Theses and Dissertations at Montana State University (MSU)
Permanent URI for this collectionhttps://scholarworks.montana.edu/handle/1/733
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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.Item Alkaline microalgae from Yellowstone National Park: physiological and genomic characterization for biofuel production(Montana State University - Bozeman, College of Agriculture, 2021) Moll, Karen Margaret; Chairperson, Graduate Committee: Brent M. Peyton; This is a manuscript style paper that includes co-authored chapters.Alternatives are needed to avoid future economic and environmental impacts from continued exploration, harvesting transport, and combustion of conventional hydrocarbons resulting in a rise of atmospheric CO 2. Microalgae, including diatoms, are eukaryotic photoautotrophs that can utilize inorganic carbon (e.g., CO 2) as a carbon source and sunlight as an energy source, and many microalgae can store carbon and energy in the form of neutral lipids. In addition to accumulating useful precursors for biofuels and chemical feed-stocks, the use of autotrophic microorganisms can further contribute to reduced CO 2 emissions through utilization of atmospheric CO 2. Most microalgal biofuel research has focused on green algae. However, there are good reasons to consider diatoms for biofuel research. Diatoms are responsible for approximately 40% of marine primary productivity, are important in freshwater systems, and are known to assimilate 20% of global CO 2. Identification and implementation of factors that can contribute to rapid growth will minimize inputs and production costs, thus improving algal biofuel viability. Nine green algae strains that were isolated from Witch Creek, Yellowstone National Park, were compared to two culture collection strains (PC-3 and UTEX395) for growth rates, dry cell weights and lipid accumulation. The strains exhibiting the fastest growth rates were WC-5, WC-1 and WC-2b. The culture collection strain was the best biomass producer and WC-5 and UTEX395 were the most productive for lipid. Based on the growth rates and lipid content, the best strains for biodiesel production were WC-1 and WC-5. In addition to the green algae strains, diatom strain, RGd-1 has previously been found to accumulate 30-40% (w/w) triacylglycerol and 70-80% (w/w) fatty acid methyl esters that can be transesterified into biodiesel. The RGd-1 was sequenced via Illumina 2x50 and PacBio RSII reads and genome comparisons revealed that the RGd-1 genome is significantly divergent from other publicly available genome sequences. RGd-1 was found to have nearly complete metabolic pathways for fatty acid elongation using acetyl-CoA in the mitochondrion or malonyl-CoA in the cytoplasm. The ability to switch between two different starting substrates may confer an advantage for fatty acid and neutral lipid biosynthesis. Further, RGd-1 was found to use the glyoxylate shunt as part of its central carbon metabolism. This carbon conservation pathway may potentially explain why RGd-1 is able to produce high concentrations of lipids. Using Illumina R MiSeq sequencing it was possible to obtain thorough community analysis of bacteria associated with RGd-1 in culture. Nine primary taxa were identified and further research will elucidate their roles as potential phycosphere bacteria that may have specific functional roles that contribute to RGd-1 health. With long-range PacBio reads, RGd-1 was found to have a potential bacterial symbiont, Brevundimonas sp.Item Rock powered life in the Samail ophiolite: an analog for early Earth(Montana State University - Bozeman, College of Agriculture, 2021) Fones, Elizabeth Marie; Chairperson, Graduate Committee: Eric Boyd; Daniel R. Colman, Emily A. Kraus, Daniel B. Nothaft, Saroj Poudel, Kaitlin R. Rempfert, John R. Spear, Alexis S. Templeton and Eric S. Boyd were co-authors of the article, 'Physiological adaptations to serpentinization in the Samail ophiolite, Oman' in the journal 'The International Society for Microbial Ecology journal' which is contained within this dissertation.; Daniel R. Colman, Emily A. Kraus, Ramunas Stepanauskas, Alexis S. Templeton, John R. Spear and Eric S. Boyd were co-authors of the article, 'Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation' in the journal 'The International Society for Microbial Ecology journal' which is contained within this dissertation.; David W. Mogk, Alexis S. Templeton and Eric S. Boyd were co-authors of the article, 'Endolithic microbial carbon cycling activities in subsurface mafic and ultramafic igneous rock' which is contained within this dissertation.Serpentinization is a geochemical process wherein the oxidation of Fe(II)-bearing minerals in ultramafic rock couples with the reduction of water to generate H 2, which in turn can reduce inorganic carbon to biologically useful substrates such as carbon monoxide and formate. Serpentinization has been proposed to fuel a subsurface biosphere and may have promoted life's emergence on early Earth. However, highly reacted waters exhibit high pH and low concentrations of potential electron acceptors for microbial metabolism, including CO 2. To characterize how serpentinization shapes the distribution and diversity of microbial life, direct cell counts, microcosm-based activity assays, and genomic inferences were performed on environmental rock and water samples from the Samail Ophiolite, Oman. Microbial communities were shaped by water type with cell densities and activities generally declining with increasing pH. However, cells inhabiting highly reacted waters exhibited adaptations enabling them to minimize stresses imposed by serpentinization, including preferentially assimilating carbon substrates for biomolecule synthesis rather than dissimilating them for energy generation, maintaining small genomes, and synthesizing proteins comprised of more reduced amino acids to minimize energetic costs and maximize protein stability in highly reducing waters. Two distinct lineages of a genus of methanogens, Methanobacterium, were recovered from subsurface waters. One lineage was most abundant in high pH waters exhibiting millimolar concentrations of H2, yet lacked two key oxidative [NiFe]-hydrogenases whose functions were presumably replaced by formate dehydrogenases that oxidize formate to yield reductant and CO 2. This allows cells to overcome CO 2/oxidant limitation in high pH waters via a pathway that is unique among characterized Methanobacteria. Finally, gabbro cores from the Stillwater Mine (Montana, U.S.A) were used to develop methods for detecting the activities of cells inhabiting mafic to ultramafic igneous rocks while controlling for potential contaminants. Optimized protocols were applied to rock cores from the Samail Ophiolite, where rates of biological formate and acetate metabolism were higher in rocks interfacing less reacted waters as compared with more extensively reacted waters, and in some cases may greatly exceed activities previously measured in fracture waters. This dissertation provides new insights into the distribution, activities, and adaptations exhibited by life in a modern serpentinizing environment.