Environmental Microbiology and Microbial Ecology Commons^™

Extracting Secondary Metabolites From Bacterial Endophytes To Suppress Or Promote Sweet Sorghum And Weeds, Mohammad R. Alsabri

Theses and Dissertations--Plant and Soil Sciences

Endophytic bacteria are ubiquitous in agricultural settings and have the potential to drastically affect plant growth both positively and negatively. These complex relationships play a key role in plant nutrition and are therefore of great interest to the agricultural community and beyond. With my dissertation work, I have had the opportunity to examine the relationship between endophytic bacteria and plants in various ways. The first part of my dissertation investigated how the microbial diversity found in soil affects the below- and above-ground traits of Sorghum bicolor. In the second section, I focused on a particular strain of bacteria that …

Long-Term Land Management Practices And Their Effect On Soil Health And Crop Productivity, Thomas Joseph Muratore Jr.

Theses and Dissertations--Plant and Soil Sciences

Agricultural intensification reliant on monocrops could change soil health in a way that does not support maximum crop productivity. Twenty-nine-year-old no-till field plots at the University of Kentucky Spindletop research farm showed a significant reduction in corn yields from continuous corn plots compared to those from plots in various types of rotation. The objective of this study was to determine what role soil microbes might play in yield reduction and how management and time effects microbial community structure. Samples were collected from the following treatments: continuous corn (CC), continuous soybean (SS), a 2-year corn/soybean rotation (CCSS), Corn in rotation with …

Tracking A Tree-Killer: Improving Detection And Characterizing Species Distribution Of Phytophthora Cinnamomi In Appalachian Forests, Kenton L. Sena

Theses and Dissertations--Plant and Soil Sciences

Phytophthora cinnamomi is a soil-borne oomycete pathogen causing root rot in susceptible host species. P. cinnamomi is thought to have originated in Southeast Asia, but has since been introduced to many regions around the world, where it causes dramatic declines in many forest tree species. In the eastern US, the primary susceptible tree species of concern are American chestnut (Castanea dentata), white oak (Quercus alba), and shortleaf pine (Pinus echinata). American chestnut, functionally eliminated in the early 1900s by the rapidly acting chestnut blight (Cryphonectria parasitica), has been the subject of decades-long …

Studies Relating Pqq Biosynthesis To Putative Peptidases And Operon Structure In Pseudomonas Species, Benjamin Diaz

Theses and Dissertations--Plant and Soil Sciences

Several bacteria isolated from the broccoli rhizosphere were assayed to compare their ability to solubilize phosphate and release pyrroloquinoline quinone (PQQ) into the surrounding media. Subsequently, their genomes were sequenced and analyzed for PQQ biosynthesis operon structure. PQQ biosynthesis genes pqqA-F were found in all isolates. The order of PQQ biosynthesis genes and predicted amino acid sequences were compared to each other and the host’s ability to solubilize phosphate and release PQQ. In all Pseudomonas species, two putative protease genes, pqqF, and pqqG, flanked the canonical pqqA-pqqE biosynthesis operon. No mechanistic studies have confirmed the function of …

Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture, Lindsey C. Slaughter

Theses and Dissertations--Plant and Soil Sciences

Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. …

Studies On Regulation Of Pqq-Dependent Phosphate Solubilization Among Rhizosphere Dwelling Bacteria, Ran An

Theses and Dissertations--Plant and Soil Sciences

Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a several different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain from soil, but in many cases it is immobilized in forms that are not available for plant uptake. Bacteria can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. In this dissertation, I studied the regulation of the glucose dehydrogenase enzyme and the PQQ coenzyme in the …

Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis

Theses and Dissertations--Plant and Soil Sciences

Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …

Tillage And Fertilization Influences On Autotrophic Nitrifiers In Agricultural Soil, Shuang Liu

Theses and Dissertations--Plant and Soil Sciences

Nitrification is a biological oxidation of NH₃ to NO₂^- and then to NO₃^-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO₃^- leaching, and reducing NO and N₂O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The …

Unveiling Novel Aspects Of D-Amino Acid Metabolism In The Model Bacterium Pseudomonas Putida Kt2440, Atanas D. Radkov

