Environmental Microbiology and Microbial Ecology Commons^™

Microbial Guardians Of The Savannah: Unraveling The Gut Microbiome For African Carnivore Conservation, Laura E. Peirson

All NMU Master's Theses

Non-invasive fecal sampling is essential for wildlife gut microbiome (GMB) research, yet field conditions often limit preservation options. I compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from carnivore kill sites were also analyzed. No significant differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples (PERMANOVA). Core bacterial communities remained consistent across sample …

Distribution, Roles And Environmental Drivers Of Bacterial Communities In The Chesapeake And Delaware Bays, Mir Alvee Ahmed

All Dissertations

In this dissertation, water samples from the Chesapeake and Delaware Bay estuaries were analyzed to see how estuarine environmental gradients drive distributions, functional potential, growth estimates and gene expressions of bacteria. To answer this, the abundant and versatile taxa– Rhodobacterales and Actinobacteriota, along with broader particle-attached (PA) vs. free-living (FL) bacterial assemblages of these Bays were analyzed using a multifaceted ‘omics approach.

The PA fraction, differing from the FL in taxonomy, distribution, functional potential and estimated growth rates across salinities, and bays harbored genes degrading complex aggregates, and surface attachment. The FL counterpart presented genes involved in nutrient uptake …

Bridging Prairie Restoration And Regenerative Agriculture With Compost Tea, April Hersey

2025 Symposium

Inland Pacific Northwest prairie is an endangered ecosystem that has been reduced by conversion to agriculture. There is growing interest in the role of soil microorganisms in prairie ecosystems, which may be crucial for restoration of the plant community through interspecies interactions within the soil near plant roots. One method for improving soil microorganism community composition is compost tea: enriched liquid compost extract. Compost tea is used in regenerative agriculture to improve crop yields and protect against pathogens, ostensibly through the activity of the added compost microbes. While research has supported compost tea application in regenerative agriculture, it has not …

The Astrobiological Figure Of Humboldt As Pioneer In The Rock Varnish Research, Jose Jordan-Soria

Homage to Alexander von Humboldt: Travels to and from Spain Throughout the Centuries / Homenaje a Alexander von Humboldt: Viajes hacia y desde España de todos los siglos

From Humboldt is particularly interesting -and little know- his description of mineral coatings on rocks 200 years ago, reported in his book Personal Narrative of Travels to the Equinoctial Regions of the New Continent during the years 1799-1804, co-written with Aimé Bonpland, for which is considerate the father of rock coating research. On June 5th 1799 set sail from A Coruña -Spain- to Cumaná -Venezuela- beginning five years of expedition. While they explored the Orinoco River system, in th eriver basin waterfalls, Humboldt observed the presence of dark coating depositions. He ascertained a manganese-rich accretion, reporting similar structures in other …

Skin Bacteriome Structure And Batrachochytrium Dendrobatidis Prevalence Differs Amongst Two Sympatric Salamanders In The San Francisco Bay Area., Aria Norwood, Jadyn Jamora, Micuel Madison, Jamiee Nguyen, Azan Yousaf, Katya Morales, Emily Vu, Obed Hernández-Gómez

Natural Sciences and Mathematics | Student Professional Publications

Microbial surveys are becoming an important component of wildlife health research, especially in cases where environmental change and infectious diseases are serious issues. Amongst amphibians, Batrachochytrium spp. have the potential to be fatal pathogens that can impact the population health of numerous species. We assessed the skin bacteriome, prevalence of Batrachochytrium dendrobatidis (Bd) and body conditions of two salamander genera with different life histories: the California slender salamander (Batrachoseps attenuatus) and members of the Pacific newt species complex (Taricha torosa and Taricha granulosa; Taricha sp.). We used 16S rRNA V4 amplicon sequencing to characterise the bacterial communities. Taricha sp. had …

Soil Degradation Of Solvent-Cast Pha Films Produced By Bacillus Tequilensis Pwf Using Waste Polyethylene Terephthalate (Pet), Rafeya Sohail, Rida Batool, Nazia Jamil

Journal of Bioresource Management

Polyhydroxyalkanoate (PHA) aliphatic polymers however efficiently biodegradable, still pose a contradiction with the principles of green chemistry. Use of bacterial strains capable of degrading synthetic plastics for the production of biopolymers i.e., PHAs may aid in reduction of plastic pollution. Bacterial strains PWA; Bacillus subtilis (MH142143), PWF; Bacillus tequilensis (MH142145), and PWG; Bacillus safensis (MH142146) were grown on waste shredded PET and PET flakes. Highest bioconversion of PET to PHA was observed using PET flakes. Strain PWF produced 40.47 % (0.815 g/L) and 31.80 % (0.626 g/L) PHA using PET flakes and shredded PET at 48 h, respectively. Whereas highest …

