Environmental Microbiology and Microbial Ecology Commons^™

Utilizing Molecular And Statistical Modeling Methods To Enhance White Nose Syndrome Detection In Bat Hibernacula, Samuel Miller

Electronic Theses & Dissertations

White Nose Syndrome (WNS) is a fungal infection in bats caused by Pseudogymnoascus destructans (Pd). Successfully identifying hibernacula infected with WNS is essential to help control and regulate the spread of WNS. Assessing the presence of WNS in bat hibernacula is usually done by visually confirming Pd on hibernating bats within infected hibernacula. This can be problematic because most visual confirmation occurs during the winter when bat populations are at their peak within hibernacula. When surveys are conducted in the winter, there is an increased chance of disturbing bats. One alternative method to visually confirming WNS on bats …

Differential Preservation Of Endogenous Human And Microbial Dna In Dental Calculus And Dentin, Allison E. Mann, Susanna Sabin, Kirsten Ziesemer, Ashild J. Vagene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-Garcia, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, Christina Warinner

Biology Faculty Articles

Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is …

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 …

Functions Of Ecosystems: Stream Metabolism As An Efficient And Effective Means To Gage The Health And Understand The Interworking Of Urban Streams In A Watershed Of Rock Island, Il, Ryan Johnson, Dr. Kevin Geedey

Celebration of Learning

Stream metabolism is a critical functional measure of stream health that integrates physical parameters like slope and discharge, with ecosystem functions like photosynthesis and respiration. Stream metabolism is widely studied; however, urban stream metabolism remains poorly understood. Stream metabolism was measured for five streams ranging from 1^st to 5^th orders from October 11^th to October 18^th 2017 and four streams ranging from 1^st to 4^th order from October 22^nd to 25^th 2017 located within an approximately 9.3 square kilometer watershed of Rock Island, IL that has an urban to suburban type of …

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 …

Examining Manganese Oxidation In Bacteria Through Bioinformatics And Environmental Sampling, T'Onna Collins

Undergraduate Theses and Capstone Projects

Manganese is an essential element for all living things. Manganese plays a role in geochemical cycles, like the nitrogen fixation cycle and the oxygen-evolving complex. The focus of this study is the manganese oxidation mechanism. Manganese oxidation plays a role in metabolic and antioxidant processes. Pseudomonas putida GB-1 is commonly used to study the process of manganese oxidation in bacteria. We used the previously identified Mn-oxidase genes, mopA, mnxG and mcoA, from P. putida GB-1 to look for conservation of manganese oxidation in other organisms. Basic Local Alignment Search Tool (BLAST) was used to find homologs of these three genes …

Sulfur Cave (Romania), An Extreme Environment With Microbial Mats In A Co2-H2S/O2 Gas Chemocline Dominated By Mycobacteria, Serban M. Sarbu, Joost W. Aerts, Jean-François Flot, Rob J.M. Van Spanning, Calin Baciu, Artur Ionescu, Boglárka M. Kis, Reka Incze, Sándor Sikó-Barabási, Zoltan Para, Botond Hegyeli, Nicu-Viorel Atudorei, Casey Barr, Kenneth Nealson, Ferenc L. Forray, Cristian Lascu, Emily J. Fleming, Wilbert Bitter, Radu Popa

International Journal of Speleology

Sulfur Cave (Puturosu Mountain, Romania) is an extreme environment, unique for displaying life in a gas chemocline. The lower part of the cave is filled with CO₂, CH₄, and H₂S of mofettic origin, while the upper part contains air that floats above the heavier volcanic gasses. S° and H₂SO₄ (from sulfur-oxidation) cover the cave wall at and below the CO₂-H₂S:O₂ gas/gas interface. On the cave wall, near the interface the pH is < 1 and unusual microbial biofilms occur on the rock’s surface. We provide context information on the geology, mineralogy, chemistry and biology to better understand this unique environment. We have used X-ray diffraction, optical microscopy, scanning electron microscopy with EDAX capabilities, stable isotope analysis and 16S and 18S rDNA amplicon sequencing. The most common taxa in the microbial biofilms are Mycobacteria, Acidithiobacillus and Ferroplasmaceae. Liquid water in this system originates solely from condensation of water …

Exploring The Microbiome: Diversity Of The Microbial Community Of Three Foam Nesting Frogs, Genus: Polypedates, Across A Developmental Gradient, Sarah Mcgrath

Masters Theses, 2010-2019

Characterization of microbial biodiversity, including that of the amphibian skin-associated microbiome, is a frontier of research recently made accessible through advances in sequencing technology. Microbial interaction with a host has been determined to have profound influences on host health across a wide range of macroscopic organisms. For amphibians, the influence of the skin-associated microbiome has been found to have particular importance, as amphibians are currently one of the fastest disappearing vertebrate groups on the planet, largely in part to skin-associated diseases caused by pathogenic microbes. Therefore, it is important to characterize the amphibian skin-associated microbiome, particularly for species with no …

