Environmental Microbiology and Microbial Ecology Commons^™

Pipeline Corrosion And Relevant Microbial Influence, Renee E. Bamberger

Williams Honors College, Honors Research Projects

This study investigated the role of microbial activity and oxygen availability in the corrosion of carbon steel pipelines with a focus on microbially influenced corrosion (MIC). Sediment collected from Old Woman Creek, Ohio, was used to simulate natural soil conditions, and carbon steel coupons were incubated under four treatments: nonsterile oxic, nonsterile anoxic, autoclaved oxic, and autoclaved anoxic over 85 days. Corrosion was assessed through mass loss measurements and the analysis of pH, sulfate, chloride, and dissolved iron concentrations. The greatest mass loss was observed in autoclaved oxic conditions, contrary to the initial hypothesis that microbial activity would greatly enhance …

Environmental Monitoring In Shallow Lakes: Public Health Threats In Urban Waters, Kyleigh E. Johnson

Theses and Dissertations

Lakes are an integral part of urban and suburban communities, providing ecological, recreational, and public health benefits. Many of these lakes are located in densely populated areas and are subject to urban influences on water quality. Algal toxins and Escherichia coli are two common recreational concerns. Algal toxins come from harmful algal blooms that are influenced by nutrient availability and temperature, while bacteria are often introduced through run-off and animal waste. Sampling every 3-4 weeks from May-October 2025 allowed for the assessment of seasonal patterns and site-specific differences across nine lakes in the Richmond area. The highest bacterial concentrations appeared …

Remediation Impacts Metal Concentrations And Metal Tolerant Bacteria In Soils Of The Missouri Tri-State Mining District, Ophelia R. Pettington

Graduate Theses/Dissertations

After over 100 years of Zn and Pb mining in the Tri-State mining district (TSMD), former mines continue to be sources of metals. Metal contaminated soils can be remediated using plant-microbe interactions. Plants manipulate their microbiome and recruit microbes to increase metal tolerance. Remediating bacteria are site-specific and identifying native microbes can accelerate remediation efforts. Studies relating microbes and metal concentrations in remediated areas in the TSMD are scarce. I collected root and bulk zone soils associated with Andropogon virginicus from remediated and non-remediated sites in Webb City, MO. I used 16S rRNA gene amplicon sequencing to evaluate the bacterial …

Elucidating The Relationship Between Water Quality And Antibiotic Resistance Of Rainwater Microbes Across Western Humboldt County, Theo P. Murphy, Eve Wendley, Justice Laskowski, Tyler Paredes

Humboldt Journal of Microbiology

Limited studies have been conducted regarding the fecal contamination and microbial dispersal through rainwater, with no known studies investigating the potential connection between antibiotic resistant microbes and water quality in rainwater. This study seeks to identify the presence of a correlation between water quality and incidence of antibiotic resistance in rainwater microbes. We hypothesize that there will be a correlation between these two variables. We additionally anticipate a high incidence of fecal contamination across rural and urban collection sites alike, with fecal contamination being more prevalent in rural areas than urban locals. To determine water quality, we measured the concentration …

The Effects Of Plastic Mulch And Irrigation On Hemp Chemistry And Leaf Endophytes, Allison Rietman, Connor Morozumi, Robert C. Pearce, Natalie Christian

Journal of Agricultural Hemp Research

As an emerging crop, cultivation techniques for industrial hemp (Cannabis sativa L.) are still being developed and optimized. For example, irrigation and plastic mulching are some management practices that have been touted for their benefits in improving crop quality. Both techniques ensure ample water availability, which has often been attributed to improving hemp cannabinoid and terpene composition. In this study, we examined how supplemental irrigation implemented in a plastic mulch system influenced the cannabinoid and terpene profiles of one cultivar of CBD hemp, Lifter. We grew industrial hemp in field with plastic mulch and applied regular irrigation to one group …

Colonization-Persistence Trade-Offs In The Human Microbiome, Liam F. Nokes

Environmental Studies Senior Theses

Understanding how diverse microbial taxa coexist in the human body without competitively excluding one another remains a key challenge in microbiome ecology. One proposed explanation is the colonization-persistence trade-off, where species with high colonization ability are poor persisters, and vice versa. We test for this trade-off across human associated microbial communities among many individuals and in multiple body sites using a large-scale participant-level meta-analysis of longitudinal microbiome datasets curated from the MGnify database. We applied island biogeography-based models to calculate effective colonization and persistence rates for microbial families and genera across 606 individuals over twenty-six studies. Regression of the log-transformed …

