Life Sciences Commons^™

Opening The Black Box: Soil Microbial Communities In Field-Based Plant-Soil Feedback Experiments, Julia Kate Aaronson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Plant-soil feedback is a process through which plants modify the properties of their associated soils, affecting their growth. PSF can play a key role in regulating plant growth and communities including altering plant invasion, rarity, and abundance. However, our understanding of the soil organisms that drive these plant growth responses is limited. Most studies treat soils as a ‘black box’ and do little to reveal which specific microbes or microbial communities may be responsible. This chapter examines two recent large PSF field experiments conducted in Minnesota, USA, and Jena, Germany. These experiments revealed that plants altered their soils, changing subsequent …

Antimicrobial Assay Of Sagebrush Roots, Lauren Rachel (Moody) Mcfadden

Undergraduate Honors Capstone Projects

Plants produce secondary metabolites for various functions, one of which is antibacterial activities. Sagebrush has historically been used by Native Americans for different medicinal purposes, suggesting that it may have secondary metabolites that would have medicinal values, including antimicrobial activities, and can be a natural source for antibiotics. This study aims to carry out the antimicrobial activity of Sagebrush root extract against a handful of bacteria. We tested the antimicrobial activity of root extract of Sagebrush against six bacteria such as Bacillus subtilis, Bacillus cereus, E. coli DHSα (Lab cloning strain), Agrobacterium tumefaciens GV3101 (Lab cloning strain), Pseudomonas …

Halotolerant Rhizosphere Bacteria: Isolation Of Rhizosphere Bacteria From Native Utah Plant Ceanothus Velutinus, Alyssa Nielsen

Fall Student Research Symposium 2021

Increasing incidences of drought forced farmers to use the secondary, degraded water for irrigation. These water sources are rich in salt concentrations. This project has started with the hopes of finding bacteria from the rhizosphere of a native to Utah plant, Ceanothus velutinus, that helps the plant survive the saltier conditions of Utah. The rhizosphere, a layer of soil attached to the roots of a plant, contains microorganisms that may contribute to the plants' abiotic and biotic stress resistance. These microorganisms are known as Plant Growth Promoting Rhizobacteria (PGPR). The roots and rhizosphere samples were collected from Tony Grove in …

Discovering Virally Encoded Proteins That Block Type Iv Crispr Immune Systems, Andrew Williams

Fall Student Research Symposium 2021

Bacteria and the viruses that infect them have been at war from the beginnings of life until today. Due to selective pressure from viral infection, bacteria have evolved various biological defense systems, including CRISPR-Cas systems that use a genetic memory of previous viral encounters to protect against future invasions. However, recently it has been shown that viruses have evolved counter-strategies to evade CRISPR systems. Virally encoded proteins called anti-CRISPRs use a variety of mechanisms to block the activity of CRISPR immune systems in order to infect bacterial cells. The Jackson lab at USU recently showed that a Type IV-A CRISPR-Cas …

Determination Of The Structure, Function, And Mechanism Of Type Iv Crispr-Cas Prokaryotic Defense Systems, Hannah Nicole Taylor

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria are under constant threat of invasion by bacteriophage (viruses which infect bacteria). To prevent bacteriophage from entering and overtaking the bacteria, bacteria utilize defense systems to identify and destroy foreign elements. One method of defense is called CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR-Associated). Many different bacteria and most archaea use CRISPR-Cas systems. There are many diverse types of CRISPR-Cas systems, each of which provides defense in a slightly different way. One such CRISPR-Cas type is called type IV. The type IV CRISPR-Cas system is poorly understood and there are very few studies published on type IV …

Sickness Behaviors Across Vertebrate Taxa: Proximate And Ultimate Mechanisms, Patricia C. Lopes, Susannah S. French, Douglas C. Woodhams, Sandra A. Binning