Phylogenetic Analysis Of Ftsz In Wolbachia: Implications For Host Specificity, Anwar Rovik, Ayu Rahayu

Makara Journal of Science

Wolbachia are the most prevalent and successful endosymbiont in invertebrates and are categorized into 21 supergroups based on genetic phylogeny. The filamenting temperature-sensitive Z (FtsZ) protein is essential for bacterial cell division and is hypothesized to play a role in Wolbachia's control of host reproduction. However, despite FtsZ's importance, little is known about its diversity and function within Wolbachia. This study investigated the variability of the FtsZ-encoding gene among Wolbachia strains and their hosts. FtsZ gene sequences were retrieved from the National Center for Biotechnology Information database, and representative sequences were randomly selected from each host species and analyzed …

Crayfish Microhabitats Provide A Close Association With Benthic Microbiomes To Support Cleaning Symbionts., Kyle J. Harris, John Hoverson, Matthew Becker, Matthew M. Cooke Mr

NEXUS: The Liberty Journal of Interdisciplinary Studies

Stream ecosystems promote variable microhabitats along a longitudinal gradient. These microhabitats support dynamic biotic assemblages. One such microhabitat in freshwater streams involves the external surface of crayfish. We investigated the microbiome of crayfish exoskeletons and the surrounding environment (water and substrate) in association with the presence and abundance of crayfish cleaning ectosymbionts (branchiobdellidans). These ectosymbionts actively consume the biofilm on crayfish as they live and reproduce in association with crayfish microhabitats. Sequenced microbes of the environment and crayfish were compared for dominant taxa. While the sample types (water, substrate, and crayfish) had significantly different microbiomes, there was not a significant …

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 …

From Epidemics To Experimental Treatments: Amphibian Mass Mortality Events And A Potential Treatment For Chytridiomycosis, Daniel Callahan

Graduate Masters Theses

Worldwide, amphibian populations have experienced dramatic declines due to a variety of threats. Among them, disease has been particularly deleterious and continues to impact populations. In the United States and Canada, the three leading causes of amphibian mass mortality events are ranavirosis, chytridiomycosis, and severe perkinsea infection, all caused by infectious pathogens. While research and policy have helped populations recover from these diseases, more work needs to be done to develop practical and efficient treatments for these infections. Of these three diseases, chytridiomycosis has had the most devastating effects on amphibian populations globally. Caused by the chytrid fungi Batrachochytrium dendrobatidis …

Impacts Of Land Development On Soil Microdiversity And Antibiotic Production, Dennis Guillen Castro, Robert Garcia, Jonathan Castro, Davida Smyth

Masters Theses (Archived)

The impact of land development on soil microbial diversity and antibiotic production is critical due to industrial expansion and the scarcity of effective antibiotics. Low Impact Development (LID) aims to preserve ecosystems, but its effectiveness in maintaining microbial diversity is uncertain. This study compares soil samples from nine sites: undisturbed (UD), residential (RD), and Madla Greenway (GW) within the VIDA development area and Texas A&M University-San Antonio campus. Isolated microbes were screened for antibiotic production and genetically characterized. Preliminary findings indicate that UD sites harbor greater microbial abundance, and a higher proportion of antibiotic-producing microbes compared to GW and RD …

Microbial Biodiversity Of The James River Rock Pool Ecosystem., Jordan C. Heydt

Masters Theses, 2020-current

Rock pools are ephemeral aquatic environments that offer a unique opportunity to study complex communities and their responses to environmental changes. The urban James River rock pool system consists of over 700 individual rock pools varying in size and depth. This unique urban freshwater ecosystem has been studied for its invertebrate, plant, and zooplankton populations but not for its microbial community composition. To fill that gap, the microbial community of this system was characterized using 16S rRNA gene sequencing, and the influence of environmental variables on the community composition was analyzed. Our findings show variation in microbial community composition across …

Microbial Community Contribution To Oxidative Stress Defense In High-Biomass Forming Cyanobacteria Harmful Algal Blooms (Chabs), Chelsea Donovan

Masters Theses, 2020-current

Cyanobacterial harmful algal blooms (cHABs) occur globally, excluding Antarctica, and often involve toxin-producing species such as Microcystis aeruginosa. These blooms threaten both ecosystems and public health, making it essential to understand their underlying drivers. Cyanobacteria generate reactive oxygen species (ROS) during photosynthesis, which can cause cellular damage unless neutralized. Some, like M. aeruginosa, lack the genetic capacity to detoxify ROS and rely on associated bacterioplankton for protection. To investigate the role of phycosphere bacteria in mitigating ROS stress, we conducted an incubation experiment using samples collected throughout the 2023 Lake Erie bloom season. Samples were treated with 10 …