Theses and Dissertations--Plant and Soil Sciences

D-amino acids (D-AAs) are the α-carbon enantiomers of L-amino acids (L- AAs), the building blocks of proteins in known organisms. It was largely believed that D-AAs are unnatural and must be toxic to most organisms, as they would compete with the L-counterparts for protein synthesis. Recently, new methods have been developed that allow scientists to chromatographically separate the two AA stereoisomers. Since that time, it has been discovered that D-AAs are vital molecules and they have been detected in many organisms. The work of this dissertation focuses on their place in bacterial metabolism. This specific area was selected due to …

Studies On The Effects Of Plant Variety And Root Exudate Compounds On The Soil Microbial Community, Márton Szoboszlay

Theses and Dissertations--Plant and Soil Sciences

Plants modify the soil environment through their root system, changing its physical properties and exuding compounds that promote or inhibit the growth of certain microorganisms. Therefore the structure of the soil microbial community is different in the rhizosphere than in the bulk soil. This dissertation introduces three research projects that investigated the effects of specific root exudate compounds on the soil microbial community structure, and plant cultivar specific differences in the rhizosphere microbiota.

The progenitor of maize is Balsas teosinte (Zea mays subsp. parviglumis). In a greenhouse experiment we compared the structure and function of its bacterial and …

The Role Of Surface Chemistry In The Toxicity Of Manufactured Cerium Dioxide Nanomaterials To Caenorhabditis Elegans, Emily Kay Oostveen

Theses and Dissertations--Plant and Soil Sciences

Manufactured CeO₂ nanomaterials (CeO₂-MNMs) are used for a wide variety of applications including diesel fuel additives and chemical/mechanical planarization media. To test the effects of CeO₂-MNM surface coating charge on to model organism Caenorhabditis elegans, we synthesized 4 nm CeO₂ with cationic (DEAE-), anionic (CM-), and neutral (DEX) coatings. In L3 nematodes exposed for 24 hours, DEAE-CeO₂ induced lethality at lower concentrations than CM- or DEX-CeO₂. Feeding slightly decreased CeO₂ toxicity, regardless of coating. In L2 nematodes exposed for 48 hours with feeding, DEAE-CeO₂ caused lethality at the …

Bacteria In Bioethanol Fermentations, Qing Li

Theses and Dissertations--Plant and Soil Sciences

To gain a better understanding of contaminating bacteria in bioethanol industry, we profiled the bacterial community structure in corn-based bioethanol fermentations and evaluated its correlation to environmental variables. Twenty-three batches of corn-mash sample were collected from six bioethanol facilities. The V4 region of the collective bacterial 16S rRNA genes was analyzed by Illumina Miseq sequencing to investigate the bacterial community structure. Non-metric multidimensional scaling (NMDS) ordination plots were constructed to visualize bacterial community structure groupings among different samples, as well as the effects of multiple environmental variables on community structure variation. Our results suggest that bacterial community structure is facility-specific, …

Managing Soil Microbial Communities With Organic Amendments To Promote Soil Aggregate Formation And Plant Health, Shawn T. Lucas

Theses and Dissertations--Plant and Soil Sciences

The effects of managing soil with organic amendments were examined with respect to soil microbial community dynamics, macroaggregate formation, and plant physio-genetic responses. The objective was to examine the possibility of managing soil microbial communities via soil management, such that the microbial community would provide agronomic benefits. In part one of this research, effects of three amendments (hairy vetch residue, manure, compost) on soil chemical and microbial properties were examined relative to formation of large macroaggregates in three different soils. Vetch and manure promoted fungal proliferation (measured via two biomarkers: fatty acid methyl ester 18:2ω6c and ergosterol) and also stimulated …

Soil Microbial Community Response To Climate Change: Results From A Temperate Kentucky Pasture, Lindsey C. Slaughter

Theses and Dissertations--Plant and Soil Sciences

Climate change is likely to alter plant species composition and interactions between plants and soil microbes that together dictate the quantity and quality of forage produced in pastures, the base of animal production in central Kentucky. This study assessed the seasonal dynamics of soil microbes and their response to increased temperature (+3^oC) and growing season precipitation (+30% of the mean annual). Total soil microbial biomass, community composition, enzyme activities, potential carbon mineralization, and catabolic responses to selected substrates were measured seasonally in the different climate treatments. In this system, seasonal variability was a dominant driving factor for all …