Biology Faculty Publications

There is nothing like a pandemic to get the world thinking about how infectious diseases affect individual behavior. In this respect, sick animals can behave in ways that are dramatically different from healthy animals: altered social interactions and changes to patterns of eating and drinking are all hallmarks of sickness. As a result, behavioral changes associated with inflammatory responses (i.e. sickness behaviors) have important implications for disease spread by affecting contacts with others and with common resources, including water and/or sleeping sites. In this Review, we summarize the behavioral modifications, including changes to thermoregulatory behaviors, known to occur in vertebrates …

Isolation & Identification Of Bacteria From The Rhizosphere Of Native Plant, Ceanothus Velutinus, And Their Potential As Biofertilizers, Katherine Webb, Hayden Johns

Student Research Symposium

Due to the ever-changing climate, plants face stressors that limit their growth. Therefore it is vital to find new ways to protect plants from biotic and abiotic stressors such as pathogen infection, drought, heavy metal poisoning, and salinity. With an increasing population, limiting the effects of stress on plant growth and development for agriculture is vital. One approach to this is focusing on beneficial plant-microbe interaction, such as plant growth-promoting rhizobacteria (PGPR). These bacteria are found in the rhizosphere- the soil that is attached to the roots of a plant. Various PGPRs share a symbiotic relationship with plants and help …

Translating -Omics Big Data: Comprehensive Understanding Of Host-Pathogen Interactions To Control Bacterial Blight In Alfalfa Using Computational Approaches, Raghav Kataria

Student Research Symposium

Plant infectious diseases are a major threat to the crops, owing to economic losses to the agriculture industry worldwide. Molecular interactions between the host and pathogen play a critical role in understanding the basis of pathogenesis. Majority of the Pseudomonas syringae strains are known to cause frost injury in plants, amongst which, P. syringae pv. syringae ALF3 is asserted to be a causal organism of bacterial stem blight in Medicago sativa (alfalfa). We elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two intense computational approaches: interolog (homology-based) and the domain-based method (based on 3D structure of …

Isolation Of Halotolerant Bacteria From The Rhizosphere Of Ceanothus Velutinus May Lead To Contributions In Plant Health In Saline Conditions, Jacob Davis

Student Research Symposium

As global temperatures have been steadily rising in the past few decades, soil salinity has been steadily increasing in many parts of the world as well. This increase in salinity has proven detrimental and especially challenging for many plant species. The soil directly in contact with the roots of plants is known as the rhizosphere. The rhizosphere hosts plant growth-promoting rhizobacteria (PGPR). PGPR plays a significant role in a plant's ability to deal with stressors such as drought, heavy metal contamination, and extreme cold temperatures. Native plants are known to show versatility to these stressors as well. One such native …

Anthropogenic Influences On Bacterial Assemblages In Stream Biofilms, Elizabeth M. Ogata

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Bacteria within biofilms are an essential component of stream ecosystems, influencing the movement of carbon (C), nitrogen (N), and phosphorus (P) in watersheds. To better understand the ecological effects of human activities on stream ecosystems, my research examined how nutrients and pharmaceuticals, common pollutants in streams worldwide, influence bacterial assemblages in stream biofilms. First, I tested how nutrients (N, P, iron) and pharmaceuticals (caffeine, diphenhydramine) influenced biofilm bacterial microbiomes (taxa present in at least 75% of samples of a contaminant treatment). Nutrients allowed taxa known for their ability to thrive in nutrient-rich environments to dominate microbiomes, pharmaceuticals supported a rich …

Fermentation Of Prebiotics In Whole Food Powders By Probiotic Bacteria Strains, Michaela Brubaker, Sumira Phatak

Research on Capitol Hill

Colorectal cancer (CRC) is the second leading cause of cancer death in the United States. Modification of the gut microbiome offers potential for CRC prevention.

