Seed Interactions With Plant Growth-Promoting Bacteria, Tammy Pheuphong, Rachel Komorek, Xiao-Ying Yu

STAR Program Research Presentations

The use of time-of-flight secondary ion mass spectrometry (ToF-SIMS) in plant biology is a relatively unexplored and quickly developing field. The majority of research in plant SIMS involves the application of ToF-SIMS to study dried wood tissues, and only a handful of studies apply SIMS on plant stems, roots, and/or seeds. Our project provides a brief description and review of previous work using SIMS on plant stems, roots, and/or seeds, along with an emphasis on the sample preparation in each study. Additionally, the use of Brachypodium distachyon (Brachypodium) as a model system for research on grasses has also become more …

Comparative Microbial Community Dynamics In A Karst Aquifer System And Proximal Surface Stream In Northwest Arkansas, Josue Rodriguez

Graduate Theses and Dissertations

Northwest Arkansas has well-developed karst systems, with numerous sinking streams and springs. Karst conduits make it easy for contaminants to enter groundwater systems, degrading the water quality and destroying fragile karst ecosystems. With the increase of urbanization, potential threats in the form of fecal contamination may prove to be more of a problem. The purpose of this research is to compare the difference between microbial communities within two different settings, a karst aquifer and a surface stream. The microbial communities within Blowing Spring Cave and Little Sugar Creek were detected and identified in water and sediment samples. Samples were also …

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 …

Plastics And Microplastics As Vectors For Bacteria And Human Pathogens, Amanda Lee Laverty

OES Theses and Dissertations

Since plastics degrade very slowly, they remain in the environment on much longer timescales than most natural substrates and can thus provide a novel habitat for colonization by bacterial communities. The full spectrum of relationships between plastics and bacteria, however, is little understood. The objective of this study was to examine marine plastic pollution as a substrate for bacteria, with particular focus on Vibrio spp., including the human pathogens, Vibrio cholerae, Vibrio parahaemolyticus, and Vibrio vulnificus.

Colonization experiments were set up in a tributary of the lower Chesapeake Bay to follow Vibrio spp. colonization and …