Environmental Microbiology and Microbial Ecology Commons^™

Investigation Of Biofilm Formation And Osmotic Stress Tolerance Of Nonmotile Escherichia Coli In Simulated Microgravity, Tyler Jenkins

Discovery Day - Daytona Beach

Simulated microgravity presents multiple physiological stressors for astronauts, including bone demineralization, muscle loss, and weakening of the immune system. Bacteria serve as viable model organisms to study physiological changes because of their abundance in the human digestive system and skin. Motility in bacteria plays a significant role in cell survival, but few studies have been conducted on microgravity’s effect on motility phenotypes. While motile strains like Escherichia coli K12 have been studied extensively under microgravity conditions, the effects of simulated microgravity on non-motile strains are largely unknown. To better understand this relationship, the nonmotile E. coli MG1655 strain was inoculated …

From Dust To Growth: Microbial Pathways To Extraterrestrial Farming, Stefani Capasso Villanueva, Nupur Kulkarni

Discovery Day - Daytona Beach

From Dust to Growth: Microbial Pathways to Extraterrestrial Farming addresses the fundamental challenge of sustaining long-term human habitation on other planets. In the era of the Artemis missions, establishing a cost-effective, bioregenerative food source is critical to reducing logistical dependency on Earth, and mitigating the physiological stressors faced by spacecrew through improved nutrition. This study initially investigated the viability of cultivating Mizuna, a proven ISS model organism, in a substrate of Martian regolith simulant amended with organic compost. Following iterative trials, it was found that the plant survival rate was extremely low, even after varying percentages of compost and simulant. …

Evaluating Soil Health And Crop Yield In Louisiana Agricultural Systems: Impacts Of Best Management Practices And Prediction Models, Hector J. Mendoza Lagos

LSU Doctoral Dissertations

The adoption of conservation management practices is critical for improving soil health, enhancing nutrient use efficiency, and sustaining crop productivity in row crop systems in Louisiana. This study evaluated the role of conservation agronomic practices, soil biochemical indicators, and machine learning predictive models to improve soil nutrient dynamics, soil health indicators, microbial communities (MC), and crop productivity on a corn (Zea mays L.) research plot scale and in a commercial forty-hectare cotton (Gassypium hirsutum L.)-corn-soybean (Glycine max L.) rotation system in northeast Louisiana. The objectives of the study were to evaluate soil nutrient dynamics and MCs under …

Dried Water Treatment Residuals Might Be An Option To Reduce Soluble Reactive Phosphorus Release From Soils, Katie B. Mckay

Biological and Agricultural Engineering Undergraduate Honors Theses

Nonpoint source pollution from agricultural landscapes contributes to freshwater eutrophication, with legacy phosphorus (P) in soils potentially driving soluble reactive phosphorus (SRP) losses to surface waters. The objectives of this study were to evaluate SRP adsorption by dried water treatment residuals (WTRs) produced by Beaver Water District, quantify reductions in soil SRP release across increasing WTR application rates, and compare dried WTR performance to prior WTR studies.

Dried WTRs (~98% solids) were assessed using batch sorption experiments and soil core incubations. Phosphorus sorption was measured by mixing WTRs with CaCl₂ solutions containing increasing SRP concentrations and fitting results to …

Biosensors For Biomedicine, Drake O'Leary

Miners Solving for Tomorrow Research Conference

This project investigated the use of engineered bacterial reporter systems to detect cellular stress responses associated with antibiotic activity. While constructs were successfully introduced and tested against known antibiotics, the reporter consistently produced a blue signal across conditions, limiting the ability to distinguish specific stress responses. This suggests issues such as leaky expression, insufficient regulatory control, or lack of specificity in the reporter design. Although results were inconclusive, this work highlights key challenges in developing reliable biosensors and provides a foundation for future optimization. Improving signal specificity and reducing background expression will be critical for enabling accurate characterization of antibiotic …

Ecovoltaic Solar Energy Development Creates Novel Microclimate, Temperature, And Soil Moisture Patterns Under Solar Panels In A Warm Desert, Juan Pinos, Seth M. Munson, Claire C. Karban, Matthew D. Petrie

