Genomics Commons^™

Characterization Of Bacterial Communities In Biscayne Bay Through Genomic Analysis, Eric Fortman

HCNSO Student Theses and Dissertations

Biscayne Bay is a shallow oligotrophic estuary in Southeast Florida. Channelization of rivers, and dredging of canals has greatly altered the historical flow of fresh water into the bay. This, coupled with the rise of a sprawling urban & suburban development, has greatly increased the nutrient load in the bay. This study examined the bacterial community at 14 stations throughout Biscayne Bay —6 stations were located at the mouths of canals; 1 upstream-canal station; 6 stations in the center of the bay; and one ocean influenced station, located near the entrance to the bay. One liter, surface water samples were …

Inferred Function And Dynamics Of Microbial Communities From The Northern Gulf Of Mexico, Deepesh Tourani

HCNSO Student Theses and Dissertations

Microbial communities, or microbiomes, are the major drivers of global biogeochemical cycles, acting as primary producers and decomposers across the water column in the oceans. Thus, they reflect changes in physicochemical properties and nutrient composition of the ocean. However, this correlation between ecological changes and the function of marine microbiomes is poorly understood. Large-scale oceanic events such as the bottom-water oxygen-depleted zone (i.e., “dead zone”) and the Deepwater Horizon oil spill in the Gulf of Mexico (GoM) render the ecosystem fragile. These events decrease survival rates of pelagic and coastal macrofauna and affect the biodiversity of the region. As part …

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to …

Isolation Of Caldatribacterium (Op9) And Investigation Of Its Potential Interactions With A Novel, Co-Cultivated Thermodesulfobacterium Species, Toshio Alvarado

Electronic Theses, Projects, and Dissertations

Atribacteria (OP9), candidate phylum with no representatives in pure culture, is found in various anaerobic environments worldwide. “Caldatribacterium”, a lineage within Atribacteria that is predicted to be a strictly anaerobic sugar fermenter based on cultivation-independent genomic analyses, is currently being maintained in lab enrichment cultures with fucose as its sole growth substrate. Metagenomics and 16S rRNA gene tag sequencing indicated that the fucose culture was a co-culture of “Caldatribacterium” and an uncultivated member of the genus Thermodesulfobacterium. Due to failed attempts to isolate “Caldatribacterium” by dilution-to-extinction and plating, it was hypothesized that “Caldatribacterium” is dependent in some way on the …

Using Single-Cell Sorting, Fish And 13c-Labeling To Cultivate And Assess Carbon Substrate Utilization Of ‘Aigarchaeota’ And Other Novel Thermophiles, Damon Kurtis Mosier

Electronic Theses, Projects, and Dissertations

‘Aigarchaeota’, a deeply branching lineage in the domain Archaea with no cultivated representatives, includes both thermophilic and hyperthermophilic microorganisms that reside in terrestrial and marine geothermal environments. The ‘Aigarchaeota’ consists of at least nine proposed genus-level groups that have been confirmed via 16S rRNA sequencing, with ‘Aigarchaeota’ Group 1 (AigG1) being the focus of this study. Based on cultivation-independent genomic data available from several AigG1 members in Great Boiling Spring (GBS), NV, and Yellowstone National Park, 22 different types of growth media were designed and tested for their ability to support growth of AigG1. One of these cultures, G1-10, was …

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 …

Ultramicrobacteria Genome Database Project, Abdullah A. Salim, Tien Tran, Andrew Putt, Terry C. Hazen

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Ultramicrobacteria (UMB) are a largely uncultured, globally abundant, and metabolically active group of bacteria. UMB have cell diameters ≤0.3μm, cell volumes ≤0.1 μm3, and small streamlined genomes. Recent findings indicate that UMB aid in bioremediation and nutrient cycling, but future investigations and comprehension of current findings are skewed by highly variable nomenclature and a lack of databases for functional, genomic, geochemical, or spatial data specific to candidate UMB. We aim to develop a user-friendly open-access database of various UMB candidates linked to an open-access online map where researchers can gather genomic, spatial, and geochemical data. Our comprehensive review of literature …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Characterization Of Immunomodulatory Microbial Factors In Medicinal Plants, Kriti Kalpana

Dissertations, Theses, and Capstone Projects

Medicinal plants are one of the biggest sources of natural products with therapeutic importance. There are currently over 28,000 plants with putative medicinal values. Plant-derived compounds have been explored extensively for various biological activities ranging from anti-cancer, immune-boosting to anti-inflammatory and anti-oxidant. Some of the most important therapeutic agents are of plant-origin, such as paclitaxel from Pacific yew (Taxus brevifolia) and artemisinin from qinghao su (a Chinese medicinal herb; a.k.a. Artemisia annua) to name a few.

The study presented in this thesis started out as classical pharmacognosy research, which focused on the identification of immunostimulatory factors in …

Impact Of Industrial Biocides On Bacterial Isolates From Hydraulic Fracturing Produced Water, Waad Ahmed Aljohani

Dissertations, Master's Theses and Master's Reports

Biocides are antimicrobial compounds that are designed to kill diverse groups of microbes in an untargeted fashion. Glutaraldehyde and DBNPA are commonly used to manage microbial growth in different industries. It is possible that biocide use may result in the development of bacterial resistance. However, resistance to DBNPA is believed to be limited under normal use conditions. We isolated a number of bacteria from produced water from a hydraulically fractured site in West Texas. We then tested the ability of these isolates to resist Glutaraldehyde and DBNPA. In this study, we found that these isolates have varying resistance to these …