Microbiology Commons^™

Microbial Literacy, Equity, And Sustainability At Cal Poly: A Policy Framework With University Housing As A Pilot Case, Joseph B. Fewel

Biological Sciences

Microorganisms play a fundamental role in human health, environmental systems, and the functioning of built environments, yet they remain largely absent from sustainability and public policy discussions. This project proposes a framework for integrating microbial literacy, equity, and health into institutional decision-making, using California Polytechnic State University (Cal Poly) as a case study and university housing as a pilot site for implementation. Drawing on interdisciplinary literature in microbiology, public health, environmental justice, and sustainability, as well as policy analysis and stakeholder interviews, this project examines how campus systems, including housing, ventilation, sanitation, food systems, and waste management, shape microbial exposure …

Synergies Of Microecology And Macroecology Elicit Insights For Creation Care, David Warners, John T. Wertz

University Faculty Publications and Creative Works

This article reports on a collection of microecological and macroecological insights that emerged from extended conversations between Calvin University professors David Warners, a botanist concentrating in restoration ecology, and John Wertz, a micro-biologist specializing in microbial ecology. Classic descriptions of ecology identify biological interactions as happening at the ecosystem, community, or population level. And yet, ecological interactions are very much occurring at the microbial level as well. Furthermore, microbial-level interactions frequently influence the quality and character of macroecological relationships and vice versa. Allowing ecological principles to be applied across all life forms broadens our comprehension of interactions that are happening …

Belowground Consequences Of Herbivory In Tomatoes And Cucumbers And Its Lasting Effects, Anthony Ignacio Barrera

Theses, Dissertations and Culminating Projects

Plants recruit soil microorganisms to help mediate biotic stressors such as herbivory, forming dynamic communities in the rhizosphere known as the root microbiome. This study investigated whether artificial herbivory could induce shifts in the root microbiome of tomato (Solanum lycopersicum) and cucumber (Cucumis sativus) and whether those shifts could be transferred to subsequent plants as a soil legacy effect. Plants were grown in sterilized or non-sterilized soil with or without simulated herbivory across two experimental phases, with Phase 2 plants receiving inoculum conditioned by Phase 1 plants. Bacterial community composition was assessed via 16S rRNA amplicon sequencing and analyzed using …

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 …

Fungal Biodiversity, Microbial Communities, And Ecosystem Function In Non-Perennial Streams, Charles T. Bond

Dissertations

A global majority of steams are non-perennial, drying at some point in time and space. Despite the vital roles that fungi and other microbes play in stream ecosystems, most research on stream microbiomes comes from perennial (continuously flowing) streams. The present series of studies addresses this research gap by examining microbial community composition and function in non-perennial streams, with an emphasis on fungi. Chapter I reviews existing scientific literature on the ecological processes that shape microbiome structure and function in non-perennial streams and outlines the varieties of fungi that may live there. Chapter II uses rDNA metabarcoding to survey fungal …

Effects Of Spatial And Temporal Variability On Bacterial Diversity And Community Composition In Roof-Harvested Rainwater Across Central Virginia, Jade Riddle

Longwood Senior Thesis Proposal

No abstract provided.

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

Rainwater Harvesting Systems Metagenomics, Jade Riddle, Julia Parsons

Spring Showcase for Research and Creative Inquiry

Climate change induced water scarcity has led to an increasing interest in non-traditional water sources such as rainwater. However, there are lingering health and safety concerns due to the lack of research into the microbial communities contained within collection systems. To address this gap, water samples were collected from rain barrels around northern Virginia for microbial analysis. Each microbe within the sample has a unique genome subject to DNA testing. Environmental DNA was prepared from the collected water samples. To characterize the microbial community, both targeted sequencing and whole genome sequencing approaches were used. Using targeted sequencing of the 16s …

Examining The Role Of Microbial Communities In Soil Carbon Cycling Across Levels Of Complexity, Chansotheary Dang

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms provide the foundation for many ecosystem processes and are important drivers of carbon and nutrient cycling. The advancement of next generation sequencing has allowed researchers to lift open the lid on the ‘black box’ in microbial ecology. While previously unculturable microbes can now be characterized with the 16S rRNA gene, answering ‘who’s there?’ is only part of the challenge. Hidden inside the ‘black box’ remains the question, ‘who’s doing what?’. Recent development in trait-based methods like quantitative stable isotope probing (qSIP) equipped microbial ecologists with the tool to connect taxon-specific traits to ecosystem processes. Despite the growing body of …

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 …

Ecology Of Viruses In Marine And Coastal Oxygen-Depleted Waters, Sophie Jurgensen

LSU Doctoral Dissertations

Deoxygenation of marine and coastal waters, both caused and exacerbated by a suite of abiotic and biotic factors, has been documented for more than sixty years. The incidence and severity of low-oxygen areas is predicted to expand globally in the coming decades. Despite their colloquial moniker “dead zones,” low-oxygen areas contain thriving and diverse microorganisms that have significant impacts on global biogeochemical cycles including contributing to positive feedback loops that further expand low-oxygen areas. While the diversity and activity of these microorganisms is beginning to be elucidated, the ecology of their viruses is particularly understudied. In this dissertation, I present …