Genetic Sequencing Using 16s Rrna For Pathogen Identification In Retropharyngeal Lymph Nodes From Wild Elk, David J. Wilson, Jacqueline P. Kurz

Human–Wildlife Interactions

Cervical region lymph nodes collected by hunters from 43 wild hunter-harvested elk (Cervus elaphus) in Utah were submitted to the Utah Veterinary Diagnostic Laboratory during fall 2009. We evaluated these lymph nodes as specimens for identification of bacterial pathogens using 16S rRNA genetic sequencing. Thirty-seven bacterial species were identified; each was found in 2 to 30 individual elk. Many common ruminant livestock pathogens were identified in elk; pathogens previously reported in elk were Pasteurella multocida and Streptococcus spp. Cervical region lymph nodes harvested from wild ruminants appear to be acceptable samples for genetic sequencing of bacteria.

The Effect Of Pure Infrared Light On The Growth Of Rhodospirrilum Rubrum, Jordan Lee Wilkes

Undergraduate Honors Capstone Projects

Scientists who study aquatic ecosystems quickly notice a diversity of pathways that different microbes and organisms can use to metabolize nutrients found in common ponds or pools. Competition for vital resources, such as light and inorganic minerals, allow only certain organisms to grow in certain niches within these ecosystems. Rhodospirillum rubrum is a gram negative, photosynthetic bacteria that competes for light within aquatic ecosystems in order to survive. R. rubrum is believed to specifically absorb light for photosynthesis at wavelengths in the range of infrared light. It was found that R. rubrum indeed can grow in "dark", anaerobic environments by …

Growth And Gas Production Of A Novel Obligatory Heterofermentative Cheddar Cheese Nonstarter Lactobacilli Species On Ribose And Galactose, Western Dairy Center, Utah State University, Megan Jane Ostler, Jeff Broadbent, Craig J. Oberg, Donald J. Mcmahon

Nutrition, Dietetics, and Food Sciences Faculty Publications

An obligatory heterofermentative lactic acid bacterium, Lactobacillus wasatchii sp. nov., isolated from gassy Cheddar cheese was studied for growth, gas formation, salt tolerance, and survival against pasteurization treatments at 63°C and 72°C. Initially, Lb. wasatchii was thought to use only ribose as a sugar source and we were interested in whether it could also utilize galactose. We conducted experiments to determine the rate and extent of growth and gas production in carbohydraterestricted (CR) de Man, Rogosa, and Sharpe (MRS) medium under anaerobic conditions with various combinations of ribose and galactose at 12, 23, and 37°C, with 23°C being the optimum …

Use Of Fourier Transform Infrared Spectroscopy For The Classification And Identification Of Bacteria Of Importance To The Food Industry, Sarah Pegram

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The aim of this work was to use Fourier Transform Infrared Spectroscopy to characterize and identify bacteria of particular significance to the food industry. FT-IR spectroscopy is a rapid technique that can be applied to all groups of bacteria. The two objectives were to determine a suitable sampling procedure to record a spectrum and to determine a suitable statistical technique to identify characteristic regions of the spectrum associated with the genus and, potentially, the species. Pure cultures of bacteria were grown in broth, suspended in saline and dried to produce a film on a halide salt crystal. These films were …

Physiological And Biochemical Aspects Of Agrobacterium-Wheat (Triticum Aestivum L.) Interactions, David L. Parrott Jr.

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Agrobacterium tumefaciens and A. rhizogenes are the causal agents of gall or hairy root disease, but normally the bacteria do not cause disease in wheat. However, both bacteria grew without inhibition when exposed to intact or wounded wheat roots or embryos, and they colonized wheat root surfaces to levels similar to dicotyledonous plants. A. tumefaciens and A. rhizogenes induced 23% cell death after a 1-h exposure to wheat embryo cells grown in 7.4 mM O₂, while the extent of cell death at 2.1 mM O₂ was 8%. Contact with A. tumefaciens or A. rhizogenes caused cultured wheat …

How Do I Keep Bacteria Out Of My Food Preparation Areas?, Charlotte Brennand

All Archived Publications

No abstract provided.

You Have The Power To Fight Bac!, Unknown Unknown

All Current Publications

No abstract provided.

