Environmental Microbiology and Microbial Ecology Commons^™

Dietary Fiber Utilization In The Gut: The Role Of Human Gut Microbes In The Degradation And Consumption Of Xylose-Based Carbohydrates, Elizabeth Drey

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

Xylans are a family of xylose-based polysaccharides naturally present in fruits, vegetables, and cereal grains. Resistant to digestion by host enzymes, xylans reach the large intestine intact, where they are utilized by members of the gut microbiome. They are initially hydrolyzed by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. These xylooligosaccharides (XOS) can then either be further hydrolyzed by primary degraders or can cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, studies have shown these species grow poorly on longer XOS and xylan substrates. In this thesis, …

Spotted Salamander Egg Masses Exhibit A Unique Internal Microbiome In Relation To Their Environment, Elizabeth Leonard

Senior Honors Theses

Microbial studies have led to various ecological and medicinal discoveries. Amphibian eggs, like those of Ambystoma maculatum, exhibit natural resistance to bacterial invasion that may be microbiome related. The purpose of this research was to sequence the external and internal microbiome of A. maculatum egg masses and compare with the environmental microbiome. It was hypothesized that the external and internal microbiome would bear more similarity to each other than the water. A significant difference was observed between the microbiome of the inside surface of the egg mass and the water but not the outside surface of the egg and …

Factors Affecting The Epizootics Of Entomopathogenic Fungi-A Review, Mirza Abdul Qayyum, Huda Bilal, Unsar Naeem Ullah:, Habib Ali, Hasnain Raza, Muhammad Wajid

Journal of Bioresource Management

Entomopathogenic fungi (EPF) specifically infect and kill insects can serve as a potential biological control agent. Several biotic and abiotic factors affect their occurrence, persistence, and epizootics caused by them. In biotic factors, fungi characters (host range, latency, spore density and dispersal, mainly host-pathogen compatibility), insect host factors (behavioral, morphological, and physiological), plant-mediated effects (plant architecture, surface chemistry, and leaf topology) are included supports or causes the barrier to mycobiopesticide. Abiotic factors which affect the EPF field persistence are mainly environmental (temperature, sunlight, humidity, rainfall) physical and chemical soil properties (soil texture, pH, E.c, moisture, C/N content, and organic matter) …

Plastic Biodegradation Through Insects And Their Symbionts Microbes: A Review, Huda Bilal, Hasnain Raza, Haseena Bibi, Tehmina Bibi

Journal of Bioresource Management

Plastic waste has recently been identified as one of the most serious environmental issues, affecting all life forms, natural habitats, and the economy, and is one of the most serious global environmental problems, second only to climate change. Seeking alternative environmentally sustainable options, such as biodegradation instead of conventional disposal, is critical in the face of this challenge. However, there is currently a lack of information about the mechanisms and efficacy of plastic biodegradation. From this perspective, this study aims to illustrate the negative environmental impacts of the plastic waste. It also addresses the role of insects and gut microbiota …

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

Masters Theses

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

The Effect Of Disturbance And Invasion On Fungal And Plant Communities Over An Elevational Gradient, Adam N. Trautwig

Doctoral Dissertations

High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also …

Response Of The Soil Bacterial Community, Resistome, And Mobilome To A Decade Of Macrolide Antibiotic Contamination, Liam Paul Brown

Electronic Thesis and Dissertation Repository

Biosolids (treated sewage sludge) are used as agricultural fertilizer but are frequently contaminated with macrolide antibiotics, to which resistance is rising among historically susceptible bacteria. To determine if the land-application of macrolides carried in biosolids could promote antibiotic resistance in soil bacteria, soil plots were exposed annually to environmentally realistic or high doses of macrolides for ten years. I sequenced the bacterial 16S ribosomal DNA, metagenomic DNA, and integron gene cassettes within the treated and antibiotic-free soil to compare the compositions and diversities of the bacterial communities, antibiotic resistance genes, and mobile genetic elements. I determined that the high dose …

Human Fecal Contamination Corresponds To Changes In The Freshwater Bacterial Communities Of A Large River Basin, Jill Mcclary-Gutierrez, Zac Driscoll, Cheryl Nenn

Freshwater Faculty Articles

Microbial water quality is generally monitored by culturable fecal indicator bacteria (FIB), which are intended to signal human health risk due to fecal pollution. However, FIB have limited utility in most urbanized watersheds as they do not discriminate among fecal pollution sources, tend to make up a small fraction of the total microbial community, and do not inform on pollution impacts on the native ecosystem. To move beyond these limitations, we assessed entire bacterial communities and investigated how bacterial diversity relates to traditional ecological and human health-relevant water quality indicators throughout the Milwaukee River Basin. Samples were collected from 16 …

A Novel Approach For Characterizing The Ultra-Micro Size-Fraction Community, Abdullah Ahmed Salim, Priscilla Nicole Pineda, Isabella Alamilla, Andrew Dean Putt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

A Novel Approach for Characterizing the Ultra-Micro Size-Fraction Community

Students: Abdullah Salim, Priscilla Pineda, Isabella Alamilla

Mentors/Supervisors: Andrew Putt, Terry C. Hazen

ABSTRACT

The ultra-micro size-fraction (UMSF) are bacteria that can pass through the 0.2 µm pore membrane filters employed in environmental surveys. Despite being ubiquitous and having high metabolic activity, UMSF remain elusive and largely uncultured. Investigations of UMSF are skewed by difficulties in culturing and a lack of techniques for measuring UMSF biogeochemical signatures. This study measures surface stream UMSF community diversity, and community response to the addition of the synthetic pharmaceutical and cosmetic carbon product cyclodextrin which …