Isolation, Sequencing, And Characterization Of Four Transmissible Antibiotic Resistance Plasmids Captured From Bacteria In Stream Sediments, Curtis J. Kapsak

Masters Theses, 2010-2019

Self-transmissible plasmids are key vectors in the transfer of resistance, catabolic, and other genes among bacteria native to environments such as streams and wetlands. The evolution of antibiotic resistance in particular is known to be powerfully affected by conjugative plasmid transfer due to the ease in which some plasmids can be horizontally transferred into a broad range of host bacteria and their ability to exchange mobile genetic elements that often contain antibiotic resistance genes.

In this study, we captured tetracycline resistance plasmids from stream sediments impacted by agricultural runoff. We selected for resistance plasmids using tetracycline, an antibiotic commonly used …

Changes In The Microbial Community Of Lubomirskia Baicalensis Affected By Red Sponge Disease, Colin Rorex

Electronic Theses and Dissertations

Lake Baikal is the oldest known lake and a unique ecosystem, home to several species of fresh water sponge. A disease outbreak affecting the dominant species, Lubormirskia baialensis, was recently reported. The cause of the disease has not been determined but one of the current hypothesis is that the increase in methane concentration is correlated to the disease outbreak. This pilot study characterized the microbiomes of sick and healthy sponges through the use of 16S rRNA sequencing. Sick sponge microbiomes shared a conserved group of taxa while the healthy sponge microbiomes had greater diversity. Indicator species analysis identified two significant …

Composition And Function Of The Bacterial Consortium Associated With The Accessory Nidamental Gland Of The Hawaiian Bobtail Squid, Jessica Bertenshaw

Honors Scholar Theses

The bacterial consortium associated with the accessory nidamental gland (ANG) of the Hawaiian bobtail squid, Euprymna Scolopes is posited to confer symbiotic benefits to the eggs of the squid when bacteria are transferred from the gland of the mother to the jelly coat, which surrounds the embryo in the egg. To characterize the composition of this community bacterial isolates from the egg jelly coat and from the ANG were identified using 16S sequencing. To elucidate the function of these bacteria, egg development experiments were performed to determine the effect of antibiotics on egg survival and the composition of the bacterial …

Antibiotic Resistant Bacteria In Water Environments In Louisville, Kentucky., Amy Priest

College of Arts & Sciences Senior Theses

Antibiotic resistant bacterial strains are an increasing problem, particularly in clinical health care settings. As a result, bacterial infections are becoming increasingly challenging to treat with more cases becoming life threatening. Aquatic environments facilitate microbial diversity and the transfer of genetic elements and thus may serve as a reservoir for antibiotic resistant microbes. Human misuse of antibiotics may further facilitate the spread of resistance in water environments. With little known about the bacteria communities in local water environments, this study aimed to learn more about these populations through the following aims: 1) identify the microbial community composition from water environments …

Detection, Activity Measurement And Phylogeny Of Ureolytic Bacteria Isolated From Elasmobranch Tissue, Yimu Yang

Master's Theses

Free-ranging marine elasmobranch tissue-associated micro-organisms were cultured from free-ranging Atlantic stingray (Dasyatis sabina) and Atlantic sharpnose sharks (Rhizoprionodon terraenovae). 16S rRNA gene phylogeny indicated bacteria community structure in both elasmobranchs were under phylum Proteobacteria, Firmicutes and Actinobacteria. By conducting split-plot ANOVA, we found the microbial richness is significantly different (P=0.0814) between two superorders of elasmobranch, which may largely due to their preferred habitats and feeding habits. Urease presentence and activity was detected in phylogenetically diverse bacterial strains. Species with high urea-hydrolyzing ability, such as Micrococcus luteus (shark blood isolate: 46.84 mU/mg protein; stingray blood isolate: 24.36 …

The Role And Contribution Of Saprotrophic Fungi During Standing Litter Decomposition Of Two Perennial Grass Species, Schizachyrium Scoparium And Schizachyrium Tenerum, Matthew Lodato

Master's Theses

In terrestrial ecosystems, most of the plant biomass produced enters the detrital pool, where microbial decomposers colonize, enzymatically degrade, and assimilate plant litter carbon and nutrients in amounts sufficient to bring about the decomposition of plant litter. Here, I estimated the biomass and production of fungi and microbial respiration associated with decaying Schizachyrium scoparium and Schizachyrium tenerum leaf litter, and constructed a partial organic matter budget estimating C flow into and through fungal decomposers. Significant losses in S. scoparium (57%) and S. tenerum (68%) leaf mass was observed during litter decomposition along with concomitant increases in fungal biomass, which reached …

