Theses and Dissertations at Montana State University (MSU)

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Pest management challenges and climate change in water limited winter wheat agroecosystems in southwestern Montana
(Montana State University - Bozeman, College of Agriculture, 2020) Nixon, Madison Grace; Chairperson, Graduate Committee: Fabian D. Menalled
Dryland winter wheat production is influenced by many environmental factors including climate, disease, and resource availability. In Montana, Bromus tectorum (cheatgrass) and Fusarium pseudograminearum (a fungus causing root crown rot) are major winter wheat pests; reducing yield and grain quality. However, little is known how climate change and resource availability impact winter wheat, B. tectorum, and F. pseudograminearum individually as well as their multi-trophic interactions. Thus, this research aimed to 1) Determine the susceptibility of B. tectorum to F. pseudograminearum and assess how CO 2 and nitrogen impact their growth, and 2) Evaluate how elevated temperature, reduced precipitation, and plant competition impact winter wheat and B. tectorum growth and reproduction. Utilizing growth chambers, high and low nitrogen treatments, fungal inoculated and uninoculated treatments, and ambient and elevated CO 2 treatments, Bromus tectorum was found to be a host of F. pseudograminearum, and the fungus significantly reduced root, shoot and total biomass, as well as primary physiological processes of B. tectorum. Fusarium pseudograminearum infection was not impacted by nitrogen or CO 2 level. Low nitrogen increased emergence and root production early on, while high nitrogen increased shoot production at later growth stages. Low nitrogen also improved stomatal conductance and transpiration rate. High CO 2 increased B. tectorum root, shoot, and biomass production, as well as intercellular CO 2. An interaction between ambient CO 2 and low nitrogen resulted in the greatest shoot relative growth rate between the first and second harvest. Field tests, using three climate treatments (ambient, increased temperature, reduced precipitation with increased temperature) and three plant competition levels (monoculture winter wheat, monoculture B. tectorum, and biculture of the two), found that for both winter wheat and B. tectorum monocultures, ambient and warmer climates produced similar yields and biomass, respectively, whereas the drier with warmer treatment reduced these factors. Additionally, B. tectorum presence increased winter wheat grain protein. A quadratic interaction model of winter wheat yield as a function of B. tectorum biomass by climate treatment suggests that at low to moderate B. tectorum biomass levels, winter wheat yield was negatively impacted by the warmer and drier treatment, whereas ambient and warmer treatment results were similar.
Delineating the determinants of carboxylation in 2-ketopropyl coenzyme M oxidoreductase/carboxylase: a unique CO 2-fixing flavoenzyme
(Montana State University - Bozeman, College of Letters & Science, 2018) Prussia, Gregory Andrew; Chairperson, Graduate Committee: John W. Peters; George H. Gauss, Florence Mus, Leah Conner, Jennifer L. DuBois and John W. Peters were co-authors of the article, 'Substitution of a conserved catalytic dyad causes loss of carboxylation in 2-KPCC' in the journal 'Federation of European Biochemical Societies letters' which is contained within this dissertation.; Jennifer L. DuBois and John W. Peters were co-authors of the article, 'A role for hisitidine 506 in carboxylate stabilization of 2-ketopropyl coenyzme M oxidoreductase/carboxylase' which is contained within this dissertation.; Gregory Andrew Prussia is not the main author of an article which is contained in this dissertation.