Extracellular Polymeric Substances In Oxygenic Photogranules: Investigation Of Their Role In Photogranulation In A Hydrostatic Environment, Wenye Camilla Kuo-Dahab

Doctoral Dissertations

The purpose of this dissertation was to assess the critical role of extracellular polymeric substances (EPS) in the photogranulation of activated sludge, in a hydrostatic environment. The first section evaluates the fate and dynamics of different fractions of EPS in sludge-based photogranulation under hydrostatic conditions. The study shows that during the transformation of activated sludge into a photogranular biomass, sludge’s base-extractable proteins selectively degrade. Strong correlations between base-extracted proteins and the growth of chlorophyll a and chlorophyll a/b ratio suggest that the bioavailability of this organic nitrogen is linked with selection and enrichment of filamentous cyanobacteria under hydrostatic conditions. The …

Soil Bacteria: Metabolic Diversity In A Wildlife Management Area, Nicholas Green

Symposium of Student Scholars

This research is part of a larger study linking the soil microbiome and processes to the aboveground plant community.

Soil samples were collected from six plots under closed canopy in the Sheffield Wildlife management area in the Piedmont ecoregion of Georgia in Paulding County. Two of the plots were located in the longleaf pine savanna where restoration of longleaf pine has been in place since 2010. Samples were collected in sterile plastic tubes at the center of each plot and 10 meters above and below the center. For each sample, soil pH and the concentration of nitrogen (N), phosphorus (P), …

Glide Another Day: Characterization Of Wild Isolates Of Predatory Myxobacteria, Daniella Krakue, Juan Vasquez, Simone Dakare

Symposium of Student Scholars

Myxobacteria belongs to a group of predatory bacteria that are found in various soil environments. They are exceptionally unique microbes who use their gliding motility to move towards prey microbes and consume them. They also have the remarkable ability to produce secondary metabolites that have antibacterial, antifungal, antiviral, and antitumor properties. For this reason, they are of interest to us so that we can understand their abilities and apply them to discover their potential as a source of novel metabolites with potential therapeutic applications. Our methodology began by collecting soil samples from various sites around the country. We then standardized …

Community Level Physiological Profiling Of The Longleaf Pine Savannah Microbiome, Gavin Treadaway

Symposium of Student Scholars

Soil microorganisms secrete chemicals into their surroundings, which the root system will uptake and in return release root exudates, which usually consist of low-molecular-weight organic compounds. These root exudates behave as signaling molecules and substrates for microorganisms to recruit beneficial soil bacteria to the plant root system, which will provide the plants with immunity to foliar diseases and pathogen infection. Studies have shown that bacteria on the root surface can protect aerial sections of the plant by promoting induced systemic resistance, a mechanism of increasing physical or chemical barriers of the plant.

The longleaf pine is an endangered species of …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Microbial Innovations For Disease Management In Honey Bees, Brendan A. Daisley

Electronic Thesis and Dissertation Repository

Arguably the most important insect pollinator, honey bees (Apis mellifera) are threatened by infectious disease, pesticide exposure, and nutritional deficits resulting from habitat loss.

The major goals of this thesis were to advance our understanding of the immune and microbiota factors underpinning synergistic interactions between the threats, and to develop a honey bee-specific probiotic with strain-level functions to alleviate cumulative stress burden.

Drosophila melanogaster was used as a high-throughput discovery platform in molecularly characterizing the effects of candidate probiotic lactobacilli and neonicotinoid-neuroimmune-microbiota mechanisms prior to experimentation in honey bees. Imd pathway activation by lactobacilli was identified to be …

Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan

Biology Theses

Fungus-growing ants (Attini: Formicidae) and their fungal cultivars participate in ant-fungus mutualism that share a 50-million-year-old coevolutionary history. Fungal cultures are grown in gardens alongside ants and a diverse collection of microbes that interact with both species in mutualistic, commensal, and antagonistic relationships. These microbes aid in digestion and detoxification of food, provide essential nutrients, help in nest hygiene, and play a dominant role in defense against pathogens and disease. Microbial communities of many model species have been shown to change in a laboratory setting as compared to their natural environment. High-throughput 16s sequencing of the V4 variable region was …

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and β-sitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis of the …

Impacts Of Soil Management On Microbial Assemblages Involved In Nitrogen Transformations In Agroecosystems In Tennessee, Usa, Jialin Hu

Doctoral Dissertations

Nutrient reduction, particularly with respect to nitrogen (N) losses, is an important goal for sustainably managed agroecosystems. Soil N-cycling microbial populations that modulate these processes are affected by agricultural management regimes. This research focused on the controls and dynamics of the major N-cycling microbial populations in high-input cotton field under agricultural management regimes and low-input native C₄ forage grass systems under pasture management practices to determine the effects of management regimes on in situ seasonal dynamics of the functional microbes responsible for N fixation, nitrification, and denitrification processes. Molecular microbial ecology methods were combined with soil physicochemical properties and …

Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells

Master's Theses

The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …

A Stable-Isotope Probing Approach To Modeling Bidirectional Nutrient Exchange In The Microcystis Phycosphere, Malia Gardner

Masters Theses, 2020-current

Cyanobacterial harmful algal blooms (cHABs) plague freshwater systems worldwide and are projected to increase in intensity in the coming decades. cHABs damage aquatic ecosystems by blocking light penetration into the water column, creating hypoxic conditions, and releasing toxins. One of the most prolific cHAB formers is the cosmopolitan genus of cyanobacteria Microcystis. Global climate change and anthropogenic loading of nutrients such as nitrogen (N) and phosphorus (P) fuel Microcystis bloom formation. Increasing global temperatures favor Microcystis because of its high optimal growth temperature. N input is of particular importance for Microcystis because it is unable to fix atmospheric N, …