Environmental Microbiology and Microbial Ecology Commons^™

Microbial Source Tracking Protocols For Differentiation Of Fecal Bacteria From Cow, Deer, And Horse, Nika Shams, Michael Beach

Symposium of Student Scholars

Microbial source tracking (MST) attempts to identify specific animal sources of fecal contamination in the environment. While traditional fecal coliform enumeration can give a general measure of contamination, the specificity imparted by modern MST provides a more informative assessment of contaminants and their likelihood to affect human health outcomes.

We have been developing an MST system that detects DNA biomarkers from the gram-negative bacterial genus Bacteroides and the family Lachnospiraceae. They are strict anaerobes found in large quantities in the intestines of animals. Unlike E. coli or Enterococci, host-specific strains of Bacteroides and Lachnospiraceae exist. To this end, we …

The Role Of Anthropogenic Influences On A Tropical Lake Ecosystem And Its Surrounding Catchment: A Case Study Of Lake Sentani, Sulung Nomosatryo, Daniel Lipus, Alexander Bartholomäus, Cynthia Henny, Iwan Ridwansyah, Puguh Sujarta, Sizhong Yang, Dirk Wagner, Jens Kallmeyer

College of Life Sciences Faculty Papers

Lake Sentani is a tropical lake in Indonesia, consisting of four interconnected sub-basins of different water depths. While previous work has highlighted the impact of catchment composition on biogeochemical processes in Lake Sentani, little is currently known about the microbiological characteristics across this unique ecosystem. With recent population growth in this historically rural area, the anthropogenic impact on Lake Sentani and hence its microbial life is also increasing. Therefore, we aimed to explore the influence of environmental and anthropogenic factors on the microbial diversity of Lake Sentani. Here, we present a detailed microbiological evaluation of Lake Sentani, analyzing 49 different …

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 …

Impact Of Glufosinate On Soil Microbial Community Dynamics, Sarobi Das

Biology Dissertations - Archive

The increasing global regulations of glyphosate due to its possible carcinogenicity and environmental hazards have necessitated the search for alternative herbicides. Glufosinate-ammonium offers a sustainable attribute due to its low toxicity and limited reported herbicide resistance cases. Despite its increasing agricultural importance, very limited studies are done on its environmental impact, especially on the soil systems. This thesis examines the ecological behavior of glufosinate in soil, precisely focusing on its effect on the dynamics of soil microbiome and the potential use of Bradyrhizobium japonicum USDA110 for bioremediation by reversing the effect of microbial dysbiosis. A series of 30-day mesocosm studies …

Unveiling The Bacterial Communities Of Aphaenogaster: Taxonomic Composition, Developmental And Species Influences, And The Impact Of Climate Change, Lily Kelleher

West Chester University Master’s Theses

Ants are vital keystone species in many ecosystems because they provide ecosystem services such as: seed dispersal, soil bioturbation, and pest control. However, ant bacterial symbioses remain largely unstudied, but these interactions are crucial because microbes play a vital role in the ants’ overall health. Today, global climate change is impacting our biodiversity, and we can use information about how changing temperatures impact the symbiotic bacterial communities associated with ants to predict future impact. Aphaenogaster rudis and A. fulva remain understudied in terms of their bacterial community and are important North American species. For this study, ants from several colonies …

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 …

Microbial And Plant Biodiversity In Appalachian Agroecosystems And Their Implications For Soil Health, Kinsey Reed Close

Graduate Theses, Dissertations, and Problem Reports (ETD)

The sustainability of agricultural landscapes depends on understanding the complex interactions between plants, soil, and microbes. In Appalachia, a region shaped by complex terrain and long histories of human and ecological interaction, small family farms produce hay, livestock, and row crops. These agroecosystems, though often treated as “artificial” by many ecologists, have the potential to support both food production and biodiversity conservation if managed with an understanding of ecological complexity. This dissertation examines how plant and microbial diversity interact with soil and management to influence nutrient cycling, soil health, and long-term resilience in Appalachian agricultural systems. A literature review revealed …

Spatial And Temporal Shifts In Bacterial Communities And Nutrient Removal In Two Springfield Wastewater Facilities, Rubina Sherchan

Graduate Theses/Dissertations

Bacterial communities play a central role in the biological nutrient removal and overall performance of wastewater treatment plants (WWTPs). However, very few is known about the spatial and seasonal dynamics of these communities. This study explores the spatial and seasonal variations in bacterial community composition across multiple treatment stages in two municipal WWTPs—Southwest (SWTP) and Northwest (NWTP)—in Springfield, Missouri. Using 16S rRNA gene amplicon sequencing, I analyzed 87 samples collected during summer and winter of 2024 from influent, sludge, aeration basins, clarifiers, and final effluent stages. I retrieved 16.4 million (summer) and 3.2 million (winter) sequences. Proteobacteria dominated both seasons …

Inoculating Soybean Plants At Different Growth Stages: Selecting Bradyrhizobium, Sinorhizobium, Or Both, Matthew R. Knoll

Graduate Theses/Dissertations

Soybean plants rely on nitrogen for growth, however atmospheric nitrogen (N2) is not a usable form and needs to be converted into different forms that are available to the plant. Nitrogen fixing bacteria such as rhizobia form symbiotic relationships with Soybeans in exchange for shelter and excess plant sugars. As a result, the plant can get the nitrogen it needs. There are four main genera of rhizobia that can form root nodules on Soybean including Bradyrhizobium, Sinorhizobium, Mesorhizobium, and Rhizobium. At this point, the effect that age of the host plant has on the selection of …

Microbial Mavericks: Turning Hazards Into Snacks, Alison G. Blanton

Biology Dissertations - Archive

Symbiotic associations with microbes are widespread across life and provide hosts with essential and beneficial functions. A growing concern in pest management is symbiont-mediated detoxification (SMD), a form of metabolic resistance to insecticides. The best-known example of SMD involves the bean bug Riptortus pedestris, where an environmentally acquired but obligate Caballeronia symbiont confers resistance to the organophosphorus insecticide fenitrothion. Motivated by this model, I began my work in another known bug-Caballeronia symbiosis: Leptoglossus phyllopus, native to the United States. I then expanded the study to include two additional U.S.-native hosts, Leptoglossus zonatus and Anasa tristis. Representative …

Characterizing Agroecosystem Effects Of Industrial Hemp On A Rotational Row Cropping System And Microbial Communities, Kent D. Pham

Theses and Dissertations--Plant and Soil Sciences

The implementation of crop rotation on a farm can have many benefits for agroecosystem health and production. This practice can potentially reduce nutrient amendments, disrupt pest and disease cycles, and increase crop yields. In Kentucky, one common rotation consists of either corn or soybean grown the first year, followed by the other crop, repeated every two years. Industrial hemp, grown for fiber or grain, is an emerging crop that has shown promise as a rotation alternative, although not much is known about its effects on soil health, agroecosystem functioning, and microbial communities. To better characterize hemp’s role within American agriculture, …

Impact Of Submarine Groundwater Discharge On Microbial Communities In A Highly Anthropized Coastal Lagoon (Mar Menor, Se Spain), Daniel Romano-Gude, Júlia Dordal-Soriano, Júlia Rodriguez-Puig, Andrea G. Bravo, Irene Alorda-Montiel, Aaron Alorda-Kleinglass, Marc Diego-Feliu, Cristina Romera-Castillo, Rebeca Mallenco-Fornies, Javier Gilabert, Jordi Garcia-Orellana, Valentí Rodellas, Clara Ruiz-González

OES Faculty Publications

Submarine groundwater discharge (SGD) supplies large quantities of nutrients and other terrestrial elements to coastal ecosystems, impacting marine biota and ecosystem functioning. Despite the relevance of prokaryotes for marine biogeochemistry, little is known about their responses to groundwater inputs. Here we explored the impact of SGD on the spatiotemporal patterns of prokaryotic communities from the Mar Menor (Murcia, Spain), a highly anthropized hypersaline coastal lagoon that receives large amounts of nutrient-polluted SGD. Using 16S rRNA amplicon sequencing, activity assays, and flow cytometry, we investigated the dynamics of prokaryotic communities across the lagoon and its connected environments (freshwater streams, groundwater, soils, …

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 …

Microbial Hydrocarbon Degradation And Carbon Cycling In Marine And Freshwater Sediments: A Comparative Metagenomic Analysis, Yogita M. Warkhade

Dissertations, Master's Theses and Master's Reports

Microbes are essential in keeping our environment balanced, especially by fixing carbon dioxide and breaking down hydrocarbons in aquatic sediments. This thesis explores how microbial communities perform these tasks in different sediment environments, including marine areas (Caspian Sea and Mediterranean Sea) and freshwater ecosystems (Great Lakes). The first part of this thesis reviews current knowledge about how microbes degrade hydrocarbons. It highlights the importance of different pathways microbes use depending on oxygen availability. The second part provides a detailed study of the microbial communities found in marine sediments from the Caspian Sea and Mediterranean Sea, showing that microbes in these …

Molecular Characterization Of Fungus-Arthropod Associations, Angie M. Martin

Graduate Theses, Dissertations, and Problem Reports (ETD)

Arthropods, or phylum Arthropoda, are the largest group of animals, accounting for over three quarters of all animal records on NCBI Taxonomy. And yet, only 40% of all deposited sequences on NCBI Nucleotide come from arthropods. Clearly, arthropods are an understudied group of animals: they are small, often drab, and lead lives very alien to our own. Arthropods have chitinous exoskeletons, segmented bodies, and jointed appendages, and include crabs, barnacles, insects, spiders, and millipedes. Since the era of DNA based studies took off in the 1980s, DNA and other small molecules have been integral to our understanding of the Earth …

Soils From Different Solidago Altissima Clones Mediate Intraspecific Interactions In Schizachyrium Scoparium, Sarah Alharbi

Masters Theses

While previous studies have examined plant intraspecific competition and soil microbial effects separately, fewer studies have investigated how these factors interact, particularly in the context of genotype-specific soil conditioning effects. Plant-soil feedbacks can significantly alter interspecific competitive outcomes, yet few studies have examined how local variation in soil conditioning influences plant responses to density-dependent competition. I investigated how soil inocula derived from four Solidago altissima clones that were previously shown to differ in their soil conditioning effects (Foster et al., 2022) affected the growth and root traits of Schizachyrium scoparium across a gradient of intraspecific competition (1, 2, or 4 …

Influence Of Thermophilic Biofilms On Proliferation Of Opportunistic Pathogens In Domestic Water Systems, Olajumoke Akinbami

Masters Theses

Domestic hot-water systems quietly grow biofilms under elevated temperatures that can serve as shelter to Opportunistic Premise Plumbing Pathogens. Although focus has been placed on microbes in domestic systems, there has been no clear conclusion on the mechanism of survival and persistence of opportunistic pathogens despite various disinfection strategies. In this study, we determined the distinction between showerhead and drip-flow biofilms at the whole-community level and analyzed the coexistence of thermotolerant organisms with opportunistic genera, such as Legionella. We sampled eight showerheads and simulated four biofilm samples in the laboratory using the drip-flow biofilm reactor.

We observed a strong …

Parallel Inquiries: Investigation Of Social Resource Use In Early Career Stem Teachers And Impacts Of Metal Pollution On Fingernail Clam Microbiome, Emily Hamada

EWU Masters Thesis Collection

No abstract provided.

Development Of A Proposed Selective Medium For The Isolation And Differentiation Of P. Sordellii, Dimyana Bottros

Honors Undergraduate Theses

Clostridium, a genus of anaerobic, spore-forming bacteria, includes clinically and ecologically significant species like Clostridium difficile and Paeniclostridium sordellii. C. difficile causes antibiotic-associated colitis, while P. sordellii is linked to fatal infections and spontaneous abortions. Recent studies found both species in marine sediments, suggesting their role in environmental and wildlife health disturbances, including the 2013 mass mortality of over 300 manatees in the Indian River Lagoon. However, isolating and differentiating P. sordellii is challenging due to the lack of selective media optimized for its growth. This thesis proposes a novel selective medium tailored to P. sordellii’s physiological …

Degradation Of Cyanobacteria And Microalgae Using Ultraviolet Radiation At 222 Nm And Its Application In The Bleaching Of Lampenflora On Cave Rock Surfaces, Keisuke Naito, Shuji Watanabe, Masuo Komukai, Takehiro Kazama, Masayuki Itoh, Masahiro Kawasaki

International Journal of Speleology

Cyanobacterial and microalgae blooms negatively affect ecological environments. One of the emerging problems of these blooms occurs in calcareous caves, where visible lighting systems in tourist caves induce the formation of photosynthetic biofilms known as lampenflora on rock surfaces. In this study, we evaluated the inactivation effect of ultraviolet (UV) light irradiation at 222 nm (rare gas halide lamp) and 254 nm (mercury lamp) on cyanobacteria and microalgae in a laboratory and on lampenflora in Ryusenshindo Cave in Japan. Based on the laboratory experiments, irradiation at 222-nm was more effective than that at 254-nm for degrading plants. The photosensitivity of …