Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands,
2022
University of Nebraska - Lincoln
Genomic Analysis Of Acetoanaerobium Sp. Vlb-1, An Anaerobic Bacterium Isolated From Nebraska's Eastern Saline Wetlands, Claire Martin
Honors Program: Senior Projects (Public)
Through the analysis of genetic code, the genomic and physiological characteristics of an environmental anaerobic bacterial isolate, Acetoanaerobium sp. strain VLB-1, can be determined and significant pathways can be identified in its significance to the environment. This particular organism was isolated from the Eastern Saline Wetlands in Lincoln, NE. With this isolate, an investigation into elemental and amino acid cycling via the Stickland reaction and the Wood-Ljungdahl pathway was conducted to determine possible metabolic products. The Stickland reaction is a relatively newly discovered pathway, observed in the genus Clostridium. A. sticklandii is the main model for this method of …
Microbial Communities And Nitrogen Dynamics In Prairie And Cropland Soils,
2022
South Dakota State University
Microbial Communities And Nitrogen Dynamics In Prairie And Cropland Soils, Bikram Kumar Das
Electronic Theses and Dissertations
Soil microbial communities are affected by many factors, such as soil nitrogen (N) and the quantity of grass-root exudates, changing seasons, fertilization method, plant diversity, and their origin. This holds for both natural and fertilized soils. This research was intended to expand the current understanding of soil microbial interactions associated with ecological functions. The objectives of the research were (I) to characterize prokaryotic soil communities, estimate functional potential, and quantify nitrogen cycle-associated prokaryotic gene expressions across three phases of the growing season, (II) to explore the diazotrophic community composition in a natural system using nifH sequencing as well as 16S …
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy,
2022
University of Montana, Missoula
An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont
Graduate Student Theses, Dissertations, & Professional Papers
Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning,
2022
Michigan Technological University
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning, Isaac Bigcraft
Dissertations, Master's Theses and Master's Reports
Carbon monoxide is well known as a toxic gas but can also be an important input and intermediary for microbial metabolisms. Carbon monoxide dehydrogenases (CODHs) serve as key enzyme complexes for a variety of microbial carbon monoxide (CO) utilization pathways. Such pathways include the Wood-Ljungdahl pathway, which is important in methanogenesis and acetogenesis, metal and sulfate reduction pathways, hydrogen production, and others. The CODH enzymes allow microbes to turn the traditionally toxic waste gas of CO into a useful carbon and energy source. Despite the flexibility of CODH enzymes, the use of carbon monoxide is still believed to be a …
Biodegradation Of Rubber Particles In Soil: Using Acclimated Bacteria Isolated From Kansas Soil To Degrade Cryogrinds In Slurry,
2022
The University of Akron
Biodegradation Of Rubber Particles In Soil: Using Acclimated Bacteria Isolated From Kansas Soil To Degrade Cryogrinds In Slurry, Shane Graham
Williams Honors College, Honors Research Projects
This study investigated the viability of bioremediating rubber cryogrind using enriched indigenous bacteria. To begin the experiment, soils from three highway roadside locations in Kansas, KS 96 and West, KS 400 and 143rd, and 199th, were collected and transported to the lab to be studied. An initial soil characterization was run on the soil samples using distilled (DI) water mixture and 0.01 M CaCl2 to assess conductivity. The soils were tested to gather a baseline of the relationship between pH and conductivity and the impact of its distance from the roadside. Bacteria were isolated from …
The Influence Of Hydrogen Peroxide On The Enrichment Of Fe(Iii) Reducing Bacteria From Acid Mine Drainage,
2022
The University of Akron
The Influence Of Hydrogen Peroxide On The Enrichment Of Fe(Iii) Reducing Bacteria From Acid Mine Drainage, Susami Seth
Williams Honors College, Honors Research Projects
It is hypothesized that the ocean of Europa, a Jupiter moon, hosts bacteria on its oceanic floor. Understanding how Fe(III) reducing bacteria (FeRB) from AMD utilize organic materials within its surrounding environment outlines how FeRB could thrive and tolerate extreme conditions. FeRB are known to tolerate metals and highly reactive oxidants species (ROS), but in this experiment, H2O2 was the experimental factor to further test FeRB tolerance. H2O2 is a common ROS and is damaging to living material such as proteins, DNA, and RNA. A range of H2O2 concentrations were fed …
Defining The Realized Niche Of The Two Major Clades Of Trichodesmium: A Study On The West Florida Shelf,
2022
Old Dominion University
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),
2022
Old Dominion University
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 …
Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest,
2022
Scripps College
Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns
Scripps Senior Theses
Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.
Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois,
2022
Scripps College
Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns
Scripps Senior Theses
This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …
Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica,
2022
Humboldt State University
Degradation And Nitrogen Cycling In The Context Of Biodiversity-Ecosystem Function Relationships In The Inquiline Bacterial Community Of Darlingtonia Californica, Megan Teigen
Cal Poly Humboldt theses and projects
Biodiversity-ecosystem function (BEF) research aims to explain how species and their environments interact with each other. Microbial communities engage in vital biogeochemical pathways in a variety of natural ecosystems, and yet there are large knowledge gaps about the specific metabolic pathways in which they are involved. Degradation specifically contributes to nitrogen cycling globally through the breakdown of large organic nitrogen compounds into small inorganic nitrogen that is necessary for the survival of many other organisms. In this study, I focused on the degradative function of the inquiline microbial communities found within the carnivorous pitcher plant, Darlingtonia californica. Darlingtonia grows in …
Cross-Kingdom Interactions Shape Soil Biogeochemistry In Natural And Agricultural Ecosystems,
2022
West Virginia University
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 …
Anthropogenic Disturbance Regimes Impact The Microbial And Chemical Composition Of Soils And Sediments Across Ecosystems,
2022
West Virginia University
Anthropogenic Disturbance Regimes Impact The Microbial And Chemical Composition Of Soils And Sediments Across Ecosystems, Gregory D. Martin
Graduate Theses, Dissertations, and Problem Reports (ETD)
Human activities have led to profound changes in the climate and environment, fundamentally changing global carbon and nitrogen cycles. Ongoing conversion of wildland for human use and the intensification of agricultural systems have dire consequences for biodiversity and the ecosystem services that support society. While natural disturbance regimes are important for the long-term maintenance of native biodiversity and ecosystem function, many disturbances are becoming increasingly frequent due to anthropogenic activities. Increasing the frequency, intensity, or duration of disturbances can prevent ecosystems from returning to their previous equilibria. Disturbance-induced changes to the local environment shape microbial communities, which in turn govern …
A Mathematical Model For Transport And Growth Of Microbes In Unsaturated Porous Soil,
2021
Embry-Riddle Aeronautical University
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),
2021
Nerja Cave Research Institute, Spain
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/Fm′) and relative electron transport rate (rETR) were determined during periods of the light, whereas the maximal quantum yield (Fv /Fm) was determined during dark periods. Increases in …
Farnesol Secretion As A Possible Driving Force For Maintaining Candida Albicans As A Diploid,
2021
University of Nebraska - Lincoln
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,
2021
Georgia College
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,
2021
University of Nebraska-Lincoln
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,
2021
Nova Southeastern University
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,
2021
Zhejiang University
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 …