Life Sciences Faculty Research

Background As solar energy development expands in desert regions, new installation practices and solar technologies seek to balance ecosystem conservation and energy generation (ecovoltaics). The Gemini Solar Project, a large ecovoltaic facility located in the northeastern Mojave Desert, employed low impact installation methods to reduce disturbance of the desert ecosystem within arrays of bifacial panels mounted on solar tracking systems. We evaluated microclimate and environmental conditions across five locations: four within-facility microsites (underneath solar panels, east and west panel driplines, and interspaces between panel rows) and one in the undisturbed desert outside the facility. Results Under panel microsites experienced lower …

Isolated Bacillus Licheniformis Sp01 From Daqing Oilfield In Reducing Chromium(Iii) Crosslinked Polymer Residue And Enhancing Oil Recovery, Xiao Hui

Student Works (2020-2029)

After polymer gel formation, the residual partially hydrolyzed polyacrylamide (HPAM) and the crosslinker (Cr3+) caused plugging and decreased oil recovery. Microorganisms can degrade HPAM to address the issues, but Cr³⁺ inhibits the process and reduces oil recovery. This study explores the underexamined biodegradation of HPAM and improved oil recovery in the presence of Cr³⁺, offering new perspectives for microbial enhanced oil recovery (MEOR) after polymer gel formation. HPAM and crude oil were innovatively used as the sole nitrogen(N) and carbon(C) sources to isolate the best-growing strain from Daqing Oilfield produced water, identified as Bacillus licheniformis SP01. The oil displacement potential …

Exploring The Interplay Of Operational Conditions, Microbial Communities, And Water Quality In Drinking Water Ozone-Biofiltration, Kara Yvonne Cunningham

Graduate Theses, Dissertations, and Problem Reports (ETD)

Ensuring reliable access to safe drinking water is a growing global challenge as water utilities face variable source water quality driven by population growth, land‑use change, and climate change impacts. To address these challenges, utilities are implementing advanced treatment technologies designed to improve reliability under variable source water conditions. Ozone-biofiltration has emerged as a treatment approach that can reduce a wide range of natural and anthropogenic contaminants. However, despite its increased use, there is limited insight into the biological processes shaping filter function or how they respond to operational and environmental changes. Advances in molecular microbiology and high-throughput sequencing now …

Regulation And Localization Of Urease In Sporosarcina Pasteurii: Implications For Coastal Protection, Amar Kosovac

UNF Graduate Theses and Dissertations

Coastal erosion is a persistent problem exacerbated by global warming. As the climate changes, the southeastern coast is likely to experience an increased frequency and intensity of storms, which can significantly damage the coastline. The coast is crucial as it serves as a habitat for numerous animals, supports tourism, and underpins infrastructure. Microbially induced calcite precipitation (MICP) is a novel method to enhance erosion resistance in sandy soils using the non-pathogenic bacterium Sporosarcina pasteurii. S. pasteurii produces urease to catalyze urea into bicarbonate, which drives the precipitation of calcium carbonate. Maximal expression of urease is a limiting factor for …

A Comprehensive Overview Of Chronic Wound Infections And Current Treatment Methods, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Chronic wound infections pose significant healthcare challenges due to persistent biofilms, antibiotic resistance, and impaired healing pathways. These wounds are characterized by prolonged inflammation, microbial colonization, and disrupted tissue regeneration, leading to substantial morbidity and healthcare costs. This article reviews current knowledge on chronic wound types, their pathophysiology, and the mechanisms underlying biofilm formation to examine the latest advancements in antimicrobial-based strategies aimed at addressing these challenges. It highlights how diverse materials and technologies have been engineered to improve infection management, enhance tissue regeneration, and overcome the limitations of traditional treatments as well as advances that leverage innovations such as …

Impact Of Shear Flow On Marine Biofilms Using Hyperspectral Imaging, Shantanu Mahesh Kore

All Theses

Various microbial communities in marine biofilms cause biofouling on submerged surfaces, posing challenges to marine industries. Despite their ecological and economic importance, biofilms' biomechanical and biochemical responses to hydrodynamic shear stress are insufficiently understood, particularly in dynamic flow conditions. To fill this gap, our study uses an innovative fiber-optic hyperspectral imaging (HSI) system and a supercontinuum laser source to examine marine biofilms' structure, composition, and detachment behavior at different shear stress levels.

