Environmental Microbiology and Microbial Ecology Commons^™

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.

Characterizing The Quorum Sensing (Qs) System In The Model Eukaryote Chlamydomonas Reinhardtii, Kirstin Donnette Cutshaw

Theses and Dissertations

Group behaviors in microorganisms are often regulated by low-molecular weight molecules that enable them to sense population density, a signaling system known as quorum sensing (QS). QS in prokaryotes has provided insight into the role ‘social’ behaviors play in the bacterial world and refined our models of virulence, bacterial motility, and more. While less common, similar behaviors are observed in certain fungi, primarily yeasts, in which QS controls cell morphology, biofilm production, and other phenotypes. We have recently pursued the potential for QS to be more broadly distributed among unicellular eukaryotes, which could significantly alter our understanding of social behaviors …

Optimizing The Expression Of Polyethylene Terephtalate Hydrolase-Encoding Synthetic Gene In Escherichia Coli Arctic Express (De3), Jocelyn Nataniel, Maria Ulfah, Dini Achnafani, Niknik Nurhayati, Gabriela Christy Sabbathini, Sri Rezeki Wulandari, Abinawanto Abinawanto, Is Helianti

Makara Journal of Science

The waste of polyethylene terephthalate (PET) plastic waste in Indonesia is a pressing concern due to its slow degradation and potential environmental damage. One promising solution is to utilize polyethylene terephthalate hydrolase from Ideonella sakaiensis (IsPETase), an enzyme that specifically degrades PET. However, inducing the expression of IsPETase synthetic gene in Escherichia coli BL21 (DE3) has been challenging because much of it remains insoluble. This study aimed to express IsPETase in E. coli Arctic Express (DE3) and optimize the conditions to enhance its production. First, pET22b(+)pelB-IsPETase was inserted into E. coli Arctic Express (DE3). The …

Metagenomic Analysis Of Antarctic Microbial Communities, David Michael Robinson

Biology ETDs

The research presented in this dissertation focuses on microbial roles in biogeochemical cycling in Antarctic aquatic environments. The major objective of my research was to examine the impact of biotic and abiotic pressures on nutrient cycling in microbially dominated systems. I used three perennially ice covered lakes in the McMurdo Dry Valleys (MDVs) along with subglacial lakes Whillans and Mercer as natural case studies. The MDVs are located in Victoria Land, East Antarctica and have been studied since 1993 as part of the McMurdo Long Term Ecological Research Project. Viruses in the MDVs were shown to be seasonally abundant and …

Degradation Of Chlorpyrifos Residue On Tropical Inceptisol Soil With Indigenous Bacteria Treatment, Asep Kurnia, Hidayatuz Zu`Amah, Baiq Nunung Sulastri, Ria Fauriah Makmur

Makara Journal of Science

The use of soil microbes is one of the most effective methods for degrading pesticide residue in soil. Microbes can accelerate the degradation of persistent pollutants including chlorpyrifos in soil. This research aims to find soil bacteria with the greatest potential to degrade chlorpyrifos residue in tropical inceptisol soil and determine its degradation index (DI). The soil used in this experiment was collected from agricultural fields in the districts of Demak, Central Java Province, Indonesia. The experiment was performed using factorial randomize complete block design composed of two factors and four replications. The first factors were made up of two …

Prochlorococcus Death By A Ubiquitous Zooplankton Filter Feeder, Avery Harman

University Honors Theses

Prochlorococcus is a globally abundant cyanobacterium that can help reveal the ecology of microorganisms in the ocean. Specifically, mortality by zooplankton such as appendicularians is globally important and Prochlorococcus can help reveal some of the choices made around feeding for this ubiquitous filter feeder. Two ecotypes of Prochlorococcus were introduced to appendicularians to determine if appendicularian feed selectively between these ecotypes. Further, a single ecotype of Prochlorococcus was fed to appendicularians over a variety of life stages to determine if retention rate changed with appendicularian life stage. My results reveal that there is no significant selection between the two Prochlorococcus …

Heavy Metals Implications To Sediment Microbiome And Coral Response To Arsenic Dosing, Dimitrios G. Giarikos, Amy Hirons, Jose V. Lopez, Abigail Renegar, Jason Gershman

SECLER Data

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, …

Characterization Of A Novel Metalloid Reductase Outer Membrane Porin Rara From Sulfurospirillum Barnesii Ses-3, Narthana Jeganathar Kanmanii

