Environmental Microbiology and Microbial Ecology Commons^™

Persistence Of Wastewater-Associated Antibiotic Resistant Bacteria In River Microcosms, Aoife P. Mahaney

Theses and Dissertations

The spread of antibiotic-resistant bacteria (ARB) associated with wastewater is a significant environmental concern, but little is known about the persistence and proliferation of these organisms in receiving water bodies after discharge. To address this knowledge gap, we performed a series of microcosm experiments in which river water was amended with either untreated or treated wastewater, and the abundance of viable ciprofloxacin-, Bactrim-, and erythromycin-resistant bacteria was monitored for 72 hours.

Both types of wastewater amendments increased the initial abundance of ARB compared to microcosms containing only river water. The increase was greatest with untreated wastewater, but that effect decreased …

Developing Methods For Analysis Of Chiral Small Molecules And D-Amino Acid Containing Peptides, Joshua I. Putman

Chemistry & Biochemistry Dissertations - Archive

This dissertation covers the development of methods to analyze chiral small molecules and d-amino acid containing peptides. The first section covers the development of liquid chromatographic chiral screening approaches for newly synthesized chiral molecules. The next part of the dissertation covers methodologies for the analysis of d-amino acid containing peptides. Lastly the bacterial degradation of three commonly used pesticides by bacteria harvested from Colorado potato beetles (Leptinotarsa decemliniata) is presented.

Twelve new azole compounds and eleven racemic ethanolamine derivatives were synthesized. These twenty-three compounds were evaluated using eight chiral columns, four macrocylic glycopeptides, a cyclodextrin derivative …

Role Of Ph And Plant Age On The Selection Of Rhizobial Endophytes In Soybean Root Nodules, Cole Alexander Roman

Graduate Theses/Dissertations

Soybeans form symbiotic relationships with nitrogen-fixing bacteria in their root nodules to acquire most of their nitrogen requirement; nitrogen is often one of the limiting nutrients in the soil. Members of the Bradyrhizobium, Sinorhizobium, Mesorhizobium, and Rhizobium genera can nodulate soybeans. Bradyrhizobium is preferentially selected over other types of rhizobia in varying environmental conditions and is often found in acidic soils. Sinorhizobium is often identified in the root nodules of soybeans in neutral and alkaline soil. So far, the potential role of soil pH on the selection of rhizobial endophytes with soybean root nodules is unknown. Likewise, …

Synthetic Microbial Communities For Plastic Upcycling, Isabel B. A. Valencia

Dissertations, Master's Theses and Master's Reports

Plastic waste and human hunger pose major threats to the health and wellbeing of populations world-wide. Using microbial methods to upcycle polyethylene terephthalate (PET) plastic into value-added compounds such as single cell protein (SCP) for human consumption is a unique solution to both these issues. Two monomers of chemically deconstructed PET (DCPET), terephthalate (TPA) and ethylene glycol (EG), have been previously shown to be biodegradable by enriched microbial communities. Using this top-down knowledge to inform the reconstruction of a minimal microbial community constructed from isolated members of these communities is a novel way to efficiently process these monomers via a …

Social Interactions And Spatial Structure Drive Community Assembly Of Bacterial Biofilm, Matthew C. Bond

Dartmouth College Ph.D Dissertations

Despite the critical nature which microbial communities play in the natural world and human civilization, the breadth of understanding remains shallow. Challenged by scale, high variability between environments, and extensive diversity, microbial ecologists strive to understand connections between a community’s structure and function, as well as the ecological and evolutionary mechanisms underlying observed natural patterning of communities. Biofilms are the predominate mode of growth for microbial communities—characterized by cellular attachment to a surface via a self-produced matrix and heterogeneous structure, often resulting in a primary growth front along the biofilm surface due to differential access to bulk nutrients (cite). This …

Borate-Based Bioactive Glasses Properties: Clinical And Biomedical Applications, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Borate bioactive glasses (BBGs) constitute the recently produced bioactive glasses (BGs) in the domain of bioactive materials, offering enhanced functionalities over conventional silicate and phosphate BGs. This advancement is primarily characterized by BBGs' rapid yet controllable degradation rates, superior bioactivity, and the ability to swiftly form a hydroxyapatite layer (HAP) upon interaction with physiological fluids. A distinguishing feature of BBGs lies in their customizability; doping with therapeutic metal ions tailors their bioactivity towards specific physiological responses, including promoting angiogenesis, antibacterial activity, and osteogenesis. This versatility of BBGs' applications extends to bone regeneration, wound healing, drug delivery systems, and potentially nerve …

Poor Water Quality As A Trigger Of Harmful Algal Blooms In Lake Manzala, Mohammed A. Hussein, Alaa Eldin Eissa, Reham M. Eltarabily, Mohamed F. Abdelghany, Mahmoud A. Elnakeeb, Eman M. Ismail, Reham H. Ragab, Amina A. Dessouki

Mansoura Veterinary Medical Journal

Objective: The current study aimed to assess the direct effects of poor water quality on the eruption of heavy harmful algal blooms and to assess the physicochemical properties of water in Lake Manzala, as well as the molecular identification of the retrieved green algae.