Comparing Microbiome Sampling Methods In A Wild Mammal: Fecal And Intestinal Samples Record Different Signals Of Host Ecology, Evolution, Melissa R. Ingala, Nancy B. Simmons, Claudia Wultsch, Konstantinos Krampis, Kelly A. Speer, Susan L. Perkins

Publications and Research

Processing of multimodal information is essential for an organism to respond to environmental events. However, how multimodal integration in neurons translates into behavior is far from clear. Here, we investigate integration of biologically relevant visual and auditory information in the goldfish startle escape system in which paired Mauthner-cells (M-cells) initiate the behavior. Sound pips and visual looms as well as multimodal combinations of these stimuli were tested for their effectiveness of evoking the startle response. Results showed that adding a low intensity sound early during a visual loom (low visual effectiveness) produced a supralinear increase in startle responsiveness as compared …

Characterizing Cultivable Bacteria From Trachymyrmex Septentrionalis Fungus Gardens, Hannah Beatty

Honors Scholar Theses

The relationship between the fungus-growing ant Trachymyrmex septentrionalis, its symbiotic cultivar fungus, and the transient and residential community of microorganisms is a diverse and complex symbiosis that has evolved over space and time. The fungus garden, comprised primarily of the cultivar fungus belonging to the family Leucocoprineae,provides an environment that hosts many bacteria, which may also play an important role in this symbiosis. Although it is known that Pseudonocardia bacteria defend the ant host against fungal pathogens, other species of bacteria that are present in these fungus gardens also likely contribute to this symbiosis. Previous studies of this …

Optimizing Genetic Manipulation Of Methanogens Through Faster Cloning Techniques, Merrisa Jennings

Biological and Agricultural Engineering Undergraduate Honors Theses

Methanogenesis is the biological production of methane. Only anaerobic archaea known as methanogens are capable of such a metabolic feat. They have strict living conditions and substrate sources which determine their rate of metabolism. This is of particular importance from a greenhouse gas reduction perspective or biogas capturing perspective. One of the best ways to optimize methanogen methane production is via genetic manipulation. The current procedures are timely though, therefore a faster cloning processes should be developed. The objective of this study was to optimize a premade genetic transformation kit known as the Gibson Kit. The Gibson Kit was supposed …

Chloride Salt Inhibition On Lipid Production In Wastewater-Grown Algae For Biofuel Production, Will Richardson

Biological and Agricultural Engineering Undergraduate Honors Theses

Algae are increasingly being recognized as useful organisms for many applications in today’s world. Their ability to remove nitrogen, phosphorus, and trace metals from water while adding oxygen to water makes them an attractive tertiary treatment technology in municipal wastewater treatment facilities. At the same time, algae produce lipids and carbohydrates that are useful for biofuel production, and they are not a human food crop unlike many biofuel feedstocks. In this study the effect of increased chloride concentrations in wastewater was assessed on the ability of two species of algae, Chlorella vulgaris and Scenedesmus dimorphus, to function as a …

Microbiome Of Commercial Broilers Through Evisceration And Immersion Chilling, John A. Handley

Graduate Theses and Dissertations

The United States poultry industry generated 38.6 billion pounds (17,500 metric ton) of meat in 2014 which averaged to 121 pounds (55 kg) per individual of the U.S that same year. Of that meat generated by the poultry industry, an estimated 1 million cases of Salmonellosis will occur. Out of the 1 million cases approximately 40, 000 to 50,000 will be confirmed cases by the CDC. Recently, the USDA has requested changes in the inspection process and are currently allowing processors more freedom to utilize innovation to drive the increase in safer and more desirable foods. The new standards set …

Predator-By-Environment Interactions Mediate Bacterial Competition In The Dictyostelium Discoideum Microbiome, R Fredrik Inglis, Odion Asikhia, Erica Ryu, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Interactions between species and their environment play a key role in the evolution of diverse communities, and numerous studies have emphasized that interactions among microbes and among trophic levels play an important role in maintaining microbial diversity and ecosystem functioning. In this study, we investigate how two of these types of interactions, public goods cooperation through the production of iron scavenging siderophores and predation by the social amoeba Dictyostelium discoideum, mediate competition between two strains of Pseudomonas fluorescens that were co-isolated from D. discoideum. We find that although we are able to generally predict the competitive outcomes between …

Assay Of The Reverse Osmosis Purified Water In The Life Science Building At Bowling Green State University, Ohio, Nicholas Mendenhall, Scott O. Rogers, Neocles B. Leontis

Honors Projects

Contaminated water sources can cause problems for scientific research and result in costly delays and failures of experiments. At Bowling Green State University, the reverse osmosis supply circulating in the Life Sciences Building has been measurably contaminated for nearly three years, corresponding to a change in servicing of the system. While servicing has been accelerated, the contamination in the system remains. The focus of this research was to identify the species of bacteria and fungi growing inside of the water system so that it might alert those servicing the system, and to begin to eliminate the contamination. Reverse osmosis water …