Toxicity And Biodegradability Of Novel Boronium Vs Conventional Ammonium-Based Antimicrobial Compounds In Wastewater Treatment Systems, Noor Shalan

Honors Theses

Quaternary ammonium compounds (QACs) are highly effective as disinfectants, herbicides, and pesticides; thus, overuse causes elevated levels of residual toxicity in domestic and industrial wastewater. QACs can be toxic to essential bacteria breaking down pollutants in wastewater treatment plants (WWTPs) and can remain untreated in effluent, harming the environment, and contributing to antibiotic resistance, posing risks to human health. Novel boronium-based antimicrobial compounds have demonstrated efficacy in eliminating bacteria, fungi, and viruses. If the boronium compounds exhibit lower residual toxicity, they could offer a promising alternative to QACs. Because these compounds are still in development, their potential toxicity to the …

Investigating Drivers In Phytoplankton Between Lentic And Lotic Ecosystems Within Twelvepole Creek Watershed, Devin Lee Farmer

Theses, Dissertations and Capstones

Harmful Algal Blooms (HABs) threaten aquatic ecosystems, local economies, and water quality. While extensively studied in lakes (lentic systems), their impact on flowing waters (lotic systems) remains underexplored. This study examined algal drivers in both ecosystems within the same watershed, focusing on Beech Fork Lake (lentic) and Twelve Pole Creek (lotic). Key environmental factors, including pH, turbidity, dissolved oxygen, and nutrient levels, were measured using in situ sensors and laboratory analysis. Water samples were analyzed for nitrogen, phosphorus, and algal biomass for comparison to environmental conditions. Phytoplankton was preserved for identification in future research. By comparing these environments, this study …

Using Bivalves As An Indicator For Fecal Bacteria, Kamala Chuss

Honors Scholar Theses

This project focuses on the integration of fecal bacteria from warm-blooded animals into bivalve tissue, and the utilization of bivalves as an indicator for fecal bacteria in waterways. Bivalves may give a more representative long-term average of fecal bacteria in water as compared to direct water testing. The primary objective is to create a standard operating procedure to use bacterial testing of bivalves as a proxy for bacteria concentration in the water. This method can be used in places where bivalves do not already exist by adding them to a body of water, or by collecting bivalves that already exist …

The Relationship Between Salvinia Molesta Infestation And The Microbial Ecology Of Wetlands At Caddo Lake, Tx, Usa, Martin Hadsell

Electronic Theses and Dissertations

Wetlands are known to host many beneficial geochemical processes such as nutrient cycling and carbon sequestration. These processes are primarily driven by the microbial communities within a wetland. The establishment of non-native invasive species within wetlands has the potential to alter the once beneficial functionality of wetland microbial communities due to the sensitivity microbes have towards environmental changes. Because of this, several metagenomic studies have been conducted to assess microbial community response to aquatic plant invasion; however, there haven’t been any studies researching the influence of Salvinia molesta (D.S. Mitch.), commonly known as Giant Salvinia, on microbial communities. The goal …

Effects Of Microplastic Biofilms On An Anthropogenically Impacted Suburban Lake, Paris M. Velasquez

Masters Theses

Plastics have been observed in every location on the planet, and their prevalence in the environment is due in part to their strong resistance to degradation. Inland lakes are susceptible to plastic pollution by highway runoff, which contains plastic fragments of brake pads, car tires, litter, and road paint. These plastics eventually enter freshwater environments and degrade into microplastics (

Heavy Metals Implications To Sediment Microbiome And Coral Response To Arsenic Dosing, Dimitrios G. Giarikos, Amy Hirons, Jose V. Lopez, Abigail Renegar, Jason Gershman

SECLER Data

No abstract provided.