Electronic Theses and Dissertations

Sulfurospirillum barnesii SES-3 is a gram-negative epsilon proteobacterium that grows anaerobically by coupling the oxidation of lactate to the reduction of arsenate. Previous work on metal and metalloid metabolism in S. barnesii had identified a redox active protein, designated RarA that when provided an artificial electron donor (i.e., reduced methyl viologen, FMN, or NADH), could reduce a variety of substrates, including arsenate, selenate, selenite, nitrite, and even phosphate. The enzyme’s inferred amino acid sequence showed weak similarity (30%) to outer membrane porins with homologs found in only certain species of Sulfurospirillum. Further, the enzyme did not contain cysteine residues …

The Influence Of A Ubiquitous Filter Feeder On Coastal Microbial Communities., Melissa Steinman, Moritz S. Schmid, Robert K. Cowen, Su Sponaugle, Kelly R. Sutherland, Anne W. Thompson

Student Research Symposium

Doliolids have a unique ability to impact the marine microbial community through bloom events and high filtration rates. Their predation on large eukaryotic microorganisms is established and evidence of predation on smaller prokaryotic microorganisms is beginning to emerge. We studied the retention of both eukaryotic and prokaryotic microbial taxa by wild-caught doliolids in the northern California Current system. We use qPCR to quantify the impact of doliolids on three important and globally abundant taxa: Synechococcus, SAR11 and diatoms. Doliolids were collected during bloom events identified at three different shelf locations with variable upwelling intensities. We discovered that in addition …

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 …

A Precious Gift: A Reflection And Resource On Water Quality And Sustainability, Mark Potosnak, Andrew Panelli, Adrienne Kalmes, Antonio Quintanilla, Dr. George Nassos, Michael Terrien, Obl. Osb

College of Science and Health Faculty and Staff Works

This reflection, prepared by Illinois Catholics concerned with the intersection of faith, environmental stewardship, and social justice, explores the theological, moral, and practical dimensions of water quality and sustainability in the state. Rooted in Scripture, and Catholic liturgy and tradition, it affirms water as a sacred gift, essential for life and a universal human right. Drawing on Catholic social teaching and Pope Francis’ Encyclical Laudato Si’: On Care for Our Common Home, it examines pressing water challenges in Illinois, including contamination from coal ash, nitrates, PFAS, and lead, as well as infrastructure, affordability, and sustainability concerns. The document offers an …

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 …

Investigating Effects Of Co-Culturing With Vibrio Fischeri On Secondary Metabolite Production Of Hawaiian Bobtail Squid Symbionts, Mariam A. Zedan

Honors Scholar Theses

Microbes are a fruitful source of natural product drug discovery since many of their secondary metabolites show defensive activity and have unique structures. However, extracting and elucidating the structure of those compounds can be challenging in vitro due to particular environmental and nutritional requirements of some bacteria. Those requirements may include proximity to other organisms that the microbes have symbiotic relationships with. Under those conditions, the organism may activate silent biosynthetic gene clusters (BGCs) responsible for production of certain secondary metabolites not typically expressed otherwise. One method of BGC induction is co-culturing with other microbes since this mimics the natural …

The Effects Of Prescribed Fire On Microbial Biomass Abundance In Longleaf Pine Ecosystems, Sarah K. Borne

Honors Theses

One of the most diverse ecosystems, longleaf pine (Pinus palustris) habitats comprise only a small fraction of the habitat they once spanned in the Gulf Coastal Plain Region of the Southeastern United States. To preserve longleaf pine ecosystems, proper prescribed burning techniques and ecosystem management are essential for preventing high intensity wildfires and increasing species diversity. Little is known about the effects of prescribed fires on carbon levels, nitrogen levels, and microbial biomass in longleaf pine forests. These components are crucial for determining how well burned areas are recovering at a microbial level compared to unburned areas. The …

Genome-Scale Metabolic Modeling Of Chitin-Degrading Microbial Systems, Aimee Kristin Kessell

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

As a major component of fungal cell walls and exoskeletons of invertebrates, chitin is widespread in soils, constituting the second most abundant biopolymer in nature. Composed of N-acetyl-D-glucosamine chains, it serves as a vital source of nutrients, including both carbon and nitrogen, for the growth of microorganisms. A solid understanding of the microbial degradation of chitin is critical for predicting their impacts on biogeochemical cycling in soil ecosystems. Organisms that degrade biopolymers (degraders) produce energetically expensive extracellular enzymes to break down complex organic carbons into simpler labile forms that are sharable with other species, including those that do not contribute …

The Influence Of Environmental Conditions On Gordonia Terrae -Specific Bacteriophage Distribution And Diversity, Gt M. Moore