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, …

Microbiome And Bacterioplankton Rrna Gene Sequence Data Collected From Gulf Of Mexico Seawater Samples, Cruises Dp03 And Dp04 From April - August 2016, Cole Easson, Lindsey Freed

DEEPEND Datasets

Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during planned DEEPEND cruise expeditions to the GOM in 2016. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable regions were generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Raw paired-end sequences were joined and quality filtered in the bioinformatics program, QIIME. Vertical baseline characterizations will track alpha and beta diversity at different depths ranging from 0 – 1500 m, assess seasonal …

Heterologous Expression Of Secreted Bacterial Bpp And Hap Phytases In Plants Stimulates Arabidopsis Thaliana Growth On Phytate., Lia R. Valeeva, Chuluuntsetseg Nyamsuren, Margarita R. Sharipova, Eugene V. Shakirov

Biological Sciences Faculty Research

Phytases are specialized phosphatases capable of releasing inorganic phosphate from myo-inositol hexakisphosphate (phytate), which is highly abundant in many soils. As inorganic phosphorus reserves decrease over time in many agricultural soils, genetic manipulation of plants to enable secretion of potent phytases into the rhizosphere has been proposed as a promising approach to improve plant phosphorus nutrition. Several families of biotechnologically important phytases have been discovered and characterized, but little data are available on which phytase families can offer the most benefits toward improving plant phosphorus intake. We have developed transgenic Arabidopsis thaliana plants expressing bacterial phytases PaPhyC (HAP family …

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). …

Mixing It Up In The Ocean Carbon Cycle And The Removal Of Refractory Dissolved Organic Carbon, Yuan Shen, Ronald Benner

Faculty Publications

A large quantity of reduced carbon is sequestered in the ocean as refractory dissolved molecules that persist through several circuits of global overturning circulation. Key aspects of the cycling of refractory dissolved organic carbon (DOC) remain unknown, making it challenging to predict how this large carbon reservoir will respond to climate change. Herein we investigate mechanisms that remove refractory DOC using bioassay experiments with DOC isolated from surface, mesopelagic and deep waters of the Atlantic Ocean. The isolated DOC was refractory to degradation by native microbial communities, even at elevated concentrations. However, when the refractory DOC was introduced to a …

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. …

Influence Of Developmental Stage, Habitat, And Captivity On Thecutaneous Bacterial Communities Of Eastern Hellbenders (Cryptobranchus Alleganiensis Alleganiensis) In West Virginia, Rachel Fern Arrick

Theses, Dissertations and Capstones

Microbes inhabit virtually all surfaces of multicellular animal hosts, with microbial cells outnumbering the hosts’ own cells 10:1. Symbiont microbes, collectively referred to as the microbiome, can have profound impacts on the metabolism, development, behavior, and disease resistance of their multicellular hosts. Because the community structure of symbiont bacteria can influence host health, the characterization of amphibian microbiomes is becoming an increasingly important tool for future conservation in the face of global amphibian declines. Eastern hellbenders are good candidates for a microbiome study because they have seen substantial declines in recent decades and learning more about the environmental and physiological …

A Cure For Salmonella: Engaging Students In Pathogen Microbiology And Bioinformatics, Sophie Jurgensen

Senior Honors Projects, 2010-2019

Advances in Next Generation Sequencing (NGS) technology have generated a vast amount of publicly available genomic data, creating a need for students with training in computational analysis. This laboratory lesson is a course-based undergraduate research experience (CURE) focusing on environmental Salmonella, a common foodborne pathogen that is of great interest to public health laboratories but is relatively less virulent than most other such pathogens. As discovery is a central tenet of CUREs, students isolate novel Salmonella enterica and related strains from stream sediment, poultry litter, or other sources in the first half of the lesson (Module 1). They also …

Bioassessment Of A Drinking Water Reservoir Using Plankton: High Throughput Sequencing Vs. Traditional Morphological Method, Wanli Gao, Zhaojin Chen, Yuying Li, Yangdong Pan, Jingya Zhu, Shijun Guo, Lanqun Hu, Jin Huang

Environmental Science and Management Faculty Publications and Presentations

Drinking water safety is increasingly perceived as one of the top global environmental issues. Plankton has been commonly used as a bioindicator for water quality in lakes and reservoirs. Recently, DNA sequencing technology has been applied to bioassessment. In this study, we compared the effectiveness of the 16S and 18S rRNA high throughput sequencing method (HTS) and the traditional optical microscopy method (TOM) in the bioassessment of drinking water quality. Five stations reflecting different habitats and hydrological conditions in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia, were sampled May 2016. Non-metric multi-dimensional scaling (NMDS) analysis showed …