Environmental Microbiology and Microbial Ecology Commons^™

Enhancing Urban Garden Capacity By Linking Biodiversity And Ecosystem Function, Mary T. Nguyen, Carleen Rauh, Shelby Gresch, Charlotte Correiro, Heidi Elmendorf, Adriane Fugh-Berman, Gina Wimp, Alexandra L. Decandia

Virginia Journal of Science

Urban agriculture broadly describes food and plant cultivation in metropolitan areas. While biodiversity is thought to support ecosystem health and resilience, the relationship between above-ground and below-ground diversity has been understudied in urban green spaces. This study examines plant, animal, bacterial, and fungal diversity across three distinct urban habitats: a turf lawn, a forb garden, and a farming space. Using bacterial 16S rRNA and fungal ITS2 sequencing, soil nutrient analyses, and surveys of vegetation and wildlife, we connect diverse philosophies in urban agriculture to their role in advancing community diversity and ecosystem function. We found that different urban gardens support …

Bacterial Community Function In Pitcher Plant Leaves As An Experimental And Mathematical Model Of Functional Dynamics, Amelia Jackson

Cal Poly Humboldt theses and projects

This work looks at two different sites with differing abiotic factors in measures of altitude, temperature and precipitation. The site with higher altitude, larger temperature range, and lower precipitation, located in Plumas National Forest (Quincy, CA), had a flat BEF trend that suggests functional redundancy The site with lower altitude, more moderate temperatures, and higher precipitation located in Six Rivers National Forest (Gasquet, CA), also had a flat BEF trend. These abiotic factors could correlate to the significantly different bacterial compositions between sites. The second portion of this work is modeling the host antagonist relationship between Eyxra moths and their …

Plant Invasion Patterns In Understory And Soil Microbial Communities Of North Central West Virginia Mixed Hardwood Forests, Isabelle Marie Uganski

Graduate Theses, Dissertations, and Problem Reports (ETD)

Invasive plants alter forest ecosystems by reducing species richness, habitat heterogeneity, and nutrient cycling as they rapidly displace native plants. Invasive plant composition can influence soil health through altering soil microbial associations and communities. By studying the mechanisms in which invasives alter above- and below-ground communities, we can better understand whole-ecosystem impacts and inform management decisions. This study examined the relationships between co-occurring invasion on above and belowground communities of mixed hardwood forests of north central West Virginia. Despite distinctive associations with aboveground characteristics (native diversity, native tree regeneration, and leaf litter density) we detected limited changes to soil microbial …

First Report Of A Bat Guano Fire From A Cave In Southeast Asia, Sopark Jantarit, Martin Ellis, Pruet Kalasuwan, Neeranuch Phusunti, Pimonsri Mittraparp-Arthorn, Jiranan Pattano, Arnon Chukamnerd, Turdtun Tong-In, Natthawut Khrueaaunruean

International Journal of Speleology

Fires occurring in cave guano are a rare and unusual phenomenon and the occurrence of such events in Southeast Asia is particularly novel. In this study, we document the first recorded instance of a bat guano fire in a tropical cave at Tham Chao Ram in Sukhothai province, northern Thailand. A bacteriological analysis was made of the guano at the fire site and from a control site within the cave. We give a comprehensive review of global reports on bat guano fires in caves, conduct an initial investigation of the physical factors at the fire site and discuss the potential …

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 …

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 …

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 …

Seasonal Detection Of Coliphages In Freshwater Bodies At Coastal Carolina University, Ella Caldwell

Honors Theses

Bacteriophages, commonly referred to as phages, are non-living viruses that only infect bacteria. As the most abundant biological entities on Earth, understanding their role in regulating microbial populations is essential. This ongoing research aims to identify naturally occurring bacteriophages that could effectively control bacteria blooms. The primary objective of this study is to detect coliphages on Coastal Carolina University's campus and determine their viral families. Coliphages are a subgroup of bacteriophages that specifically infect coliform bacteria. Water samples were collected across multiple sites on campus, and polymerase chain reaction (PCR) was employed to amplify the viral DNA from the potential …

Life After Death: Investigating The Resistance And Recovery Of Fungal Communities To Foundation Tree Mortality, Jessie F. Marlenee

Biology ETDs

Tree mortality can have cascading effects on the composition and resilience of interacting fungal communities. Yet, little is known about the impact tree mortality, distinct from abiotic drivers (i.e., drought), has on these communities. This dissertation focuses on the resilience of fungal communities to experimental tree mortality in a piñon-juniper woodland. In chapter one, I found that piñon mortality reduced piñon fine root biomass and piñon mycorrhizal fungal diversity, whereas juniper mycorrhizal fungi were unaffected by juniper mortality. In chapter two, I revealed that piñon mortality altered the composition and spatial structure of mycorrhizal and saprotrophic fungi in the soil, …

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 …

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 …

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 …

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 (

Exploring Biosignatures And Biogeochemical Processes In Lanzarote Lava Tubes: Implications For Martian Analog Research, Vera Palma, Ana Z. Miller, Francesco Sauro, Bogdan P. Onac, José M. De La Rosa, Sara Gutiérrez-Patricio, Beatriz Cubero, José A. Gonzalez-Perez, Jesus Martínez-Frías, A Teresa Caldeira

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Exploring Pristine Microbial Ecosystems From The Uninhabited Volcanic Selvagens Islands, Pedro N. Jiménez-Morillo, Sara Gutiérrez-Patricio, Vera Palma, Ana Teresa Caldeira, Nicasio Tomás Jiménez-Morillo, Ana Z. Miller

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Microbial Colonization Of New Lava Tubes Formed By The Fagradalsfjall Volcano’S Eruption (Iceland), Ettore Lopo, Francesco Sauro, Ana Zelia Miller, Bogdan Petroniu Onac, Martina Cappelletti

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Onsite Microbial Analyses In One Of The Most Remote Quartzite Subterranean Environment On Earth: Imawarì Yeuta On Venezuelan Tepuis, Martina Cappelletti

FRONTIERS UNBOUND: Exploring Extreme Environments

No abstract provided.

