Environmental Microbiology and Microbial Ecology Commons^™

Cross-Kingdom Interactions Shape Soil Biogeochemistry In Natural And Agricultural Ecosystems, Jennifer Lynne Kane

Graduate Theses, Dissertations, and Problem Reports (ETD)

Microorganisms influence life on earth in innumerable ways, including in medical, industrial, environmental, and agricultural contexts. Given the increasingly apparent consequences of climate warming, interest in how to better predict and manage Earth’s carbon sinks has never been greater. Soil, the largest terrestrial carbon sink, harbors an incredibly taxonomically and functionally diverse microbial community. These soil-dwelling microbes govern the fate of soil carbon and nutrients by cycling organic matter as they live, grow, and die. It has only been relatively recently that technological advancement has allowed for in-depth surveys of the vast diversity of soil microbes. High throughput analytical capabilities …

Defining The Realized Niche Of The Two Major Clades Of Trichodesmium: A Study On The West Florida Shelf, Kristina A. Confesor, Corday R. Selden, Kimberly E. Powell, Laura A. Donahue, Travis Mellett, Salvatore Caprara, Angela N. Knapp, Kristen N. Buck, P. Dreux Chappell

OES Faculty Publications

The cyanobacterium Trichodesmium plays an essential role supporting ocean productivity by relieving nitrogen limitation via dinitrogen (N-2) fixation. The two common Trichodesmium clades, T. erythraeum and T. thiebautii, are both observed in waters along the West Florida Shelf (WFS). We hypothesized that these taxa occupy distinct realized niches, where T. thiebautii is the more oceanic clade. Samples for DNA and water chemistry analyses were collected on three separate WFS expeditions (2015, 2018, and 2019) spanning multiple seasons; abundances of the single copy housekeeping gene rnpB from both clades were enumerated via quantitative PCR. We conducted a suite of statistical …

Evidence For Metabolic Diversity In Meso-Neoproterozoic Stromatolites (Vazante Group, Brazil), Flavia Callefo, Fresia Ricardi-Branco, Mirian Mírian Liza Alves Forancelli Pacheco, Alexandre Ribeiro Cardoso, Nora Noffke, Verônica De Carvalho Teixeira, Itamar Tomio Neckel, Lara Maldanis, Emma Bullock, Dina Bower, Adalene Moreira Silva, Dario Ferreira Sanchez, Fabio Rodrigues, Douglas Galante

OES Faculty Publications

Deciphering the evolution of ecological interactions among the metabolic types during the early diversification of life on Earth is crucial for our understanding of the ancient biosphere. The stromatolites from the genus Conophyton cylindricus represent a datum for the Proterozoic (Meso to Neoproterozoic) on Earth. Their typical conical shape has been considered a result of a competition between microorganisms for space, light and nutrients. Well-preserved records of this genus from the "Paleontological Site of Cabeludo ", Vazante Group, São Francisco Craton (Southern Brazil) present in situ fossilized biofilms, containing preserved carbonaceous matter. Petrographic and geochemical analyses revealed an alternation between …

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 …

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 …

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 …

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. …

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 …

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 …

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. …

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 …

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 …

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, …

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 …

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 …