Environmental Microbiology and Microbial Ecology Commons^™

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.

Fiddler Crab Gut Microbiomes As An Indicator For Eutrophication Due To Waste-Water Contamination In Estuaries, Madison L. Geraci

Honors Theses

Estuaries are unique biogeochemical zones in coastal systems that provide a myriad of ecological functions: providing habitat for critically important fishery species, diverse species of plants and animals, and contributing to nutrient cycling. Estuaries are vulnerable to anthropogenic stressors as they are intersections between marine and terrestrial communities and are often the hotspot of coastal development and activity. Estuarine sediments act as repositories for anthropogenic contaminants, including excess nutrient runoffs and waste-water pollution that can cause states of eutrophication. Microorganisms are sensitive to these environmental changes, presenting a unique opportunity of being useful bioindicators of environmental stress. Isolating microorganisms from …

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 …

Patterns Of Epiphytic Bacterial Growth On Flower Surfaces: Relationships With Flower Longevity And Environmental Factors, Rita Nkem Afagwu

Graduate Theses/Dissertations

Flowers host diverse communities of epiphytic bacteria, which can impact floral functions, pollinator interactions, and overall plant fitness. However, little is known about how the abundance of these bacteria change as flowers age, and how these shifts may correlate with floral longevity. In this study I investigate the change in bacterial abundance across the lifespan of a flower from anthesis (opening of bud to flower) to senescence (wilting of flower) and to explore the potential implications for floral longevity. We tracked the age of the flowers by determining the average age to senescence in flowers of 8 plant species over …

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 …

Scale And Habitat Effects On Measurement Of Streptomyces Biogeography And Biodiversity, Terilyn A. Stoflet

Cal Poly Humboldt theses and projects

Bacteria in the genus Streptomyces are detected in most soils around the world, as well as on and in seeds, plants, animals, insects and the wind. Currently, more than 700 valid species of Streptomyces have been identified worldwide. Streptomyces produce the majority of antibiotics, antivirals and antifungals, as well as important agricultural bioactive molecules due to their unique genetic capabilities. Their distinct genetic abilities allow them to produce an unlimited amount of biosynthetic gene clusters, or BGC’s. Although many compounds come from Streptomyces, scientists have not discovered the biogeographic patterns of this genus. The biogeography of Streptomyces is a …

A Comparison Of Adenosine Triphosphate With Other Metrics Of Microbial Biomass In A Gradient From The North Atlantic To The Chesapeake Bay, Alexander B. Bochdansky, Amber A. Beecher, Joshua R. Calderon, Alison N. Stouffer, Nyjaee N. Washington

OES Faculty Publications

A new, simplified protocol for determining particulate adenosine triphosphate (ATP) levels allows for the assessment of microbial biomass distribution in aquatic systems at a high temporal and spatial resolution. A comparison of ATP data with related variables, such as particulate carbon, nitrogen, chlorophyll, and turbidity in pelagic samples, yielded significant and strong correlations in a gradient from the tributaries of the Chesapeake Bay (sigma-t = 8) to the open North Atlantic (sigma-t = 29). Correlations varied between ATP and biomass depending on the microscopic method employed. Despite the much greater effort involved, biomass determined by microscopy correlated poorly with other …

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 …

Breaking Virulent: The Coincidental Evolution Of Virulence Factors In Bacteria., Rhiannon Emmanuelle Cecil

Electronic Theses and Dissertations

Understanding how innocuous organisms can evolve to be pathogenic to humans is of increasing global concern. Further, understanding how existing pathogens may evolved to be more virulent is also vital to our ability to provide healthcare to people afflicted with diseases that promote chronic bacterial infections, such as cystic fibrosis. With the rise of antibiotic resistance in both bacteria and fungi it is paramount that new therapeutics are identified. Understanding what mutations occur that result in increased virulence in microbes can potentially provide new targets for antimicrobial drugs to combat antibiotic resistance. The Coincidental Evolution Hypothesis is a fundamental hypothesis …

Distinguishing Community Assembly Through Functional Redundancy Models., Sandra A. Tsiorintsoa, Sharon Bewick, Matthew Macauley

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay

Dartmouth College Ph.D Dissertations

The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …

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 …

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 …

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 …

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 …

Causes And Consequences Of Lasr Mutant Selection In Pseudomonas Aeruginosa Populations, Dallas L. Mould