Biology Theses

Bacteriophages are viruses that infect a diverse range of bacteria, with certain strains serving medical and industrial significance. Actinobacteriophages are viruses that specifically infect Phylum Actinobacteria hosts including the environmentally abundant Gordonia terrae. Some species of Gordonia, including G. terrae, have also been isolated from human infections. The isolation and characterization of novel phages that can infect Gordonia can therefore be significant to both genomics and potential phage therapy. Actinobacteriophages that infect these bacteria have been isolated from soil environments, but optimal environmental parameters for isolation have not been fully evaluated. This study examined the relationships between environmental …

Identification Of Plant Growth Promoting Rhizobacteria For Ballona Wetlands Restoration, Caroline Ehren, Michelle Lum

Honors Thesis

The Ballona Wetlands Ecological Reserve (BWER) is home to many California native plant species which contribute to ecosystem services of flood and erosion mitigation, water quality improvement, carbon sequestration, and habitat provisions for threatened and endangered species. Plant growth promoting rhizobacteria (PGPR) improve plant tolerance to abiotic stressors and suppress pathogens through the alteration of nutrient absorption, water uptake, and enzymatic activity, and have potential in conservation strategies by aiding revegetation methods. Eight bacterial strains were isolated from native Frankenia salina and Baccharis pilularis in the BWER to determine whether these microbes act as PGPR. The strains were characterized using …

Effect Of Assay Medium Ph On Inhibitory Ability Of Streptomyces, Trevor Swan, Miriam Gieske

Undergraduate Research Symposium 2024

Streptomyces bacteria from soil often produce antibiotics which inhibit growth of other microbes. When comparing Streptomyces’ inhibitory ability between different soils, it may be important to match the pH of the medium used in assays to the pH of the soil they came from. We assayed Streptomyces isolates collected from a long-term agricultural experiment with nitrogen-fertilized and non-fertilized treatments to determine their ability to inhibit growth of other bacteria by producing antibiotics. Average soil pH was 6.8 in fertilized soil and 7.2 in non-fertilized soil. We dotted isolates on a glucose-asparagine agar medium adjusted to different pH values and overlaid …

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 …

Validation Of A Passive Sampler For Tracking Harmful Algal Toxins In Natural Waters, Hailee Eiker

Honors Theses

Algal blooms that produce toxins that are harmful to the health of people, animals, and the environment are known as harmful algal blooms (HABs). Recently, rising global temperatures, nutrient pollution, and an increase in the frequency of extreme hydrologic events have made HABs a bigger problem. This has all led to greater cultural eutrophication which is a major contributor to the spread of HABs. Cyanobacteria make up the bulk of HABs in freshwater systems, microcystins being among the cyanotoxins that are most frequently reported and studied. Taking grab samples of water is the current standard procedure for sampling cyanotoxins, however, …

A Review On Bioremediation Of Heavy Metals And Hydrocarbons Through Plant Growth-Promoting Bacteria And Composting, Hafsa Saleem, Hadia Farooq, Rimsha Mazhar, Sadaf Shakil, Sahar Fazal

Journal of Bioresource Management

Soil is an important ecosystem component; it serves as a habitat for many microscopic organisms that play an important role in the ecosystem's maintenance and crops grown in soil. Unfortunately, human activities have adversely affected not only the environment but also the soil health. Soil has been contaminated with heavy metals hydrocarbons and hydrocarbon-based products that are affecting soil health and the growth of plants. In this review two methods of heavy metal remediation are discussed; one is the role of plant growth-promoting bacteria (PGPB) in the enhancement of phytoremediation and the other is composting. PGPB help plants to grow …

Novel Microbiological Medium Developed For The Isolation Of Bacteria Associated With Estuarine Anemones, Parker K. Lund, Catalina Cuellar-Gempeler

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Out of the nearly one trillion species of microbiota estimated to inhabit Earth only ten thousand have been cultured in the laboratory. Culturing continues to play a vital role in determining the physiology and ecologic function of individual bacteria in microbial communities and for microbes associated with host organisms one of the major challenges is developing microbiological media that mimics the bacteria’s natural environment enough to promote growth. Here, we target bacteria associated with the estuary anemones Diadumene lineata and Metridium senile by developing a novel medium that uses anemone tissue as the sole source of nutrients. We further measured …

The Diversity Of Wolbachia Across The Turtle Ants (Formicidae: Cephalotes Spp.), Corey Reese, Leland C. Graber, Manuela O. Ramalho, Corrie S. Moreau

Biology Faculty Publications

Wolbachia is a widespread and well-known bacterium that can induce a wide range of changes within its host. Ants specifically harbor a great deal of Wolbachia diversity and are useful systems to study endosymbiosis. The turtle ants (Cephalotes) are a widespread group of tropical ants that rely on gut microbes to support their herbivorous diet for their survival, yet little is known of the extent of this diversity. Therefore, studying their endosymbionts and categorizing the diversity of bacteria within Cephalotes hosts could help to delimit species and identify new strains and can help lead to a further understanding of how …