Procedures: Subsurface water samples were collected from three different sites in September 2023 for water quality assessment. Moreover, morphological and molecular identification of suspected harmful algae is the most reliable diagnostic tool for this eruption.

Results: This study was conducted in the northern and northeastern regions of Lake Manzala. These regions receive large amounts of municipal, …

Co-Divergence Of Lemur Hosts And Gut Microbiomes Across Multiple Evolutionary Scales, Mariah E. Donohue

Theses and Dissertations--Biology

This dissertation bridges micro- and macroevolutionary approaches to understand the co-diversification of animal hosts and their gut microbiomes at different evolutionary timescales. I examined these dynamics using wild lemurs, a diverse Primate clade endemic to the island of Madagascar.

First, I tested the relative effects of host phylogenetic relationships, diet, and habitat in shaping the gut microbiome through deep evolutionary time and across distinct microbial kingdoms. I designed a natural experiment sampling feces from rainforest and dry forest lemur communities with similar phylogenetic assemblages and considerable variation in dietary strategy. Then, I amplified and sequenced two metabarcoding genes, the V4 …

Interactions Between Multiple Stressors, Nanomaterials And A Pathogen, In Caenorhabditis Elegans, Jarad Cochran

Theses and Dissertations--Plant and Soil Sciences

Metal and metal oxide nanoparticles (NP), which have received interest for use in agriculture, show in vitro and in vivo toxicity at relatively low concentrations. Silver nanoparticles (Ag NP) and zinc oxide nanoparticles (ZnO NP) cause adverse effects in model soil organisms under environmentally relevant conditions. In most toxicity assessments of nanomaterials, model organisms are exposed to a single stressor. Though single stressor experiments are essential to understanding the fate and effects of released NP, in nature, organisms are affected by multiple stressors, including pathogens, which might exacerbate or mitigate negative effects of NP exposure. There is limited research on …

The Sewage Microbiome Dynamics Of Different Serving Neighborhoods In Charleston, Illinois, Sandra Chiamaka Okoye

Masters Theses

The complex microbial ecosystem within sewage systems holds significant implications for environmental and public health. Unlike studies on wastewater treatment plant microbiomes, upstream sewage systems have not been studied widely. This research investigated the dynamic sewage microbiome across diverse serving neighborhoods in Charleston, Illinois, encompassing residential, hospital, industrial, and university areas. Drawing upon recent advancements in microbiome research, the study aimed to unravel the spatial and temporal variations in microbial structures. Three times between June to December 2023 sewage samples were collected from manholes in the areas mentioned above. Community DNA was extracted and sequenced for the V4-V5 region of …

Dust-Driven Mechanism For Marine Particle Aggregation: Interactions Between Clay Minerals, Heterotrophic Bacteria And Organic Matter Influences Aggregation In Marine Systems, Vignesh Gokuladas Menon

Dartmouth College Master’s Theses

Atmospheric dust deposition plays a crucial role in marine biogeochemical cycles, yet mechanisms underlying its impact on particle dynamics remain unclear. This study investigates the synergistic interactions between marine heterotrophic bacteria and clay minerals in seawater, focusing on their effect on Transparent Exopolymer Particles (TEP) production and organoclay aggregation. Field experiments in the Gulf of Maine and laboratory roller tank studies were conducted using natural microbial communities and model heterotrophic bacterial strains (Alteromonas sp. EZ55, Marinobacter adhaerens HP15, and Sulfitobacter sp. NAS-14.1). Results demonstrate that clay exposure significantly enhances TEP production by bloom-associated heterotrophic bacteria, with increases up to …

A Comparison Of Adenosine Triphosphate With Other Metrics Of Microbial Biomass In A Gradient From The North Atlantic To The Chesapeake Bay, Alexander B. Bochdansky, Amber A. Beecher, Joshua R. Calderon, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

A new, simplified protocol for determining particulate adenosine triphosphate (ATP) levels allows for the assessment of microbial biomass distribution in aquatic systems at a high temporal and spatial resolution. A comparison of ATP data with related variables, such as particulate carbon, nitrogen, chlorophyll, and turbidity in pelagic samples, yielded significant and strong correlations in a gradient from the tributaries of the Chesapeake Bay (sigma-t = 8) to the open North Atlantic (sigma-t = 29). Correlations varied between ATP and biomass depending on the microscopic method employed. Despite the much greater effort involved, biomass determined by microscopy correlated poorly with other …