Global CO 2-emissions are continuously rising, accelerating the impact of associated environmental processes such as climate change, deforestation, and ocean acidification. As a consequence, there is great interest in processes that can mitigate the increase in anthropogenic CO 2. The biological incorporation of a CO 2 molecule into an organic substrate is catalyzed by enzymes known as carboxylases. Although carboxylases employ diverse CO 2-fixing mechanisms and play broad physiological roles in Nature, they follow three general paradigms: 1). The formation of a reactive ene-intermediate nucleophile. 2). Protection of this reactive nucleophile from potential competing electrophiles (other than CO 2) by excluding solvent from the active site. 3). Electrostatic complementation of the negatively-charged carboxylation intermediate and product. 2-ketopropyl coenzyme M oxidoredutase/carboxylase (2-KPCC) is the only known carboxylating member of the FAD-containing, NAD(P)H-dependent disulfide oxidoreductase (DSOR) enzymes. The members of this family catalyze redox reactions and several well-characterized members catalyze the reductive cleavage of disulfide substrate. 2-KPCC performs the reductive cleavage of a thioether bond and subsequently carboxylates it's intermediate. How 2-KPCC has integrated the paradigms of carboxylation using a scaffold purposed for reductive cleavage is unknown. In this work, the paradigms mentioned above are identified in 2-KPCC and the methods by which 2-KPCC integrates carboxylation chemistry with reductive cleavage are discussed. Essential to the redox chemistry catalyzed by many DSOR members is a conserved His-Glu catalytic dyad, which serves to stabilize the electronic interaction between the FAD cofactor and the redox-active cysteine pair in the reactive state. 2-KPCC has substituted the catalytic His and Glu with Phe and His, respectively. We show that the Phe substitution is critical for excluding protons (as competing electrophiles) from the active site and the downstream His substitution acts to stabilize the negative charge on the carboxylated product, acetoacetate. Individually, each substitution plays an essential role in carboxylation. We show through a detailed spectroscopic study that by substituting both catalytic dyad residues the protonated and electronic state of the redox-active cysteine pair and FAD cofactor are affected, altering the DSOR active site to accommodate the unique cleavage and CO 2-fixation reaction catalyzed by 2-KPCC. Thus, this research has furthered the understanding of how the prototypical reductive cleavage reactions catalyzed by DSOR enzymes can be coordinated with a carboxylation reaction by a mechanism analogous to that shared by established carboxylase enzymes.
Sequence stratigraphic framework of the late Devonian (Frasnian) Duperow Formation in western and central Montana
(Montana State University - Bozeman, College of Letters & Science, 2019) Steuer, Christopher Johann; Chairperson, Graduate Committee: David W. Bowen
The Late Devonian Duperow Formation in western and central Montana and it's equivalent lower Jefferson Formation, is comprised of shallow marine carbonate strata deposited on the western margin of North America. It has produced significant volumes of oil and natural gas in the Alberta and Williston basins where the sequence stratigraphic framework of the formation is well-documented. However, in western and central Montana, the Duperow remains largely understudied. Additionally, at Kevin Dome, in northwest Montana, the Duperow hosts a large naturally occurring carbon-dioxide (CO^2) accumulation which is a potential economic resource and an analog for CO^2 sequestration over geologic time scales. The goal of this study is to determine the facies relationships and sequence stratigraphic architecture of the Late Devonian Duperow Formation in western and central Montana. This interpretation could help in exploration for oil and natural gas and provide useful information to aid in future carbon sequestration efforts. Multiple data sets are used in this study to best constrain depositional environments on the platform during Duperow deposition. Seven measured sections, three drill cores with associated well-logs, and forty-one thin sections are used to characterize facies, facies associations, parasequences, parasequence sets and sequences of the Duperow Formation and to construct the sequence stratigraphic framework within which these strata occur. Ten lithofacies comprising six lithofacies associations allow the interpretation of six depositional environments responsible for deposition of the Duperow Formation. The Duperow thins from the west and north onto the Central Montana Uplift, a paleohigh at the time, and thickens into the Central Montana Trough, a sub-basin on the platform. Two 2nd order and seven 3rd order sequences are interpreted from measured sections. Sequences are comprised of a transgressive systems tract and a highstand systems tract with no evidence for lowstand strata on the shelf. Transgression across the Central Montana Uplift did not occur until after the basal sequence boundary of the upper 2nd order sequence. Prior to this transgression, sequences lapped out before reaching the Central Montana Uplift. Overall, the Duperow in central and western Montana exhibits retrogradational stacking and thus is part of the transgressive systems tract of a lower-order megasequence.
The reactive form of a C-S bond-cleaving CO 2-fixing flavoenzyme
(Montana State University - Bozeman, College of Letters & Science, 2019) Mattice, Jenna Rose; Chairperson, Graduate Committee: Jennifer DuBois; Thesis includes a paper of which Jenna R. Mattice is not the main author.
