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Item Rhizobiome dynamics in plant growth promotion and abiotic stress response(Montana State University - Bozeman, College of Agriculture, 2023) Goemann, Hannah Marie; Chairperson, Graduate Committee: Brent M. PeytonSoil microorganisms play vital roles in global nutrient cycling. Understanding the complex relationships between plants and soil microbes and their implications is one of the greatest challenges facing microbial ecology today. Soil microbes can play beneficial roles in supporting plant growth by increasing access to nutrients, water, and decreasing plant stress signaling under abiotic stresses such as drought and heat. With increasing climate variability due to climate change, it is imperative to make scientifically informed management decisions to best support global biodiversity and plant productivity in natural and agroecosystsms. In this dissertation I summarize four separate investigations of plant-microbe interactions. The first is using nitrogen-fixing cyanobacterial biofertilizers to promote plant growth of perennial second generation bioenergy crops switchgrass (Panicum virgatum) and tall wheatgrass (Agropyrun elongatum). The second and third studies seek to better understand plant-microbe carbon exchange under drought stress in the native North American prairie grass blue grama (Bouteloua gracilis). The final study explores the potential microbial contribution to heat tolerance of panic grass (Dichanthelium lanuginosum) across a natural soil temperature gradient in Yellowstone National Park. Next-generation amplicon sequencing using the Illumina Miseq platform is the primary technique utilized across the three studies to investigate microbial community dynamics. The main results of the biofertilizer study were that tall wheatgrass is better suited to the SW Montana growing season than switchgrass, and similar plant yields were achieved with the cyanobacterial biofertilizer as with urea chemical fertilizer without negatively impacting the microbial community diversity. The first blue grama study found that severe and mild drought had distinct, phylogenetically linked responses within the blue grama rhizobiome with Planctomycetes, Thermoproteota (ammonia-oxidizing archaea), and Glomeromycetes (arbuscular mycorrhizal fungi) exhibiting notably altered relative abundances. The second blue grama study found that climate legacy plays an important role in shaping blue grama drought response. Finally, from the D. lanuginosum study in Yellowstone National Park we learned that pH and temperature both strongly influence community composition, and that D. lanuginosum selects for unique community members in its rhizosphere at higher temperatures. Collectively, these studies contribute to furthering our understanding of the dynamics of plant-associated microbiomes.Item Microbial adaptation to cultivation stress using storage compounds(Montana State University - Bozeman, College of Agriculture, 2022) Arnold, Adrienne Dale; Chairperson, Graduate Committee: Ross Carlson; This is a manuscript style paper that includes co-authored chapters.Methanotrophs and green algae are microorganisms that grow on single carbon substrates. Methanotrophs are bacteria that use methane as their carbon source, and green algae are eukaryotic phototrophs that grow on CO 2. They are of interest both as primary producers in the environment and as biological catalysts for the conversion of greenhouse gases into value-added compounds. Understanding how methanotrophs and green algae adapt to cultivation stresses is key to understanding carbon cycling in the environment and in industrial settings. This work uses stoichiometric metabolic modeling to investigate the role of carbon storage compounds in the metabolism of C1-utilizing organisms. Storage compounds are accumulated as intracellular reserves of polysaccharides or lipids, which can be catabolized under stress conditions to provide carbon and energy to the cell. Catabolism of carbon storage compounds often results in the excretion of multi-carbon organic compounds that can be utilized as carbon substrates by other members of the microbial community. In silico metabolic models were developed for methanotroph and algal systems and used to examine the breakdown of storage compounds in response to common cultivation stresses. For the aerobic methanotrophs, predictions focused on the use of polyhydroxybutyrate and glycogen in adaptation to O 2 limitation. For the green algae, starch and triacylglycerol reserves are analyzed as sources for compatible solutes, which are produced by cells in response to high salinity conditions. Metabolic modeling of storage compound utilization by methanotrophs and algae helps elucidate the role of these organisms as primary producers and presents an opportunity for industrial production of multi-carbon compounds from single carbon substrates.Item Genomic composition of green algae grown in high alkaline conditions(Montana State University - Bozeman, College of Agriculture, 2023) Goemann, Calvin Lee Cicha; Chairperson, Graduate Committee: Blake Wiedenheft; This is a manuscript style paper that includes co-authored chapters.Algae are responsible for 50% of global oxygen production and sequestration of CO 2 from the atmosphere. Algal photosynthesis plays a critical role in all aquatic ecosystems converting sunlight and CO2 into usable biomass. Algal growth and biomass production can be coopted to produce industrially relevant bioproducts like triacylglycerol (TAGs) that can be converted into biodiesel and provide a sustainable carbon-neutral alternative to fossil fuels. In high-stress environments, algae produce high levels of TAGs. Multiple stresses including nitrogen limitation and high pH impact algae physiology, but little is known about how algae shift their metabolism to produce TAGs in response to these stresses. This topic remains relatively unexplored due to the limited availability of complete algae genomes. Here we sequence and annotate the complete telomere-to-telomere genome of an alkali-tolerant green algae Chlorella sp. SLA-04. Genomic analysis supports a reclassification of Chlorophyta green algae and illuminates how SLA-04 adapts to diverse environmental conditions. Additionally, transcriptomic analysis revealed how Chlorella sp. SLA-04 rewires carbon metabolism in high alkaline and nutrient-deplete conditions to produce TAGs while minimizing photosynthetic oxidative stress. Together, we double the amount of publicly available telomere-to-telomere green algal genomes and use this resource to explore how algae respond to diverse environmental conditions in their native and industrial settings.