Antibiotic Resistance In A Coastal River In Mississippi, Usa – Potential Drivers, Shuo Shen, Wei Wu, Eric A. Saillant, Darrell Jay Grimes

Gulf and Caribbean Research

Wastewater treatment plants (WWTPs) are major sources of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in water bodies. Most studies on the impact of WWTPs on antibiotic resistance have focused on freshwater systems, with little information on coastal and estuarine waters with variable salinity. This study monitored seasonal levels of ARGs at the effluent and downstream of the Pascagoula— Moss Point WWTP in the lower Pascagoula River, a coastal river in southeastern Mississippi, USA. Surface water samples were collected seasonally at upstream, outflow, and 3 downstream sites from February to November 2016. Bacterial resistance to sulfamethazine, tetracycline, and …

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 …

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 …

Connecting The Nebraska Water Quality Index To The Aquatic Microbial Community Of The North Platte River Basin, Nebraska, Paula R. Guastello

School of Natural Resources: Dissertations, Theses, and Student Research

The Nebraska Water Quality Index, under development by the Nebraska Department of Environment and Energy, summarizes in a single value eight environmental parameters that have been monitored in Nebraska for nearly 20 years. Water quality parameters including those used in the Nebraska Water Quality Index have been shown in previous studies to impact bacterial growth. As such, this index has the potential to correlate with the freshwater microbial community. Here, I relate the Nebraska Water Quality Index to microbial community composition and structure using 16S rRNA gene amplicon sequence data collected from the North Platte River Basin, Nebraska. This index …

Considerations For The Use Of Mycorrhizal Fungi Inoculants In Coal Mine Reclamation And Reforestation In Appalachia: A Guide Of Best Practices And Management Recommendations, Cole Hansen Reistrup

Master's Projects and Capstones

Nearly all terrestrial plants form symbiotic relationships with mycorrhizal fungi. These beneficial soil microbes support plant health by increasing plants’ access to nutrients and water, protecting them from pathogens, improving soil properties, and more. A challenge to restoring forests on coal mined land in Appalachia is that mine soils are often degraded in a number of ways, including lacking mycorrhizal fungi, which makes mine soils difficult for trees to grow upon. Substantial improvements to coal mine reforestation success have been made since the development of the Forestry Reclamation Approach in 2005 that provides guidelines for how to create a suitable …

Assessing Functional Biodiversity For The Future Of Plants, Planet, And People, Ali Loker

Doctor of Plant Health Program: Dissertations and Student Research

Biodiversity plays a critical role in supporting life in global ecosystems and its links to ecosystem services and sustainability are recognized by scientific and non-scientific communities. Growing awareness of the importance of biodiversity is accelerated by discussions of its loss, and how to design interventions to conserve and mitigate a biodiversity crisis. Stakeholders are funding and implementing assessment strategies at various scales to help direct conservation efforts. There is also growing interest in measuring and communicating biodiversity outcomes.

Functional biodiversity characterizes the multiplicity of life forms into groups based on their diverse contributions to natural and agro-ecosystems. Assessing functional biodiversity …

Changes And Relationships Of Soil Aluminum, Organic Matter, And Hydrogen Ion Concentration With Rye Cover Crop, Arron Wilder

Cal Poly Humboldt theses and projects

Soil acidity is a common agricultural problem worldwide, as approximately 50% of all potentially arable soils are affected by pH limitations. At soil pH 3+) is considered to be the chemical form of aluminum in acid soil that hinders plant growth the most. Potentially, soil organic matter (SOM) can ameliorate the toxic effects of Al³⁺ on plants and microbes by binding with Al³⁺, thus preventing Al³⁺ (and other species of aluminum) from interacting in the rhizosphere. Increasing SOM also increases soil health indicators (i.e., microbial activity, soil water holding capacity, aggregate stability, porosity, etc.) while the …

Rapid Bacterial And Fungal Successional Dynamics In First Year After Chaparral Wildfire, M. Fabiola Pulido-Chavez, James W. J. Randolph, Cassandra A. Zalman, Loralee Larios, Peter M. Homyak, Sydney I. Glassman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rise in wildfire frequency and severity across the globe has increased interest in secondary succession. However, despite the role of soil microbial communities in controlling biogeochemical cycling and their role in the regeneration of post-fire vegetation, the lack of measurements immediately post-fire and at high temporal resolution has limited understanding of microbial secondary succession. To fill this knowledge gap, we sampled soils at 17, 25, 34, 67, 95, 131, 187, 286, and 376 days after a southern California wildfire in fire-adapted chaparral shrublands. We assessed bacterial and fungal biomass with qPCR of 16S and 18S and richness and composition …

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 …

Genomic Analysis And Characterization Of Surface Properties Of Naphthalene Degrading Acinetobacter Isolates, Gunn Emilie Berge

Graduate Theses and Dissertations (2019 - present)

No abstract provided.