Atmospheric carbon dioxide (CO 2) is used as a carbon source for building biomass in plants and most engineered synthetic microbes. Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme on earth, is used by these organisms to catalyze the first step in CO 2 fixation. 1,2 Microbial processes that also fix carbon dioxide or bicarbonate have more recently been discovered. My research focuses on a reaction catalyzed by 2-KPCC (NADPH:2-ketopropyl-coenzyme M oxidorectuase/ carboxylase), a bacterial enzyme that is part of the flavin and cysteine-disulfide containing oxidoreductase family (DSORs) which are best known for reducing metallic or disulfide substrates. 2-KPCC is unique because it breaks a comparatively strong C-S bond, leading to the generation of a reactive enolacetone intermediate which can directly attack and fix CO 2. 2-KPCC contains a phenylalanine in the place where most other DSOR members have a catalytically essential histidine. This research focuses on studying the unique reactive form of 2-KPCC in presence of an active site phenylalanine.
The coenzyme M biosynthetic pathway in proteobacterium Xanthobacter autotrophicus Py2
(Montana State University - Bozeman, College of Letters & Science, 2018) Partovi, Sarah Eve; Chairperson, Graduate Committee: John W. Peters; Florence Mus, Andrew E. Gutknecht, Hunter A. Martinez, Brian P. Tripet, Bernd Markus Lange, Jennifer L. DuBois and John W. Peters were co-authors of the article, 'Coenzyme M biosynthesis in bacteria involves phosphate elimination by a unique member of the aspartase/fumarase superfamily' submitted to the journal 'Journal of biological chemistry' which is contained within this thesis.
The metabolically versatile bacterium Xanthobacter autotrophicus Py2 has been the focus of many studies within the field of bioenergy sciences, as it contains two unique CO 2 fixing enzymes, and can utilize unconventional substrates such as propylene and acetone as the sole supplemented carbon source while fixing CO 2 in the process. Unexpectedly, coenzyme M (CoM) was found to play a crucial role as a C 3 carrier in the pathway for propylene metabolism in the late 1990s. Previously, CoM was thought to be present solely as a C 1 carrier in methanogenic archaea for nearly 30 years. Though CoM biosynthesis has been characterized in methanogenic archaea, bacterial CoM biosynthesis remained uncharacterized. In X. autotrophicus Py2, four putative CoM biosynthetic enzymes encoded by xcbB1, C1, D1, and E1 have been identified through informatics and proteomic approaches. XcbB1 is homologous to the archaeal ComA which catalyzes the addition of sulfite to phosphoenolpyruvate, and forms the initial intermediate, phosphosulfolactate, in one of the methanogen CoM biosynthetic pathways. The remaining genes do not encode homologues of any of the previously characterized enzymes in methanogen CoM biosynthesis, suggesting bacteria have a unique pathway. The production of phosphosulfolactate by ComA homolog XcbB1 was verified, indicating that bacterial CoM biosynthesis is initiated in an analogous fashion to the PEP-dependent methanogenic archaeal CoM biosynthesis pathway. XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS), and XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to D-cysteine desulfhydrases. Direct demonstration of activities for XcbB1 and C1 strengthens their hypothetical assignment to a CoM biosynthetic pathway, and puts firm contraints on our proposed functions for XcbD1 and E1. Known AFS members catalyze beta-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. We demonstrate herein that XcbC1 catalyzes a beta-elimination reaction on the substrate phosphosulfolactate to yield sulfoacrylic acid and inorganic phosphate. To our knowledge, beta-elimination reactions releasing phosphate is unprecedented among the AFS, indicating XcbC1 is a unique phosphatase. This work will serve as the framework for future studies aimed at uncovering the final stages of the biosynthetic pathway. By elucidating the XcbB1 and XcbC1 reactions, we have made significant strides towards understanding bacterial CoM biosynthesis which evaded characterization in previous years.
Mesoscale, radiometrically referenced, multi-temporal hyperspectral data for CO 2 leak detection by locating spatial variation of biophysically relevant parameters
(Montana State University - Bozeman, College of Letters & Science, 2017) McCann, Cooper Patrick; Chairperson, Graduate Committee: Kevin S. Repasky
Low-cost flight-based hyperspectral imaging systems have the potential to provide valuable information for ecosystem and environmental studies as well as aide in land management and land health monitoring. This thesis describes (1) a bootstrap method of producing mesoscale, radiometrically-referenced hyperspectral data using the Landsat surface reflectance (LaSRC) data product as a reference target, (2) biophysically relevant basis functions to model the reflectance spectra, (3) an unsupervised classification technique based on natural histogram splitting of these biophysically relevant parameters, and (4) local and multi-temporal anomaly detection. The bootstrap method extends standard processing techniques to remove uneven illumination conditions between flight passes, allowing the creation of radiometrically self-consistent data. Through selective spectral and spatial resampling, LaSRC data is used as a radiometric reference target. Advantages of the bootstrap method include the need for minimal site access, no ancillary instrumentation, and automated data processing. Data from a flight on 06/02/2016 is compared with concurrently collected ground based reflectance spectra as a means of validation achieving an average error of 2.74%. Fitting reflectance spectra using basis functions, based on biophysically relevant spectral features, allows both noise and data reductions while shifting information from spectral bands to biophysical features. Histogram splitting is used to determine a clustering based on natural splittings of these fit parameters. The Indian Pines reference data enabled comparisons of the efficacy of this technique to established techniques. The splitting technique is shown to be an improvement over the ISODATA clustering technique with an overall accuracy of 34.3/19.0% before merging and 40.9/39.2% after merging. This improvement is also seen as an improvement of kappa before/after merging of 24.8/30.5 for the histogram splitting technique compared to 15.8/28.5 for ISODATA. Three hyperspectral flights over the Kevin Dome area, covering 1843 ha, acquired 06/21/2014, 06/24/2015 and 06/26/2016 are examined with different methods of anomaly detection. Detection of anomalies within a single data set is examined to determine, on a local scale, areas that are significantly different from the surrounding area. Additionally, the detection and identification of persistent anomalies and non-persistent anomalies was investigated across multiple data sets.
Development of a micro pulsed LIDAR and a singly-resonant optical parametric oscillator for CO 2 DIAL for use in atmospheric studies
(Montana State University - Bozeman, College of Letters & Science, 2017) Chantjaroen, Chat; Chairperson, Graduate Committee: Kevin S. Repasky
According to the Fifth Assessment Report (AR5) from the Intergovernmental Panel on Climate Change (IPCC), aerosols and CO 2 are the largest contributors to anthropogenic radiative forcing--net negative for aerosols and positive for CO 2. This relates to the amount of impact that aerosols and CO 2 can have on our atmosphere and climate system. CO 2 is the predominant greenhouse gas in the atmosphere and causes great impacts on our climate system. Recent studies show that a less well known atmospheric component--aerosols, which are solid particles or liquid droplets suspended in air, can cause great impact on our climate system too. They can affect our climate directly by absorbing and scattering sunlight to warm or cool our climate. They can also affect our climate indirectly by affecting cloud microphysical properties. Typically sulfate aerosols or sea salts act as condensation nuclei for clouds to form. Clouds are estimated to shade about 60% of the earth at any given time. They are preventing much of the sunlight from reaching the earth's surface and are helping with the flow of the global water cycle. These are what permit lifeforms on earth. In the IPCC report, both aerosols and CO 2 also have the largest uncertainties and aerosols remains at a low level of scientific understanding. These indicate the need of more accurate measurements and that new technologies and instruments needs to be developed. This dissertation focuses on the development of two instruments--a scannable Micro Pulsed Lidar (MPL) for atmospheric aerosol measurements and an Optical Parametric Oscillator (OPO) for use as a transmitter in a Differential Absorption Lidar (DIAL) for atmospheric CO2 measurements. The MPL demonstrates successful measurements of aerosols. It provides the total aerosol optical depth (AOD) and aerosol lidar ratio (S a) that agree well with an instrument used by the Aerosol Robotic Network (AERONET). It also successfully provides range-resolved information about aerosols that AERONET instrument is incapable of. The range-resolved information is important in the study of the sources and sinks of aerosols. The OPO results show good promise for its use as a DIAL transmitter.