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 …

From The Organismal To Biosphere Levels: Environmental Impacts On The Amphibian Microbiota, Obed Hernandez-Gomez, Jessica Hua

Natural Sciences and Mathematics | Faculty Scholarship

This review summarizes the role of environmental factors on amphibian microbiotas at the organismal, population, community, ecosystem, and biosphere levels. At the organismal-level, tissue source, disease status, and experimental manipulations were the strongest predictors of variation in amphibian microbiotas. At the population-level, habitat quality, disease status, and ancestry were commonly documented as drivers of microbiota turnover. At the community-level, studies focused on how species’ niche influence microbiota structure and function. At the ecosystem-level, abiotic and biotic reservoirs were important contributors to microbiota structure. At the biosphere-level, databases, sample banks, and semi-natural experiments were commonly used to describe microbiota assembly mechanisms …

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, …

Host-Microbe Interactions In Non-Native Estuarine Anemones: Biogeography And Temperature, Parker K. Lund

Cal Poly Humboldt theses and projects

Non-native species are increasing in prevalence around the world, resulting in negative economic and ecological impacts. However, the broad distributions of non-native species also offer a system for investigating the response of host-associated microbial communities to environmental factors across a range of ecological scales. At the broadest scale, I investigated the geography of microbial communities in the non-native estuarine anemone Diadumene lineata on the west coast of the United States of America. Across latitudes, microbial community composition was very similar and displayed a high percentage of Klebsiella spp. at all sites. However, the communities in California tended to exhibit higher …

Community Ecology And Disease Dynamics In Pacific Oysters: Unraveling Microbiome-Pathogen Interactions In The Wild, Victoria E. Cifelli

Cal Poly Humboldt theses and projects

In the context of multispecies microbial assemblages, disruptions can occur when there are alterations in host conditions, such as the onset of a disease. Notably, viruses have the potential to reshape a host's microbial community. However, the role of the host's habitat and environment, which could be pivotal in communities with shifting niche space and habitat filters, is often overlooked in host-microbe-pathogen interactions. Recognizing the importance of these factors, I employed a field-based approach to understand microbial community dynamics in the presence of disease. To address the influence of geographical location, I conducted an analysis involving healthy and infected oysters …

Fine-Scale Genetic Structure In Rhizosphere Microbial Communities Associated With Chamaecrista Fasciculata (Fabaceae), Mahboubeh Hosseinalizadeh Nobarinezhad, Lisa E. Wallace

Biological Sciences Faculty Publications

Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of …

Death Of A Bacterium: Exploring The Inhibition Of Staphylococcus Aureus By Burkholderia Cenocepacia., Tiffany Brandt

Electronic Theses and Dissertations

Antimicrobial resistance is a phenomenon of increasing concern as antimicrobial overuse and misuse eliminate current therapeutic options, ushering society into a post-antimicrobial era. Antibiotic discovery and synthesis efforts are urgently needed to counter the increasing burden of antimicrobial resistance. Staphylococcus aureus is a causative agent of a variety of clinical manifestations including bacteremia, endocarditis, soft tissue infection, osteomyelitis, and device-related infections. S. aureus infection presents additional treatment challenges due to its capacity for biofilm formation, which is a mode of growth that confers protection from antibiotics and physical elimination, and the emergence of antibiotic resistant strains, including methicillin-resistant S. aureus …

Microbial Sociality In Biofilms, Swetha Kasetty

Dartmouth College Ph.D Dissertations

Biofilms are communities of microorganisms attached to surfaces through various self-secreted matrix materials. Biofilms are dynamic communities with extensive interactions between their residents. Microorganisms compete, cooperate, and communicate with each other in biofilms. These ecological interactions determine the emergence or loss of strains/species and are critical in the formation and proliferation of biofilms. Furthermore, most natural biofilms are formed by multiple microbial species and strains and these interactions within the biofilm dramatically influence community composition and structure over time. Microbial interactions also influence clinically relevant outcomes such as antibiotic resistance and host virulence. In this thesis we explore the potential …

Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen

Cal Poly Humboldt theses and projects

Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …

Microbial Community And Soil Responses To Land Management Practices In Remnant And Restored Tallgrass Prairies, Desirae Marie Klimek

Graduate Research Theses & Dissertations

Critical ecosystem functions, such as decomposition and nutrient cycling, are driven by microbial communities within soil. As such, it is important to examine the effect of restoration practices, such as the presence of native grazers and prescribed burning, on these microbes and the soil they inhabit. The Nachusa Grasslands provides a chronosequence of restored tallgrass prairies ranging in restoration age from 5 to 33 years, as well as remnant prairies, and agricultural fields. These sites were sampled seasonally from 2013-2020 and microbial ribosomal RNA genes were surveyed to characterize soil microbial communities and assess how common restoration practices affect these …

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. …

Responses Of Wetland Soil Microbial Communities To Different Types Of Anthropogenic Stress, Grace Ann Cagle