To detect spectral and spatial heterogeneity in live biofilms without labeling, we created a custom imaging pipeline that captures reflectance spectra in the 600-850 nm range, targeting microbial …

The Antibiofilm Efficacy Of Copper And Zinc-Enhanced Borate Bioactive Glasses On Polymicrobial Biofilms, Sarah Fakher, David J. Westenberg

Biological Sciences Faculty Research & Creative Works

Healthcare-acquired infections (HAIs) are a significant global challenge driven by biofilm-forming pathogens. Polymicrobial biofilms, involving interactions between multiple microbial species, exacerbate treatment difficulties due to their enhanced resistance to antimicrobial therapies. Borate bioactive glasses (BBGs) are an emerging class of biomaterials that have attracted significant interest in infection control. The incorporation of copper and zinc into the BBG matrix can effectively disrupt biofilm formation and bacterial colonization. This study investigates the antibiofilm efficacy of copper and zinc-doped BBGs against polymicrobial biofilms formed by S. epidermidis, E. coli, and P. aeruginosa. Using static and dynamic biofilm models, BBGs were applied through …

Watershed-Level Survey Of Antimicrobial Resistance From Onsite Wastewater Systems, Trey Franklin Clark

Graduate Theses, Dissertations, and Problem Reports (ETD)

The emergence of antimicrobial resistance (AMR) has quickly become one of the largest global health and development threats. Research related to environmental modes of transmission of AMR has accelerated in recent years, and the US Environmental Protection Agency is particularly interested in this emerging contaminant. Knowledge of how onsite (decentralized) wastewater treatment systems contribute to this issue is lacking, so this research serves to analyze and quantify the environmental dissemination of AMR and fecal contamination from these sources at a watershed level while using statistical analysis to assess relationships between physiochemical, spatial, and sampling parameters. This research surveyed four watersheds …

Boosting The Power Performance Of Microbial Fuel Cells By Using Dual Nanomaterial-Modified Carbon Felt Electrodes, Krishna Thapa, Wenyan Liu, Yuwei Zhang, David J. Westenberg, Yishu Zhou, Risheng Wang

Chemistry Faculty Research & Creative Works

Innovative design enhancements to microbial fuel cells (MFCs) are pivotal for improving their viability as renewable energy sources. This study introduces a dual approach to electrode modification, integrating polyaniline (PANI) and gold nanoparticles (AuNPs) on carbon felt (CF) anodes coupled with a unique cathode composed of DNA origami and chitosan. The synergistic effect of PANI and AuNPs significantly increases the hydrophilicity and conductivity of the anode, leading to a considerable surge in power density. Concurrently, the biocompatible DNA origami and chitosan-functionalized cathode facilitates efficient electron transfer without relying on conventional catalysts. Together, these modifications yield a 52.42% increase in the …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

The Ecological Responses To Hydroperiod Of Wetland Plant Species Determined By Manipulated Soil Surface Elevation (Marsh Organs), Brandon Wolff

LSU Master's Theses

As sea level rise, subsidence, and abandonment of natural deltaic processes due to a highly engineered Mississippi River continue to threaten Louisiana’s coastal wetlands, the need for a system-wide understanding of natural wetland land-building and preservation processes has never been greater. A key component of any wetland is the ever-changing water environment that periodically floods and dries the marsh platforms. The flooding depth, duration, and frequency, known as the hydroperiod, along with salinity and soil fertility are key determining factors of vegetation and marsh types at a particular location. Different types of vegetation will have different growth characteristics such as …

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 …

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 …

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 …

Enhancing Urban Water Quality Through Biological-Chemical Treatment: Aquatic Macroinvertebrate Community And Temporal Chlorophyll-A Response, Matthew Chaffee

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

With a growing human population, urbanization is impeding a plethora of natural waterways. Of these, urban ponds play a vital role in nutrient sequestration, flood prevention, and habitat sanctuaries. However, nutrient loading can reduce habitat effectiveness and promote harmful algae blooms. To reduce internal nutrient loads, a biological-chemical treatment strategy consisting of floating treatment wetlands (FTWs) and lanthanum were applied to two urban retention ponds, Densmore and Wilderness Ridge Ponds. To measure effectiveness, chlorophyll-a samples were collected and correlated with Sentinel-2. A novel band algorithm termed 3BR1 produced a strong correlation (R² = 0.72) to physical chlorophyll-a …

Human Microbiome Transfer In The Built Environment Differs Based On Occupants, Objects, And Buildings, Andrew J. Hoisington, Christopher E. Stamper, Katherine L. Bates, Maggie A. Stanislawski, Michael C. Flux, Teodor T. Postolache, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Compared to microbiomes on other skin sites, the bacterial microbiome of the human hand has been found to have greater variability across time. To increase understanding regarding the longitudinal transfer of the hand microbiome to objects in the built environment, and vice versa, 22 participants provided skin microbiome samples from their dominant hands, as well as from frequently and infrequently touched objects in their office environments. Additional longitudinal samples from home environments were obtained from a subset of 11 participants. We observed stability of the microbiomes of both the hand and built environments within the office and home settings; however, …

The Kinetics Of Biocontaminant Inactivation: A Comparative Study With Bacillus Globigii And Bacillus Anthracis, Leigh M. Durden

Theses and Dissertations

Bacillus anthracis has been a biological threat for decades and after the 2001 terrorist attack via the U.S. Postal Service where five people died, there was heightened awareness and inquiry on the subject (Goel, 2015; Greenberg et al., 2010; Nicholson & Galeano, 2003; Spotts Whitney et al., 2003). The health risk to humans makes this biological agent, a Tier 1 agent and one of the most likely to be used in an attack (Anthrax as a Bioterrorism Weapon | CDC, n.d.; Driks, 2009; Rose & Rice, 2014). B. anthracis is one of most resistant and potent biological warfare agents as …

Investigating The Effectiveness Of Microplastic Removal And The Relationship Between Microplastics, Bacterial Communities, And Nitrogen Cycling In The Natural Treatment Systems At The Arcata Wastewater Treatment Facility, Fiona Connor

Cal Poly Humboldt theses and projects

This thesis addressed two challenging aspects of microplastic research, including the quantification of microplastics in organic-rich water, and the investigation of how microplastics impact microorganisms and related nutrient-cycling. Two projects were designed and executed to address specific research objectives relating to these broad topics. The first objective was to develop and implement methods to determine the effectiveness of microplastic removal across the natural treatment systems at the Arcata Wastewater Treatment Facility (AWTF). The second objective was to observe how microplastics found in domestic wastewater impact the bacterial communities and nitrogen cycling in freshwater treatment wetland sediment through a bench-scale experiment, …

Optimizing Sample Collection And Data Interpretation For Effective Wastewater-Based Epidemiology In Combined Sewer Systems, Christopher Allen Anderson

Graduate Theses, Dissertations, and Problem Reports (ETD)

COVID-19 has spurred growth in the science surrounding wastewater-based epidemiology (WBE) pertaining to the detection of severe acute respiratory virus 2 (SARS-CoV-2) in waste streams as an early warning signal for public health. However, the highly variable wastewater environment has made it difficult to standardize an approach for sampling and analysis, especially in locations using combined sewer infrastructure. This study addresses knowledge gaps of WBE via three specific aims: (1) to compare diurnal fluctuations of SARS-CoV-2 and the human fecal indicator, pepper mild mottle virus (PMMoV) in wastewater treatment plant (WWTP) influent samples collected during dry versus wet weather conditions; …

Application Of A 14c-Assay To Assess Methanotrophic Biodegradation Of Tce In Low Ph Groundwater, Evan Groome

All Theses

Current biological strategies for remediating trichloroethylene (TCE) in low pH aquifers (i.e., pH14C-TCE assay was developed to determine pseudo first-order rate constants for the degradation of TCE in microcosms containing soil and groundwater from the Boeing Michigan Aeronautical Research Center (BOMARC) superfund site, where the pH ranges from 4.1 to 4.9. The ¹⁴C-TCE assay was also adapted to calculate soil-normalized rate constants for data from this site, as well as data that Szwast²¹ collected from the Beltsville Agricultural Research Center (BARC). In addition to natural attenuation, biostimulation through amendments of methane and nutrients were also assessed. This treatment …

Effects Of Continuous In Situ Low-Dose Ionizing Radiation On Microorganisms, Molly E. Wintenberg

All Dissertations

Precise detection and monitoring of nuclear fuel cycle, enrichment, and weapon development activities are critical for supporting warfighter preparation in chemical, biological, radiological, nuclear, and explosives (CBRNE) operations, clandestine activities, and nuclear compliance. A biological sensing system could serve as an alternative to traditional detection methods by using organic material naturally present in the environment to discreetly detect residual trace nuclear material. Microorganisms provide an optimal platform for an alternative sensing system; however, their response to low levels of ionizing radiation is poorly characterized. Combining the power of next-generation sequencing and transcriptomic analysis, this dissertation takes an approach to obtain …

Biodegradation Of Rubber Particles In Soil: Using Acclimated Bacteria Isolated From Kansas Soil To Degrade Cryogrinds In Slurry, Shane Graham

Williams Honors College, Honors Research Projects

This study investigated the viability of bioremediating rubber cryogrind using enriched indigenous bacteria. To begin the experiment, soils from three highway roadside locations in Kansas, KS 96 and West, KS 400 and 143^rd, and 199^th, were collected and transported to the lab to be studied. An initial soil characterization was run on the soil samples using distilled (DI) water mixture and 0.01 M CaCl₂ to assess conductivity. The soils were tested to gather a baseline of the relationship between pH and conductivity and the impact of its distance from the roadside. Bacteria were isolated from …

A Temporal Analysis Of The Microbiota And Biofouling Development On Artificial Substrates In The Port Everglades Inlet, Florida, Denise Swack

All HCAS Student Capstones, Theses, and Dissertations

A pilot project was deployed in Port Everglades Inlet, Florida that aimed to evaluate the biofilm composing the microbiome on ecologically engineered artificial substrates used to build Coastal Marine Infrastructure. In April of 2017, an Articulated Concrete Block Mattress comprised of an ecological engineered concrete substrate and a standard smooth surface control substrates were compared. This study will provide a profile on the microbiome community on artificial substrates within Port Everglades Inlet on bio-enhancing concrete-based solutions in our Coastal Marine Infrastructure. To study the microbial community, the 16s rRNA technology was used in Illumina’s high-throughput DNA sequencing. Samples were collected …

Characterizing The Dormancy And Repair Of A Circumneutral Passive Remediation System Receiving Iron And Sulfate-Rich Amd, Garrett Struble

Electronic Theses and Dissertations

The Wingfield Pines remediation system is a ~20-acre circumneutral, gravity-fed system constructed in 2009 to passively remediate Fe from an ~2000 gallon/minute effluent. In 2017, a fracture to the system’s underground cavern caused the AMD effluent to bypass the system, flowing directly into Chartiers Creek and leaving the system decommissioned between 2017-2019. Soil slurry and water samples were collected in the weeks prior to the system’s reinstalment in September 2019 through January 2020 in order to determine the effect of the repair on remediation efficiency and microbial community composition. This study acted as the first to describe the temporary decommissioning …

A Novel Jumbo Phage Phima05 Inhibits Harmful Microcystis Sp., Ampapan Naknaen, Oramas Suttinun, Komwit Surachat, Eakalak Khan, Rattanaruji Pomwised

Civil and Environmental Engineering and Construction Faculty Research

Microcystis poses a concern because of its potential contribution to eutrophication and production of microcystins (MCs). Phage treatment has been proposed as a novel biocontrol method for Microcystis. Here, we isolated a lytic cyanophage named PhiMa05 with high efficiency against MCs-producing Microcystis strains. Its burst size was large, with approximately 127 phage particles/infected cell, a short latent period (1 day), and high stability to broad salinity, pH and temperature ranges. The PhiMa05 structure was composed of an icosahedral capsid (100 nm) and tail (120 nm), suggesting that the PhiMa05 belongs to the Myoviridae family. PhiMa05 inhibited both planktonic and aggregated …