Assessing The Activity Of Antimicrobial Peptides Against Common Marine Bacteria Located In Rotifer (Brachionus Plicatilis) Cultures, Chelsea Woods, Lindsey Woolley, Gavin Partridge, Mengqi Chen, Evan F. Haney, Robert E.W. Hancock, Nicky Buller, Andrew Currie

Fisheries Research Articles

Rotifers are used as the first feed for marine fish larvae and are grown in large cultures that have high loads of organic matter and heterotrophic bacteria; these bacteria are passed on to the developing fish larvae and can potentially lead to bacterial infections. A modified minimum inhibitory concentration (MIC) protocol for antimicrobial peptides was used to determine the potency of ten antimicrobial peptides (AMPs) in artificial seawater relevant to a rotifer culture (salinity of 25‰) against common marine pathogens. All of the AMPs had antimicrobial activity against the bacterial isolates when the salt concentration was approximately zero. However, in …

Evaluating Soil Health Changes Following Cover Crop And No-Till Integration Into A Soybean (Glycine Max) Cropping System In The Mississippi Alluvial Valley, Alexandra Gwin Firth

Theses and Dissertations

The transition of natural landscapes to intensive agricultural uses has resulted in severe loss of soil organic carbon (SOC), increased CO₂ emissions, river depletion, and groundwater overdraft. Despite negative documented effects of agricultural land use (i.e., soil erosion, nutrient runoff) on critical natural resources (i.e., water, soil), food production must increase to meet the demands of a rising human population. Given the environmental and agricultural productivity concerns of intensely managed soils, it is critical to implement conservation practices that mitigate the negative effects of crop production and enhance environmental integrity. In the Mississippi Alluvial Valley (MAV) region of Mississippi, USA, …

Development Of A Methodology For The Quantification Of Reaerosolization Of A Biological Contaminant Surrogate Particle From Military Uniform Fabric, George D. Cooksey

Theses and Dissertations

During a mass casualty medical evacuation after a bioaerosol attack, a decontamination method is needed that is effective at both decontamination and preventing the secondary hazard of biological particles reaerosolizing from contaminated clothing. However, neither the efficacy of current decontamination methods nor the risk of biological particle reaerosolization is significantly explored in existing literature. The goals of this thesis were to develop a repeatable methodology to quantify the reaerosolization of a biological contaminate off Airman Battle Uniform (ABU) fabric swatches, and to test the efficacy of one decontamination method (high-volume, low-pressure water) using 1 mpolystyrene latex (PSL) spheres as a …

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

The Effects Of Hydrologic Heterogeneity On Harmful Algal Blooms In Freshwater Reservoir, Lake Sinclair, Georgia, Margaret Blackledge

Biology Theses

Aquatic habitats are frequently studied after a major water quality problem like the occurrence of an algal bloom. In this study, A proactive rather than a reactive response was considered, where the complexity of conditions conducive to uncontrolled cell growth were studied before a bloom took place by sampling regularly. This study aimed to monitor water quality by monthly sampling of algal communities for approximately one year. As the base of the aquatic food web, algae are a highly diverse group of organisms with varying sensitivity to physical and chemical changes in the environment. Four shallow sites were monitored at …

Soil Microbial Community Dynamics In Response To Prescribed Extreme Fires Following Juniperus Virginiana Invasion In The Loess Canyons Of Nebraska, Julie A. Fowler

School of Natural Resources: Dissertations, Theses, and Student Research

In Nebraska and other regions of the Great Plains, the conifer Juniperus virginiana (eastern redcedar) is converting grasslands to dense woodlands. This is driven by the interacting drivers of fire suppression, altered grazing regimes, climate change and other anthropogenic factors, impacting the provisioning of ecosystem services. This vegetation state transition modifies water resource regulation and biogeochemical cycles leading to altered edaphic properties including soil microbial community composition. To restore these grasslands and control J. virginiana spread, prescribed extreme burns are implemented as a management tool through local prescribed burn associations. We hypothesized that the alternative state transition to dense J. …