Dartmouth College Ph.D Dissertations

Change is the only constant in life, and these changes, though random in nature, can have consequences. Quorum sensing is heterogeneous in phenotype and prone to negative selection. In P. aeruginosa, the regulator LasR is frequently non-functional in phylogenetically diverse isolates. Through repeated experimental evolution and mathematical modeling, we show that differences in growth enable lasR mutant evolutionary success and this requires a system enabling metabolic choices, known as carbon catabolite repression (or catabolite repression). The differences in catabolite repression between wild type and lasR mutants enable altered metabolite preferences, and the resulting differences in metabolic states enable intraspecies …

The Response Of Microcystis And The Microbiome To Exogenous Hydrogen Peroxide, Bryan A. Puma

Masters Theses, 2020-current

Microcystis spp. produce prolific annual blooms in freshwater systems worldwide. The success of these blooms depends heavily on the Microcystis spp. overcoming environmental factors such as oxidative stress caused by reactive oxygen species (ROS) like hydrogen peroxide. Most Microcystis genomes do not contain many genes for responding to oxidative stress, including those that encode the enzyme catalase. Other cyanobacteria such as Prochlorococcus that also lack hydrogen peroxide degrading enzymes have been shown to benefit from partnerships with heterotrophic bacteria. Microcystis spp. may also receive similar benefits from heterotrophic bacteria in the phycosphere. To test this hypothesis, we examined the …

Variation In Synthetic Floral Microbiome Composition Is Largely Ignored By Foraging Bumblebees, Nevin P. Cullen

2023 Midwest Ecology & Evolution Conference

Most flowers are occupied by diverse communities of microbes, which can alter floral attractiveness to key pollinators and floral fitness by interacting with floral traits. Different species of flower often acquire unique communities of microbes. Consequently, pollinators are frequently forced to choose between two flowers with distinct floral microbiomes while foraging. However, it is currently unknown whether pollinators have an inherent preference for flowers containing one floral microbiome over another, and whether microbial preference is modified by variation in floral traits. We investigated this knowledge gap using distinct bacteria and yeasts cultured from a nickel-hyperaccumulating plant and its non-accumulating relative. …

An Optimal Patch Use Model For Nitrogen Foraging In Arbuscular Mycorrhizal Fungi, Xin Lin

2023 Midwest Ecology & Evolution Conference

Optimal Foraging Theory has been widely used to study animal foraging behaviors, but has seldom been applied to symbiotic microbes like arbuscular mycorrhizal (AM) fungi. To date we know little about how AM fungi make decisions to forage in different nutrient patches. To help address this gap we here apply Optimal Foraging Theory to understand how AM fungi forage for nitrogen. We focus on nitrogen because AM fungi need more nitrogen than their plant hosts and soil nitrogen availability can shift the relationship between AM fungi and their hosts from mutualism to parasitism. We present a stochastic dynamic programming model …

Elevated Co2 Drives Community And Network Structural Change Within Foliar Microbiomes Of Soybean, Connor Morozumi

2023 Midwest Ecology & Evolution Conference

Microbiomes within plants can play large roles in determining responses to stress or perturbation, increasingly common in a rapidly changing world. For example, foliar endophytes are known to increase stress tolerance to drought and decrease herbivory among many other effects. How these microbes are likely to respond to global change themselves is poorly understood. Global changes, such as increased atmospheric CO₂, which can influence host plant physiological processes, have the potential to directly and indirectly alter microbiome community structure. Here, we assessed community and network structure of bacterial and fungal phyllosphere microbiomes within soybean (Glycine max). …

Initial Steps In Testing The Stress Gradient Hypothesis For Selenium Exposure In Soil Bacteria, Kristian J. Harris

2023 Midwest Ecology & Evolution Conference

The Stress Gradient Hypothesis (SGH) states that interspecific interactions should shift from competitive to facilitative interactions as environmental stress increases. Selenium (Se) is a naturally occurring metalloid that acts as an environmental pollutant and as an essential micronutrient. Due to its metallic properties, Se acts as an oxidative stress and can be toxic to plants and animals. Given this, Se in soil systems acts as an abiotic stress that influences species composition and species interactions. Within soils, bacteria and fungi have evolved to tolerate Se via detoxification and Se processing for respiration and studies show that metal detoxification traits like …