Application Of Environmental Dna Metabarcoding To Differentiate Algal Communities By Littoral Zonation And Detect Unreported Algal Species, Sergei Bombin, Andrei Bombin, Brian Wysor, Juan M. Lopez-Bautista

Arts & Sciences Faculty Publications

Coastal areas are the most biologically productive and undoubtedly among the most complex ecosystems. Algae are responsible for most of the gross primary production in these coastal regions. However, despite the critical importance of algae for the global ecosystem, the biodiversity of many algal groups is understudied, partially due to the high complexity of morphologically identifying algal species. The current study aimed to take advantage of the recently developed technology for biotic community assessment through the high-throughput sequencing (HTS) of environmental DNA (eDNA), known as the “eDNA metabarcoding”, to characterize littoral algal communities in the Northern Gulf of Mexico (NGoM). …

Scale And Habitat Effects On Measurement Of Streptomyces Biogeography And Biodiversity, Terilyn A. Stoflet

Cal Poly Humboldt theses and projects

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a …

Examining The Role Of Microbial Communities In Soil Carbon Cycling Across Levels Of Complexity, Chansotheary Dang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms provide the foundation for many ecosystem processes and are important drivers of carbon and nutrient cycling. The advancement of next generation sequencing has allowed researchers to lift open the lid on the ‘black box’ in microbial ecology. While previously unculturable microbes can now be characterized with the 16S rRNA gene, answering ‘who’s there?’ is only part of the challenge. Hidden inside the ‘black box’ remains the question, ‘who’s doing what?’. Recent development in trait-based methods like quantitative stable isotope probing (qSIP) equipped microbial ecologists with the tool to connect taxon-specific traits to ecosystem processes. Despite the growing body of …

In Vitro Assessment Of The Anti-Biofilm Effectiveness Of Copper And Zinc Enhanced Borate Bioactive Glass Using Processed Microscopic Images, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

The escalating burden of nosocomial infections presents a formidable challenge to healthcare systems worldwide, leading to increased morbidity, prolonged hospital stays, and elevated healthcare costs. These infections are often resistant to conventional antibiotic therapies due to their association with biofilms which contribute to the persistence and resistance of pathogens. In addressing the challenge of biofilm-associated nosocomial infections, borate bioactive glasses (BBGs) have emerged as promising biomaterials. Doping these glasses with antimicrobial metals could potentially harness their antibacterial properties to prevent biofilm formation. This study undertakes a rigorous evaluation of the anti-biofilm efficacy of copper and zinc-doped BBGs by employing processed …

Microbes Mediated Keratin Extraction From Poultry Waste And Assessment Of Its Efficacy In Growth Promotion Of Zea Mays And Triticum Aestivum, Imran Ahmad, Aisha Waheed Qurashi, Roheela Yasmeen

Journal of Bioresource Management

Feathers are a waste product of the poultry industry and are considered a major pollutant of the environment. Soil associated with poultry farms is a rich source of indigenous bacteria that are involved in biodegradation of keratin of the feathers of Gallus gallus domesticus. The present study was designed to understand the role of microbes in the degradation of a feather’s keratin and its possible utilization as a bio-protein for plants. In our studies, Keratinolytic activity was high at 37-45 ℃ and at 7.5-9.5 pH. Pseudomonas aeruginosa was identified by 16S rRNA sequencing as the most active keratinolytic strain. …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Isolation And Characterization Of Microbes From Agricultural Fields And Their Evaluation For The Control Of Plant Pests, Hira Liaqat Ali, Sumaira Mazhar, Afeefa Chaudhry

Journal of Bioresource Management

Plant diseases due to pests cause huge loss to crop fields every year. For the control of plant pest, pesticides are under use. Fusarium wilt is caused by phytopathogen Fusarium oxysporum. More than 100 species were affected due to this disease caused by this virus. Fungi also affect onion plant crop yield every year, when chemical pesticides are applied to onion crop field. It will increase the cost of onion production and it is also dangerous for the environment and living organism other than the targeted pests. A number of microorganisms like fungi, bacteria and nematode are currently being …

Developing Disinfection Strategies For Controlling Human Norovirus, Sars-Cov-2, And Clostridioides Difficile Endospores In Long-Term Care Facilities, Jinge Huang

All Dissertations

Long-term care facilities (LTCFs) provide an environment favorable for the transmission of three critical human pathogens: human norovirus (HuNoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and Clostridioides difficile. Given residents in LTCFs are susceptible to infections due to their advanced ages and compromised immune systems, effective environmental surface disinfection plays a crucial role in controlling the spread of human pathogens within these settings and, therefore, mitigates the risk of infections caused by these pathogens. This dissertation aimed to assess the efficacy of various types of disinfectants against two HuNoV surrogates [feline calicivirus (FCV) and Tulane virus (TuV)], two …