Toxicity Of Aspen Wood Leachate To Aquatic Life: Laboratory Studies, Barry R. Taylor, J. Stephen Goudey, N. Bruce Carmichael

Aspen Bibliography

Trembling aspen (Populus tremuloides Michx.), a common hardwood tree throughout Canada, is being harvested at increasing rates for use in paper and building materials. Piles of aspen logs have been observed to produce a dark, watery, acutely toxic leachate. A laboratory study was undertaken to elucidate the nature, strength, and persistence of aspen leachate toxicity and the chemical composition of the leachate. Leaching from aspen chips in the laboratory was rapid, with 1% mass loss in the first 24 h. Another 2 weeks of immersion was necessary to remove all remaining leachable material (3% total)> Fresh aspen leachate derived …

Mechanisms For Soil Moisture Effects On Activity Of Nitrifying Bacteria, John M. Stark, M. K. Firestone

Biology Faculty Publications

Moisture may limit microbial activity in a wide range of environments including salt water, food, wood, biofilms, and soils. Low water availability can inhibit microbial activity by lowering intracellular water potential and thus reducing hydration and activity of enzymes. In solid matrices, low water content may also reduce microbial activity by restricting substrate supply. As pores within solid matrices drain and water films coating surfaces become thinner, diffusion path lengths become more tortuous, and the rate of substrate diffusion to microbial cells declines. We used two independent techniques to evaluate the relative importance of cytoplasmic dehydration versus diffusional limitations in …

Mechanisms For Soil Moisture Effects On Activity Of Nitrifying Bacteria, John M. Stark, M. K. Firestone

John M. Stark

Moisture may limit microbial activity in a wide range of environments including salt water, food, wood, biofilms, and soils. Low water availability can inhibit microbial activity by lowering intracellular water potential and thus reducing hydration and activity of enzymes. In solid matrices, low water content may also reduce microbial activity by restricting substrate supply. As pores within solid matrices drain and water films coating surfaces become thinner, diffusion path lengths become more tortuous, and the rate of substrate diffusion to microbial cells declines. We used two independent techniques to evaluate the relative importance of cytoplasmic dehydration versus diffusional limitations in …

Identification Of Potential Adhesins Shared Among Isolates Of Actinobacillus Species And Actinobacillus-Like Bacteria Cultured From Ram Lambs With Clinical Epididymitis, Yu-Wen Liu

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Ram lamb epididymitis, a serious reproductive disease of sheep, is caused principally by bacteria belonging to the genera Haemophilus and Actinobacillus. Six bacteria were studied: the American Type Culture Collection (ATCC) of Actinobacillus seminis (ATCC 15768), ATCC of Actinobacillus actinomycetemcomitans (ATCC 29522), field isolates of A seminis (86722 and 4101) and field isolates of Actin obacillus- like bacteria (Y136 and D107). The objectives of this study were to quantitate the adhesion of these 6 bacteria to bovine kidney epithelial cells (BKECs) and ram epididymal epithelial cells (REECs), evaluate the effect of rabbit polyclonal antibody prepared against ATCC 15768 …

Changes In The Rheology And Microstructure Of Ropy Yogurt During Shearing, J. A. Teggatz, H. A. Morris

Food Structure

Rheological and microstructural changes that occurred in ropy yogurt during shearing were observed. Yogurt made with an exopolymer-producing (ropy) strain of Lactobacillus delbrueckii subsp. bulgaricus and non-ropy strain of Streptococcus thermophilus was subjected to an increasing shear rate from 0-833 s-1 using a Haake Rotovisco RV2. Shear stress niticeably increased to a peak value and then decreased to a plateau value as the shear rate continued to increase. Samples taken at eight different shear rates were examined by scanning electron microscopy (SEM). At low shear rates, the exopolysaccharide (EPS) existed as a filamentous network attached to the lactobacilli and casein …

Microbiological Immunocytochemistry: A Review Of Current Trends And Applications, Julian E. Beesley

Scanning Microscopy

It has been considered worthwhile to update previous reviews of microbiological immunocytochemistry in order to identify areas of current importance in this continually expanding area of research. Publications in virology, bacteriology and protozoology indicate a continued interest in immunocytochemistry. Deployment of colloidal gold techniques is almost universal in these applications. The post-embedding technique was the most widely applied technique although a few studies employed the immunonegative stain, pre-embedding and immunoreplica techniques, thereby reflecting the use of colloidal gold in all other areas of the biological sciences.