Antibacterial And Anticancer Activities Of A Fosmid Clone From Atlantis Ii Red Sea Brine Pool., Marina Nabil

Theses and Dissertations

Antimicrobial resistance (AMR) and cancer are among the top global human health issues requiring urgent control practices. AMR caused 5 million death cases around the world in 2019. This number is expected to reach 10 million deaths by 2050. Cancer deaths reached 10 million in 2020. Additionally, anticancer drug resistance is a common cause of death among cancer patients. Screening for novel compounds is one of the strategies recommended by the World Health Organization (WHO) to control drug resistance in microbial and cancer cells. Marine natural products (MNPs) are characterized by chemically diverse structures with various bioactivities, especially in extreme …

A Survey Of Fusarium Oxysporum In Georgia Hemp Farms And Vegetable Gardens, Christopher D. Burt

Georgia Journal of Science

Recent changes in U.S. federal law have recognized the genetic and chemical differences between hemp and marijuana (Cannabis sativa L.), resulting in the legalization of hemp in the United States. The barriers to this plant’s growth in the state of Georgia are not well understood due to its prohibition for the past 80 years. Among the many possible obstacles is fungal disease. Fusarium oxysporum (Schlecht. emend. Snyder & Hansen) is a fungus that damages various crops and was previously researched as a biocontrol agent for C. sativa. Thus, this study surveyed hemp farms in Georgia to determine the prevalence …

Effectiveness Of Mycorrhizae And Vermicompost Seed Inoculation For Germination, Vegetative Growth, Cannabinoid Content, And Cured Flower Weight Of Cbd-Rich Hemp (Cannabis Sativa L.), Hannah Boyer, Nicole Wagner, Merritt Drewery

Journal of Agricultural Hemp Research

Effective germination and vigorous growth of hemp cultivars is paramount to cultivators’ ability to produce high-quality hemp products. Beneficial bacteria and fungi are known symbionts to plants and are used in regenerative agriculture to increase plant health and crop yield. This pilot study investigated the effect of microbial seed inoculation on germination rate, plant height, cured flower weight, and cannabinoid content of cannabidiol (CBD)-rich hemp (Cannabis sativa L). The experiment included a control and the following treatments: 1) seed inoculation of Great White ^â Premium Mycorrhizae (GW), 2) seed inoculation of vermicompost (V), and 3) seed inoculation of Great …

The Ecological Responses To Hydroperiod Of Wetland Plant Species Determined By Manipulated Soil Surface Elevation (Marsh Organs), Brandon Wolff

LSU Master's Theses

As sea level rise, subsidence, and abandonment of natural deltaic processes due to a highly engineered Mississippi River continue to threaten Louisiana’s coastal wetlands, the need for a system-wide understanding of natural wetland land-building and preservation processes has never been greater. A key component of any wetland is the ever-changing water environment that periodically floods and dries the marsh platforms. The flooding depth, duration, and frequency, known as the hydroperiod, along with salinity and soil fertility are key determining factors of vegetation and marsh types at a particular location. Different types of vegetation will have different growth characteristics such as …

The Influence Of Environmental Parameters On Gordonia Terrae - Specific Bacteriophage Abundance And Diversity, Gt M. Moore, Uqueen C. Wheeler, Indiren Pillay

Graduate Research Showcase

Bacteriophages are viruses that infect a wide variety of host bacteria with some strains having medical and industrial significance. These highly abundant and genetically bacterial viruses constitute a large amount of unexplored genetic information. Because bacteriophages are highly specific, they can be used therapeutically to combat bacterial infections by selecting a phage to target and kill harmful bacteria. Thus, phage therapy is currently being explored to aid in the fight against antibiotic resistance. Actinobacteriophages are viruses that specifically infect Phylum Actinobacteria hosts including the environmentally abundant Gordonia terrae. Some species of Gordonia, including G. terrae, have also …

The Presence Of Pathogenic Leptospira In San Juan Bay Estuaries And Its Relationship To Fecal Pollution Sources, Jodel M. Nicholas, Dave Bachoon Dr.

Graduate Research Showcase

The northern coastal zones of Puerto Rico, including the San Juan Bay and Rio Grande de Loiza watersheds, are increasingly becoming focal points of environmental concern due to wastewater originating from human activity. This runoff, which consists of effluents from sewage treatment, septic tanks, and animal husbandry, enters coastal lagoons and estuaries, posing critical threats to these vital ecosystems. This study aims to determine the presence of Leptospira in over 100 samples from 16 sub-basins over 2 years as well as identify the major sources of fecal pollution using molecular source tracking techniques. End point PCR assays for Leptospira (LipL32), …