LSU Doctoral Dissertations

Microorganisms are the major drivers of biogeochemical transformations of carbon and nitrogen in wetlands. These processes are crucial for ecological sustainability and are heavily impacted by human activities. How anthropogenic stress affects the microbial drivers of carbon storage and nutrient cycling in wetlands is not well understood. I investigated the response of wetland soil microbial communities to three different types of anthropogenic stress using DNA sequencing. First, I studied the effect of warming on microbial carbon processing in a peatland underlaid by permafrost by comparing the abundances of specific genes between sites subjected to five years of warming and controls. …

Analysis Of 316 Omnitrophota (Op3) Genomes Reveals A Diverse And Ubiquitous Candidate Phylum Of Putative Syntrophs, Predators, And Free-Living Nanobacteria Encoding Giant Open-Reading Frames., Cale O. Seymour

UNLV Theses, Dissertations, Professional Papers, and Capstones

Candidate bacterial phylum Omnitrophota has never been isolated and is poorly understood. In this study, we explored the genomics, phylogeny, taxonomy, distribution, cell size, and predicted physiology of Omnitrophota based on 316 genomes. Phylogenomic concordance identified seven classes accommodating 144 species. Calibration of genome-based taxonomy to ribosomal SSU profiling revealed most Omnitrophota classes are prevalent in the Earth Microbiome Dataset, particularly in soils and sediments. Fluorescence-activated cell sorting and differential size filtration experiments showed ultra-small (<400 >nm) cells are common across the phylum, as are parasitism-related genes, including a conserved tight adherence (Tad) complex and ATP/ADP translocase. However, nucleotide and …

Construction And Analysis Of Three Multi-Partite Synthetic Microbial Communities, Alexander J. Lazzara, Jacob K. Fanning

Honors Theses

Microbial Communities are of interest to molecular biologists hoping to understand the nature of metabolic interactions between co-existing, or possibly mutualistic, organisms. These interactions are ubiquitous in nature, but understanding the molecular mechanisms involved remains challenging and not well understood. Here, we design three tri-partite microbial circuits based on possible interactions among involved microbes, which are discussed and may suggest mutualistic interactions. Carbon and nitrogen molecular pathways and the intracellular metabolism of each microbe is discussed. We present minimal growth media that will ensure that organisms utilize available resources, which may originate from metabolic processes in neighboring microbes, simulating a …

Shifts In The Microbiota Associated With Male Mosquitoes (Aedes Aegypti) Exposed To An Obligate Gut Fungal Symbiont (Zancudomyces Culisetae), Jonas Frankel-Bricker

University Author Recognition Bibliography: 2020

Research characterizing arthropod-associated microbiota has revealed that microbial dynamics can have an important impact on host phenotypic traits. The influence of fungi on these interactions are emerging as targets for research, especially in organisms associated with global human health. A recent study demonstrated colonization of a widespread gut fungus (Zancudomyces culisetae) in a larval mosquito (Aedes aegypti) digestive tract affected microbiomes in larvae and newly emerged adult females (Frankel-Bricker et al. Appl Environ Microbiol, 2020. https://doi.org/10.1128/AEM.02334-19) but did not investigate these processes in males. The objective of the study presented here was to assess fungal influences …

Microbial Community Structures In Three Bahamian Blue Holes, Meghan J. Gordon

USF Tampa Graduate Theses and Dissertations

This study used 16S rDNA metagenomics and water chemistry to conduct an examination of microbial community dynamics and biogeochemistry in three physically adjacent, sunlit blue holes with variable hydrologic regimes on San Salvador Island, Bahamas. Church and Watling’s Blue Holes are holomictic with relatively clear waters, while Inkwell Blue Hole hosts density stratification and waters stained brown with tannins. Based on water color and clarity and physicochemical profiles, I hypothesized Church and Watling’s Blue Holes would be dominated by oxigenic photoautotrophs, and that the bottom layer of Inkwell would be characterized by euxinic (anoxic and sulfidic) conditions and host primarily …

The Effect Of Historic Shipwrecks On Sediment Microbiomes In The Northern Gulf Of Mexico, Melissa Brock

Master's Theses

Microorganisms are ubiquitously distributed across all aquatic habitats, but it is the environmental conditions of a habitat that determine which microorganisms can thrive in terms of abundance or metabolic activity. Habitats that experience consistent physical and chemical environmental conditions repeatedly favor specific taxonomic groups which may result in a microbial assemblage that is commonly associated with that habitat (i.e., a core microbiome). Core microbiomes have been identified for a variety of natural marine habitats including methane seeps, wood falls, octocoral, and deep-sea sediments. However, it was unknown if the presence of man-made structures on the seafloor, including historic shipwrecks, also …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Parasitic Microbiome Project: Grand Challenges, Nolwenn M. Dheilly, Joaquín Martínez Martínez, Karyna Rosario, Paul J. Brindley, Raina N. Fichorava, Jonathan Z. Kaye, Kevin D. Kohl, Laura J. Knoll, Julius Lukeš, Susan L. Perkins, Robert Poulin, Lynn Schriml, Luke R. Thompson

Faculty Publications

No abstract provided.