Establishment Of Bacteroides In The Gut And Its Role In The Cystic Fibrosis Gut-Lung Axis, Rebecca A. Valls

Dartmouth College Ph.D Dissertations

In the quest to understand the complex interplay between the gut microbiota and cystic fibrosis (CF), a disease characterized by chronic upper respiratory complications and an exacerbated proinflammatory response, our lab engaged in a collaborative study with Dartmouth-Hitchcock Medical Center (DHMC) to characterize the gut microbiota of pediatric CF patients. Initial analyses established a connection between gut microbial composition and respiratory health, particularly highlighting a scarcity of Bacteroides species compared to healthy controls. In following investigations, we utilized random forest models to understand how stool microbiota may influence clinical outcomes of these pediatric CF patients, including: age, upper respiratory infections, …

Archaeal Diversity In The Anna's Hummingbird Microbiome, Lauren E. Chance

Honors Scholar Theses

The microbial communities that are present in and on vertebrates are collectively called the microbiome. The composition of a microbiome is dependent upon the host, the environment, and evolution. There has been extensive research on the bacterial composition of host-associated microbiomes, however, there has been much less work on the archaeal composition of host-associated microbiomes. Archaea have previously been assumed to primarily exist in extreme environments, but this may not be true and has been influenced by their generally low abundance and methodological difficulties in detection. It is possible they are consistent members of diverse host-associated microbiomes.

Archaea-specific PCR primers …

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 …

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 …

Temporal Distribution Of Potential Waterborne Pathogens In Sequiota Spring, William J. Durstock

Graduate Theses/Dissertations

Waterborne pathogens from human fecal matter pose a significant health risk in karst environments, where domestic wastewater can easily be transferred to the shallow groundwater system via old, leaky septic tanks and damaged sewer lines. This study monitored fecal indicator bacteria (FIB) and potential pathogens in Sequiota Spring located in the karst region of southwest Missouri, using Microbial Source Tracking (MST) and Illumina DNA sequencing of bacterial 16S rRNA genes. MST identified high levels of human fecal indicator bacteria (HFIB) (up to 110,000 cells/L) in July 2020. By June 2022, HFIB levels had dropped significantly (55-fold reduction) after the City …

Effects Of Subchronic Oral Pfos Exposure Via Drinking Water On Gut Microbiota Composition, Emma Ann Loder

Graduate Theses/Dissertations

Perfluorooctanesulfonic acid (PFOS) has been phased out of production in the United States, but because of its resistance to degradation and its persistence in the environment, PFOS can be found in drinking water across America. Oral exposure to PFOS has been linked to adverse developmental, immunological, hepatic, and endocrine health. Oral PFOS exposure may alter the gut microbiota and cause dysbiosis, which is implicated in the pathology of inflammatory diseases like Crohn’s disease, diabetes, and ulcerative colitis. The goal of the study was to investigate the effects of subchronic oral PFOS exposure on the composition of the gut microbiota. Adult …

How Environmental Variation Affects Bumblebee Cognition And The Gut Microbiome, Parker Madison Campbell

Graduate Theses/Dissertations

This master's thesis examines the influence of environmental variables on cognitive processes in Bombus impatiens, focusing on the effects of ingested microbial communities on gut microbiota and their subsequent impact on associative color learning. The study implemented controlled feeding trials with isolated microbe species (Candida bombi, Metschnikowia reukaufii, Lactobacillus micheneri and a control with no microbes) to analyze shifts in gut microbial composition in foraging bees. Results indicated minor alterations in the microbial profiles of bees, yet no statistically significant correlation was found between these modifications and variations in learning or memory performance. Furthermore, the study assessed the impact of …

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 …

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 …

Sympatric Soil Microbe Interactions Between Streptomyces And Fusarium Isolates, Lehren A. Olk-Szost

All NMU Master's Theses

Interkingdom interactions between soil bacteria and fungi may play a critical role in occurrence of disease suppressive soils, yet our understanding of these interactions remains limited. Streptomyces are well-known producers of antimicrobial compounds important to medicine and agriculture. Production of these secondary metabolites is often mediated by quorum sensing. Most Streptomyces research occurs in single species experiments, yet new metabolites have been discovered in interspecies co-culture experiments. Interspecies, intergenic, and interkingdom co-culture research will likely reveal many valuable compounds, and strengthen our understanding of complex ecological interactions in soil microbiomes. Interactions between sympatric Streptomyces and Fusarium isolates from disease suppressive …

Reproduction, Early Development, And Larval Rearing Of The Climbing Perch Anabas Testudineus (Teleostei: Anabantidae) In Captivity, Frolan A. Aya, Reylan C. Gutierrez, Luis Maria B. Garcia

The Philippine Agricultural Scientist

Induced spawning, early development, and larval rearing of the climbing perch Anabas testudineus were examined under captive conditions. Five female climbing perch [125.33 ± 3.27 mm SL; 70.67 ± 5.59 g BW] were paired with apparently mature males (108.50 ± 3.97 mm SL; 39.27 ± 4.70 g BW) and induced to spawn with 5,000 IU human chorionic gonadotropin (hCG) + 0.5 mL Ovaprim kg BW^-1. All hCG + Ovaprim-injected fish spawned 9 – 11 h after hormone administration but saline-injected fish (control group) failed to spawn. Mean egg production per female, fertilization and hatching rates, and larval production …

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …