Environmental Microbiology and Microbial Ecology Commons^™

A Mathematical Model For Transport And Growth Of Microbes In Unsaturated Porous Soil, Harihar Khanal, Andrei Ludu, Ramesh Chandra Timsina, Kedar Nath Uprety

Publications

In this work, we develop a mathematical model for transport and growth of microbes by natural (rain) water infiltration and flow through unsaturated porous soil along the vertical direction under gravity and capillarity by coupling a system of advection diffusion equations (for concentration of microbes and their growth-limiting substrate) with the Richards equation. (e model takes into consideration several major physical, chemical, and biological mechanisms. (e resulting coupled system of PDEs together with their boundary conditions is highly nonlinear and complicated to solve analytically. We present both a partial analytic approach towards solving the nonlinear system and finding the main …

Monitoring Photosynthetic Activity Using In Vivo Chlorophyll A Fluorescence In Microalgae And Cyanobacteria Biofilms In The Nerja Cave (Malaga, Spain), Yolanda Del Rosal, Juan Muñoz-Fernández, Paula S.M. Celis-Plá, Mariona Hernández-Mariné, Félix Álvarez-Gómez, Salvador Merino, Félix L. Figueroa

International Journal of Speleology

The characterization of the most common photosynthetic biofilms in the Nerja Cave by the continuous monitoring of the in vivo chlorophyll a (Chl a) fluorescence and the incorporation of the irradiance as a new environmental variable related to previous studies in the cave, have allowed us to improve our knowledge about the photosynthetic pattern of the biofilms of the cave. Effective quantum yield (ΔF/F_m′) and relative electron transport rate (rETR) were determined during periods of the light, whereas the maximal quantum yield (F_v /F_m) was determined during dark periods. Increases in …

Determining Effects Of Management Practices On Potato Early Dying And Soil Microbiome And Assessing Risk Of Fungicide Resistance In Verticillium Dahliae, Kedi Li

Electronic Theses and Dissertations

Potato early dying (PED) is a yield-constraining soilborne disease of potato, caused by Verticillium spp. with V. dahliae being the predominant causal agent. Since the pathogen inhabits soil for long periods, PED management aims to reduce the population of V. dahliae in soil. Benzovindiflupyr and azoxystrobin are effective chemicals and frequently used in the control of V. dahliae. In this study, field trials were conducted at Aroostook Farm, Presque Isle, ME in 2019 and 2020. Chemical and biological products have been studied for PED control, and fungicide resistance was also examined. To evaluate fungicide resistance, benzovindiflupyr was characterized on …

Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid, Kenneth Nickerson, Cory Boone, Kory Parker

Kenneth Nickerson Papers

Candida albicans is a pathogenic dimorphic fungus which is invariably found as a diploid in patients. C. albicans secretes the sesquiterpene farnesol both as a quorum sensing molecule which blocks the yeast to hypha conversion and as a virulence factor for pathogenicity. 20-25 μM farnesol kills other competing yeasts and fungi, often by triggering apoptosis, and yet wild type diploid C. albicans tolerates 300-500 μM farnesol. The recent availability of 10 haploid strains of C. albicans (5 mating type aand 5 mating type α) allowed us to compare their production of and sensitivity to farnesol. On average, the heterozygous diploid …

The Effects Of Hydrologic Heterogeneity On Harmful Algal Blooms In Freshwater Reservoir, Lake Sinclair, Georgia, Margaret Blackledge

Biology Theses

Aquatic habitats are frequently studied after a major water quality problem like the occurrence of an algal bloom. In this study, A proactive rather than a reactive response was considered, where the complexity of conditions conducive to uncontrolled cell growth were studied before a bloom took place by sampling regularly. This study aimed to monitor water quality by monthly sampling of algal communities for approximately one year. As the base of the aquatic food web, algae are a highly diverse group of organisms with varying sensitivity to physical and chemical changes in the environment. Four shallow sites were monitored at …

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. …

A Temporal Analysis Of The Microbiota And Biofouling Development On Artificial Substrates In The Port Everglades Inlet, Florida, Denise Swack

All HCAS Student Capstones, Theses, and Dissertations

A pilot project was deployed in Port Everglades Inlet, Florida that aimed to evaluate the biofilm composing the microbiome on ecologically engineered artificial substrates used to build Coastal Marine Infrastructure. In April of 2017, an Articulated Concrete Block Mattress comprised of an ecological engineered concrete substrate and a standard smooth surface control substrates were compared. This study will provide a profile on the microbiome community on artificial substrates within Port Everglades Inlet on bio-enhancing concrete-based solutions in our Coastal Marine Infrastructure. To study the microbial community, the 16s rRNA technology was used in Illumina’s high-throughput DNA sequencing. Samples were collected …

Rhizobium Symbiotic Capacity Shapes Root-Associated Microbiomes In Soybean, Yuanhui Lu, Bin Ma, Wenfeng Chen, Klaus Schlaeppi, Matthias Erb, Erinne Stirling, Lingfei Hu, Entao Wang, Yunzeng Zhang, Kankan Zhao, Zhijiang Lu, Shudi Ye, Jianming Xu

Environmental Science and Geology Faculty Research Publications

Root-microbiome interactions are of central importance for plant performance and yield. A distinctive feature of legumes is that they engage in symbiosis with N₂-fixing rhizobia. If and how the rhizobial symbiotic capacity modulates root-associated microbiomes are still not yet well understood. We determined root-associated microbiomes of soybean inoculated with wild type (WT) or a noeI mutant of Bradyrhizobium diazoefficiens USDA 110 by amplicon sequencing. UPLC-MS/MS was used to analyze root exudates. The noeI gene is responsible for fucose-methylation of Nod factor secreted by USDA 110 WT strain. Soybean roots inoculated with the noeI mutant showed a significant decrease …

Response Of Soil Viral And Microbial Functional Diversity To Long-Term Agricultural Management In Jackson, West Tennessee, Ning Duan

Doctoral Dissertations

Soil microbial communities are a critical component for ecosystem stability and function. Viruses, as an important biotic controller, have the potential to regulate the abundance and diversity of bacterial communities through infection. Soil is known to harbor abundant and diverse viral assemblages but their ecological role and influence on microbial processes has not been fully elucidated. Microbes can be influenced by viruses not only from infection but though biogeochemical feedbacks of the “microbial (bacterium–phage–DOC) loop” or “viral shunt”. However, we know relatively little about the microbial community and function under the regulation of viruses in soil and how they respond …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

Determining The Ecological And Physiological Factors Contributing To The Competitive Success Of Prochlorococcus In The Oligotrophic Ocean, Benjamin C. Calfee

Doctoral Dissertations

Prochlorococcus is a genus of extremely successful marine cyanobacteria. This success is realized through its pervasive biogeographical range and presence in almost all open ocean environments where it usually it the dominant phytoplankton. Limited capabilities of culturing and genetic manipulation of this organism have resulted in assumptions about this success overwhelmingly based on field observations. These studies have assumed adaptations for resource uptake and utilization in nutrient limited environments to cause dominance of Prochlorococcus over other photosynthetic microbes. In an attempt to definitively explain this through laboratory culture, we developed a culturing system to assay questions of nutrient limitation effects …

High Arctic Permafrost Microbial Characterizations: Siberian And Svalbard Microbiology Of Ancient And Active Layer Permafrost, Katie Sipes

Doctoral Dissertations

Permafrost is soil that has remained frozen for at least two years. The active layer is a surface portion above the permafrost that experiences seasonal thaw and refreezing. The environmental characteristics of permafrost and active layer are different but are directly related to each other. As the climate continues to warm, the active layer will expand into the permafrost and the continuously frozen soil will be subjected to seasonal thawing. The organisms that inhabit both the active layer and the permafrost soil will respond differently to the climate based on where in the soil they are present and the soil …

Quantification Of Soil Microbial Biomass In The Mcmurdo Dry Valleys, Antarctica, Emily Ruth Reynebeau

Biology ETDs

Quantifying microbial biomass is important for understanding microbial contribution to

nutrient cycling and population flux. Widely accepted biomass estimation methods are

sufficient for well-studied and high biomass systems, though are often not sensitive enough

for systems with extremely low biomass. The McMurdo Dry Valleys of Antarctica are

characterized as an extremely harsh environment with severe restrictions on life, with

perhaps some of the lowest biomass in the world. We measured prokaryote biomass across

Taylor and Wright Valleys using four estimation metrics to determine the most appropriate

method for this ecosystem. The chloroform fumigation method was not sensitive enough

for the …

Assessment Of Bacteriological Quality Of Drinking Water In Some Primary And Secondary Schools In Mukalla City-Hadhramout/Yemen, Eidha Ali Bin Hameed, Khaled Saleh Bin Alshikh Bubkr

Hadhramout University Journal of Natural & Applied Sciences

Assessment of faecal contamination and detection enumeration of coliforms and other microorganisms in water is one of the measurements to determine the hygienic quality of water. This study aimed to assess the drinking water in some primary and secondary schools in Mukalla city-Hadhramout/Yemen to estimate the bacterial contamination of drinking water and its safety to the public. The water samples were studied for bacteriological analysis in which was inoculated into culture media using two methods, the presumptive test for the most probable number (MPN) and confirmatory test for bacterial identification. Also, some physiochemical properties of water such as temperature, total …

Dietary Fiber Utilization In The Gut: The Role Of Human Gut Microbes In The Degradation And Consumption Of Xylose-Based Carbohydrates, Elizabeth Drey

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Xylans are a family of xylose-based polysaccharides naturally present in fruits, vegetables, and cereal grains. Resistant to digestion by host enzymes, xylans reach the large intestine intact, where they are utilized by members of the gut microbiome. They are initially hydrolyzed by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. These xylooligosaccharides (XOS) can then either be further hydrolyzed by primary degraders or can cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, studies have shown these species grow poorly on longer XOS and xylan substrates. In this thesis, …

Spotted Salamander Egg Masses Exhibit A Unique Internal Microbiome In Relation To Their Environment, Elizabeth Leonard

Senior Honors Theses

Microbial studies have led to various ecological and medicinal discoveries. Amphibian eggs, like those of Ambystoma maculatum, exhibit natural resistance to bacterial invasion that may be microbiome related. The purpose of this research was to sequence the external and internal microbiome of A. maculatum egg masses and compare with the environmental microbiome. It was hypothesized that the external and internal microbiome would bear more similarity to each other than the water. A significant difference was observed between the microbiome of the inside surface of the egg mass and the water but not the outside surface of the egg and …

Factors Affecting The Epizootics Of Entomopathogenic Fungi-A Review, Mirza Abdul Qayyum, Huda Bilal, Unsar Naeem Ullah:, Habib Ali, Hasnain Raza, Muhammad Wajid

Journal of Bioresource Management

Entomopathogenic fungi (EPF) specifically infect and kill insects can serve as a potential biological control agent. Several biotic and abiotic factors affect their occurrence, persistence, and epizootics caused by them. In biotic factors, fungi characters (host range, latency, spore density and dispersal, mainly host-pathogen compatibility), insect host factors (behavioral, morphological, and physiological), plant-mediated effects (plant architecture, surface chemistry, and leaf topology) are included supports or causes the barrier to mycobiopesticide. Abiotic factors which affect the EPF field persistence are mainly environmental (temperature, sunlight, humidity, rainfall) physical and chemical soil properties (soil texture, pH, E.c, moisture, C/N content, and organic matter) …

Plastic Biodegradation Through Insects And Their Symbionts Microbes: A Review, Huda Bilal, Hasnain Raza, Haseena Bibi, Tehmina Bibi

Journal of Bioresource Management

Plastic waste has recently been identified as one of the most serious environmental issues, affecting all life forms, natural habitats, and the economy, and is one of the most serious global environmental problems, second only to climate change. Seeking alternative environmentally sustainable options, such as biodegradation instead of conventional disposal, is critical in the face of this challenge. However, there is currently a lack of information about the mechanisms and efficacy of plastic biodegradation. From this perspective, this study aims to illustrate the negative environmental impacts of the plastic waste. It also addresses the role of insects and gut microbiota …

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has been widely …

The Effect Of Disturbance And Invasion On Fungal And Plant Communities Over An Elevational Gradient, Adam N. Trautwig

Doctoral Dissertations

High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also …

Response Of The Soil Bacterial Community, Resistome, And Mobilome To A Decade Of Macrolide Antibiotic Contamination, Liam Paul Brown

Electronic Thesis and Dissertation Repository

Biosolids (treated sewage sludge) are used as agricultural fertilizer but are frequently contaminated with macrolide antibiotics, to which resistance is rising among historically susceptible bacteria. To determine if the land-application of macrolides carried in biosolids could promote antibiotic resistance in soil bacteria, soil plots were exposed annually to environmentally realistic or high doses of macrolides for ten years. I sequenced the bacterial 16S ribosomal DNA, metagenomic DNA, and integron gene cassettes within the treated and antibiotic-free soil to compare the compositions and diversities of the bacterial communities, antibiotic resistance genes, and mobile genetic elements. I determined that the high dose …

Human Fecal Contamination Corresponds To Changes In The Freshwater Bacterial Communities Of A Large River Basin, Jill Mcclary-Gutierrez, Zac Driscoll, Cheryl Nenn

Freshwater Faculty Articles

Microbial water quality is generally monitored by culturable fecal indicator bacteria (FIB), which are intended to signal human health risk due to fecal pollution. However, FIB have limited utility in most urbanized watersheds as they do not discriminate among fecal pollution sources, tend to make up a small fraction of the total microbial community, and do not inform on pollution impacts on the native ecosystem. To move beyond these limitations, we assessed entire bacterial communities and investigated how bacterial diversity relates to traditional ecological and human health-relevant water quality indicators throughout the Milwaukee River Basin. Samples were collected from 16 …

A Novel Approach For Characterizing The Ultra-Micro Size-Fraction Community, Abdullah Ahmed Salim, Priscilla Nicole Pineda, Isabella Alamilla, Andrew Dean Putt

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

A Novel Approach for Characterizing the Ultra-Micro Size-Fraction Community

Students: Abdullah Salim, Priscilla Pineda, Isabella Alamilla

Mentors/Supervisors: Andrew Putt, Terry C. Hazen

ABSTRACT

The ultra-micro size-fraction (UMSF) are bacteria that can pass through the 0.2 µm pore membrane filters employed in environmental surveys. Despite being ubiquitous and having high metabolic activity, UMSF remain elusive and largely uncultured. Investigations of UMSF are skewed by difficulties in culturing and a lack of techniques for measuring UMSF biogeochemical signatures. This study measures surface stream UMSF community diversity, and community response to the addition of the synthetic pharmaceutical and cosmetic carbon product cyclodextrin which …

Extracellular Polymeric Substances In Oxygenic Photogranules: Investigation Of Their Role In Photogranulation In A Hydrostatic Environment, Wenye Camilla Kuo-Dahab

Doctoral Dissertations

The purpose of this dissertation was to assess the critical role of extracellular polymeric substances (EPS) in the photogranulation of activated sludge, in a hydrostatic environment. The first section evaluates the fate and dynamics of different fractions of EPS in sludge-based photogranulation under hydrostatic conditions. The study shows that during the transformation of activated sludge into a photogranular biomass, sludge’s base-extractable proteins selectively degrade. Strong correlations between base-extracted proteins and the growth of chlorophyll a and chlorophyll a/b ratio suggest that the bioavailability of this organic nitrogen is linked with selection and enrichment of filamentous cyanobacteria under hydrostatic conditions. The …

Soil Bacteria: Metabolic Diversity In A Wildlife Management Area, Nicholas Green

Symposium of Student Scholars

This research is part of a larger study linking the soil microbiome and processes to the aboveground plant community.

Soil samples were collected from six plots under closed canopy in the Sheffield Wildlife management area in the Piedmont ecoregion of Georgia in Paulding County. Two of the plots were located in the longleaf pine savanna where restoration of longleaf pine has been in place since 2010. Samples were collected in sterile plastic tubes at the center of each plot and 10 meters above and below the center. For each sample, soil pH and the concentration of nitrogen (N), phosphorus (P), …

Glide Another Day: Characterization Of Wild Isolates Of Predatory Myxobacteria, Daniella Krakue, Juan Vasquez, Simone Dakare

Symposium of Student Scholars

Myxobacteria belongs to a group of predatory bacteria that are found in various soil environments. They are exceptionally unique microbes who use their gliding motility to move towards prey microbes and consume them. They also have the remarkable ability to produce secondary metabolites that have antibacterial, antifungal, antiviral, and antitumor properties. For this reason, they are of interest to us so that we can understand their abilities and apply them to discover their potential as a source of novel metabolites with potential therapeutic applications. Our methodology began by collecting soil samples from various sites around the country. We then standardized …

Community Level Physiological Profiling Of The Longleaf Pine Savannah Microbiome, Gavin Treadaway

Symposium of Student Scholars

Soil microorganisms secrete chemicals into their surroundings, which the root system will uptake and in return release root exudates, which usually consist of low-molecular-weight organic compounds. These root exudates behave as signaling molecules and substrates for microorganisms to recruit beneficial soil bacteria to the plant root system, which will provide the plants with immunity to foliar diseases and pathogen infection. Studies have shown that bacteria on the root surface can protect aerial sections of the plant by promoting induced systemic resistance, a mechanism of increasing physical or chemical barriers of the plant.

The longleaf pine is an endangered species of …

Insights Into Halophilic Microbial Adaptation: Analysis Of Integrons And Associated Genomic Structures And Characterization Of A Nitrilase In Hypersaline Environments, Sarah Sonbol

Theses and Dissertations

Hypersaline environments are extreme habitats that can be exploited as biotechnological resources. Here, we characterized a nitrilase (NitraS-ATII) isolated from Atlantis II Deep brine pool. It showed higher thermal stability and heavy metal tolerance compared to a closely related nitrilase.

We also studied integrons in halophiles and hypersaline environments. Integrons are genetic platforms in which an integron integrase (IntI) mediates the excision and integration of gene cassettes at specific recombination sites. In order to search for integrons in halophiles and hypersaline metagenomes, we used a PCR-based approach, in addition to different bioinformatics tools, mainly IntegronFinder.

We found that integrons and …

Microbial Innovations For Disease Management In Honey Bees, Brendan A. Daisley

Electronic Thesis and Dissertation Repository

Arguably the most important insect pollinator, honey bees (Apis mellifera) are threatened by infectious disease, pesticide exposure, and nutritional deficits resulting from habitat loss.

The major goals of this thesis were to advance our understanding of the immune and microbiota factors underpinning synergistic interactions between the threats, and to develop a honey bee-specific probiotic with strain-level functions to alleviate cumulative stress burden.

Drosophila melanogaster was used as a high-throughput discovery platform in molecularly characterizing the effects of candidate probiotic lactobacilli and neonicotinoid-neuroimmune-microbiota mechanisms prior to experimentation in honey bees. Imd pathway activation by lactobacilli was identified to be …

Comparative Microbiome Analysis Of The Funfus Gardening Ant Species Trachymyrmex Arizonensis, Chase D. Rowan

Biology Theses

Fungus-growing ants (Attini: Formicidae) and their fungal cultivars participate in ant-fungus mutualism that share a 50-million-year-old coevolutionary history. Fungal cultures are grown in gardens alongside ants and a diverse collection of microbes that interact with both species in mutualistic, commensal, and antagonistic relationships. These microbes aid in digestion and detoxification of food, provide essential nutrients, help in nest hygiene, and play a dominant role in defense against pathogens and disease. Microbial communities of many model species have been shown to change in a laboratory setting as compared to their natural environment. High-throughput 16s sequencing of the V4 variable region was …