A fiber optic array for the detection of sub-surface carbon dioxide at carbon sequestration sites
(Montana State University - Bozeman, College of Engineering, 2014) Soukup, Benjamin John; Chairperson, Graduate Committee: Kevin S. Repasky
A fiber sensor array for sub-surface CO 2 concentrations measurements was developed for monitoring geologic carbon sequestration sites. The fiber sensor array uses a temperature-tunable distributed feedback (DFB) laser outputting a nominal wavelength of 2.004 microns. Light from this DFB laser is directed to one of the four probes via an in-line 1x4 fiber optic switch. Each of the probes is placed underground and utilizes filters that allow only soil gas to enter the probe. Light from the DFB laser interacts with CO 2 within the probe before being directed back through the switch. The DFB laser is tuned across two CO 2 absorption features where a transmission measurement is made, allowing the CO 2 concentration to be retrieved. This process is repeated for each probe, allowing CO 2 concentration measurements to be made as a function of time for each probe. The fiber sensor array was deployed for fifty-eight days at the Zero Emission Research Technology (ZERT) field site and for a twenty-eight day period at the Kevin Dome geologic carbon sequestration site. Background measurements indicate the instrument can monitor background levels as low as 1,000 parts per million (ppm). During a thirty-four day sub-surface CO 2 release, elevated CO 2 concentrations were readily detected by each of the four probes with values ranging to over 60,000 ppm.
Effect of permafrost thaw on methane and carbon dioxide exchange in two western Alaska peatlands
(Montana State University - Bozeman, College of Agriculture, 2013) Johnston, Carmel Eliise; Chairperson, Graduate Committee: Stephanie A. Ewing; Stephanie A. Ewing, Jennifer W. Harden, Paul C. Stoy, Ruth K. Varner, Kimberly P. Wickland, Joshua Koch, Christopher Fuller and Mark T. Jorgenson were co-authors of the article, '2.0 effect of permafrost thaw on CO 2 and CH 4 exchange in a western Alaska peatland chronosequence' submitted to the journal 'Environmental research letters' which is contained within this thesis.; Stephanie A. Ewing, Merritt R. Turetsky, Jennifer W. Harden, A. David McGuire and Miriam Jones were co-authors of the article, '3.0 effect of recent permafrost thaw on the spatial distribution of CO 2 and CH 4 exchange in a western Alaska peatland' submitted to the journal 'Environmental research letters' which is contained within this thesis.
Methane (CH 4) causes about 20% of greenhouse gas radiative forcing despite its relatively short lifetime (~10 y) and low concentration (1800 ppb) in the atmosphere. Wetlands are the largest natural source of CH 4, amounting to 22% of CH 4 production globally, with emission of CH 4-C by both diffusion and ebullition pathways. Permafrost peatlands store about 10% of permafrost C and 5% of global belowground C; hence CH 4- C emission with peatland permafrost thaw is of concern. We quantified temporal and spatial aspects of CH 4 and CO 2 emissions from northern peatlands using two approaches: (1) a ~1000 y thaw chronosequence in remote western Alaska (Innoko Flats Wildlife Refuge; May-September, 2011), and (2) lateral transects in intermediate age (~20-500 y) collapse-scar bog features at a well-instrumented site near Fairbanks, Alaska (Alaska Peatland Experiment (APEX)/Bonanza Creek Long Term Experimental Research site; June-September, 2012). At Innoko Flats, peak CH 4 production was observed in features aged 30-590 y since thaw, which had warmer soils than younger sites and shallower water tables than older sites. Average surface flux at these 30-590 y sites (+2.52 ± 0.98 mg CH 4-C m -2 hr -1) was greater than estimated ebullition flux (0.13 ± 0.05 mg CH 4-C m -2 hr -1) based on an observed rate of 0.78 ± 0.33 mL m -2 hr -1. Net ecosystem exchange of CO 2-C (NEE) did not differ among chronosequence features, and offset CH 4-C emissions by a factor of 2 to 400 when considered as 100-y global warming potential. At APEX, bogs reflecting <100 y since most recent thaw showed high variability in CH 4 exchange, but rates were generally consistent with levels at the Innoko 30-590 y sites (mean of 5.42 ± 1.16 mg CH 4-C m -2 hr -1). APEX bogs showed greater balance between CH 4-C efflux and CO 2-C influx, with CH 4-C fluxes offsetting 80-140% of NEE during the growing season when considered as 100-y global warming potential. We argue that CH 4 contributes most significantly to post-thaw C loss over timescales of decades to centuries in these northern peatlands.
Biological and geochemical controls on CO2 equilibria in free water wetlands
(Montana State University - Bozeman, College of Engineering, 1999) Sharp, Thomas Robert

Theses and Dissertations at Montana State University (MSU)

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