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 …

Under Ice Photosynthetic Primary Production And Dark Carbon Fixation In A Temperate Freshwater System, Vanessa Cubillos Tellez

Dissertations, Master's Theses and Master's Reports

Ice-covered lakes are vulnerable to environmental change, especially those in the Northern Hemisphere where ice cover is rapidly declining due to global warming. These changes can alter metabolic processes and disrupt carbon cycling driven by primary producers who form the base of the food chain and are key to sustaining ecosystem function. Photosynthetic primary production and dark carbon fixation under the ice in the Keweenaw Waterway, a temperate freshwater system that is ice-covered for ~3 months out of the year, were studied using a carbon isotopic labeling (14C-bicarbonate) technique. Water samples were collected weekly during ice cover and monthly during …

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 …

Microbial Communities In The Guana Tolomato Matanzas National Estuarine Research Reserve: An Assessment Of The Responses Of Spartina Alterniflora Epiphytes To Nitrogen Enrichment, And A Characterization Of Benthic Cyanobacterial Diversity, Anne C. Hurley

UNF Graduate Theses and Dissertations

Elevated nitrogen and phosphorus inputs from anthropogenic sources, which can lead to significant increases in algal biomass and changes in algal community composition, poses a serious threat to estuarine ecosystems worldwide. While numerous studies have addressed the impacts of nutrient enrichment on epiphytic algae in seagrass habitats, few have investigated potential nutrient-driven changes to epiphytes on emergent salt marsh plants, such as Spartina alterniflora. Epiphytic microalgae on S. alterniflora play an important role in food availability in salt marsh ecosystems, and epiphytic nitrogen-fixing cyanobacteria also provide an important source of nitrogen for salt marsh consumers. The first study included …

Guano Among Bat Species From Two Regions Shows Influence Of Geography And Diet On Bacterial Community, Rahma Ahmed, Thomas Mcelroy, Shannon Whitney, Lydia Moore

Symposium of Student Scholars

Studies of bat guano have shown that the diversity and structure of associated microbial communities can be related to factors such as host phylogeny, life history and reproductive stage, geography, and diet. Many insectivorous bat species in the southeastern U.S. have generalist diets that may shift seasonally to take advantage of abundant prey species or maximize caloric intake. Seasonal shifts in prey availability or consumption should be reflected in a guano microbiome change. We also expected to detect distinct guano microbiomes within species. Within species, distinct microbial communities related to geography, and finally life history and reproductive stage. We compared …

Combining Isotopic And Genetic Analyses To Quantify Microbial Facilitation Of Recalcitrant Resource Use By Terrestrial And Aquatic Consumers, Alexi Christina Besser

Biology ETDs

Quantifying the flow of energy and nutrients through food webs is foundational to understanding the structure and function of ecosystems. Here, I utilize the stable carbon and nitrogen isotope analysis of individual amino acids to trace the movement of essential amino acids through terrestrial and freshwater food webs in New Mexico, USA. I first explore isotopic patterns among co-occurring terrestrial plants and aquatic algae. I then combine this molecular isotopic approach with 16S and 18S rRNA sequencing to demonstrate the importance of gut microbiota as sources of essential amino acids to wild mammalian hosts. Next, I explore the roles of …

Algae And Cyanobacteria In The Aphotic Habitats Of Veternica Cave (Medvednica Mt., Croatia) And Selected Caves Of The Dinaric Karst (South-Eastern Europe), Najla Baković, Tanja Pipan, Robert Baković, Roman Ozimec, Josip Rubinić, Renata Matoničkin Kepčija

International Journal of Speleology

Microphototrophs (algae and cyanobacteria) in karst environments have been intensively studied in aquatic epigean habitats. In recent decades knowledge about the communities inhabiting cave entrances and lampenflora has grown substantially, but the data about the communities in aphotic cave zone are scarce. This study aimed to investigate spatio-temporal presence of microphototrophs in the aphotic zone of Veternica Cave (Mt. Medvednica karst) and to present additional preliminary data from 22 caves of the Dinaric karst. The data were collected over ten years, in parallel with research on cave phagotrophic protists. In addition to the remains of microphototrophs, living algae and cyanobacteria …