Relationship Between Prodigiosin Production And Batrachochytrium Dendrobatidis Metabolite Concentration, Nautica Ek Hagg

Honors Thesis

Batrachochytrium dendrobatidis (Bd) is a pathogenic fungus that has been causing extirpations of amphibian species across the globe. The microbiome on the skin of amphibians is known to be a key factor in infection dynamics. It has been established that one species of cutaneous bacteria, Serratia marcescens, and a secondary metabolite with antifungal properties it produces, prodigiosin, has shown a promising ability to decrease the growth of Bd. However, when Serratia marcescens is grown in the same media with added metabolites produced by Bd, there is an observed decrease in the production of the bacteria’s protective metabolite, prodigiosin. This experiment …

Fine-Scale Spatial Patterns In Microbial Activity And Community Composition In Shoreline Marine Sediments, Elizabeth Basha

Honors Theses

Coastal environments of the Gulf of Mexico host diverse and dynamic microbial communities essential for biogeochemical cycling, yet the fine-scale environmental drivers of microbial function and community structure in these systems remain underexplored. This study investigated the relationships between sand moisture content, microbial extracellular enzyme activity, and bacterial community composition along beach transects on Biloxi East Beach, Mississippi. Sand was sampled at five points along four transects spanning a gradient from submerged intertidal zones to dry upper beach sands. Extracellular enzyme activities linked to carbon, nitrogen, and phosphorus cycling (β-glucosidase, N-acetylglucosaminidase, phosphatase, phenol oxidase, and peroxidase) were measured, and bacterial …

Evaluation Of Phenotypic Antimicrobial Resistance From Bacterial Pathogen Isolates In Bison, Aleena M. Kallan

Honors Capstones

Bison, the American buffalo, are increasingly utilized for food consumption due to their high protein content. Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen that leads to severe clinical infections and becomes antimicrobial-resistant (AMR). Specifically, fluoroquinolone antibiotics can complicate human treatment when infected with resistant STEC. This study aims to determine the presence of STEC in bison reservoirs and their antimicrobial resistance. Fecal samples (n=320) from bison herds were collected, followed by specific culture-based isolation for STEC. Polymerase chain reaction (PCR) was employed for pathogen confirmation, with 25.6% prevalence. PCR targeting gene, gyrA (resistant to fluoroquinolone), was tested …

Microbial Community And Water Quality Assessment Of Crassostrea Virginica Habitats In Southeast Florida, Stacy Brown

All HCAS Student Capstones, Theses, and Dissertations

Eastern oysters (Crassostrea virginica) are essential habitat-forming species that contribute significantly to coastal water quality due to their filter-feeding behavior. Unlike other coastal regions in the Gulf of Mexico and Northeastern United States, oysters are not commercially managed in Southeast Florida and as a result sparse data exists on locations of the Eastern oyster habitat. Similarly, the benefits of oyster reefs to water quality are also not fully documented in Southeast Florida. Although beneficial and often referred to as keystone habitat building species, populations of C. virginica are not currently listed as protected species so little work has …

The Impacts Of Management Practices On Industrial Hemp Chemistry, Physiology, And Microbiome Ecology., Allison Marie Rietman

Electronic Theses and Dissertations

Agroecology incorporates ecology and agronomy to inform crop management. Industrial hemp (Cannabis sativa L.) is a prime system to investigate agroecological questions because it has only recently been authorized for commercial cultivation and its sensitivity to biotic and abiotic stressors is unresolved. Here, I investigate how some conventional management choices, including the application of fungicide, plastic mulch, and irrigation, impact the physiology, chemistry, and microbial ecology of industrial hemp. Overall, I found that industrial hemp can be both resilient and resistant to these stressors, an important development for the industry. In Chapter II, I tested the impacts of fungicide application …

Biological Reduction Of Perchlorate In Martian Regolith Simulant Using Azospira Oryzae, Brianna Bernhardt

Honors Program: Senior Projects (Public)

Establishing a sustainable human presence on Mars will require in-situ resource utilization (ISRU) to reduce costly and inefficient resupply missions. Despite containing many of the requirements for agriculture, Martian regolith is contaminated with toxic levels of perchlorate (ClO₄^-), threatening human health and agricultural success. Biological remediation using perchlorate-reducing bacteria offers a promising approach to address these challenges. This study investigated the perchlorate-reducing ability of Azospira oryzae, a facultative anaerobe capable of converting ClO₄^- to chloride (Cl^-) through dissimilatory respiration. A. oryzae was cultured in Martian regolith simulant (MGS-1) amended with 0.0%, 0.5%, …

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 …