Effect Of Bacterial Inoculant On Alfalfa Haylage: Ensiling Characteristics And Milk Production Response When Fed To Dairy Cows In Early Lactation, Barb Kent

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Third-cutting alfalfa hay harvested at bud stage in each of 2 yrs, treated with a live bacterial inoculant, packed in polyethylene-bonded bags and allowed to ensile. In both years, treated haylage had a lower pH, and a period effect was found for pH and mold count, regardless of treatment. In year 1, there was a period effect found for acid detergent fiber. In year 2, mean lactic-acid-producing bacteria numbers (log 10) were significantly higher for treated haylage (9.69 and 10.36) for control and treated haylage, respectively). Regardless of treatment, lactic-acid-producing bacteria numbers and water soluble carbohydrates significantly declined through time. …

Preparation Of Biological Samples For Transmission X-Ray Microanalysis: A Review Of Alternative Procedures To The Use Of Sectioned Material, D. C. Sigee

Scanning Microscopy

Although transmission X-ray microanalysis of biological material has traditionally been carried out mainly on sectioned preparations, a number of alternative procedures exist. These are considered under three major headings - whole cell preparations, analysis of cell homogenates and biological fluids, and applications of the technique to microsamples of purified biochemicals. These three aspects provide a continuous range of investigative level - from the cellular to the molecular.

The use of X-ray microanalysis with whole cell preparations is considered in reference to eukaryote (animal) cells and prokaryotes - where it has particular potential in environmental studies on bacteria. In the case …

Studies On The Occurrence And Elemental Composition Of Bacteria In Freshwater Plankton, K. N. Booth, D. C. Sigee, E. Bellinger

Scanning Microscopy

The occurrence and cation content of bacteria in a eutrophic freshwater lake (Rostherne Mere, Cheshire, UK) were investigated over a one year sampling period in relation to cation changes in the lake surface water and phytoplankton.

Scanning electron microscope examination of trawl-net and filtered samples demonstrated bacterial association with Anabaena, Aphanizomenon and diatoms. Direct counts of associated and unassociated bacteria showed that increases in bacterial population relate to population decline of major algal constituents.

Spectrophotometric determination of selected cation levels in the lake water demonstrated wide fluctuations throughout the sampling period, with elevated levels of transition metals before and at …

Vertical Migration Of Onychiurus Subtenuis (Collembola) In Relation To Rainfall And Microbial Activity, M. Hassall, S. Visser, D. Parkinson

Aspen Bibliography

No abstract provided.

The Electron Microscope Detection And X-Ray Quantitation Of Cations In Bacterial Cells, D. C. Sigee, M. H. El-Masry, R. H. Al-Rabaee

Scanning Electron Microscopy

Electron microscope autoradiography and X-ray microanalysis have been used for the detection and quantitation of cations in the bacterium Pseudomonas tabaci. These techniques differ in the information they provide (relating to either cation uptake or in situ levels), their applicability to different cations, their sensitivity and their spatial resolution. With uptake of ⁶³Ni²⁺, high resolution autoradiography (involving gold latensification and physical development) demonstrated a high degree of cation localisation to the central nucleoid area (glutaraldehyde-fixed cells) and within this to the constituent chromatin (acetic-alcohol preparations).

X-ray microanalysis of whole bacterial cells revealed the presence of substantial levels …

Discoloured Wood Of Aspen Caused By Increment Boring, G. Laflamme

Aspen Bibliography

No abstract provided.