Dissertations / Theses on the topic 'Plant Sciences'

Cynipid gall formation is achieved by the intimate insect-plant interaction where by cynipid wasps redirect host plant development to form novel structures to protect and nourish the developing larva. To investigate the molecular mechanisms involved in this interaction, and extend our understanding of plant development, four approaches were taken. 1) A PCR based approach to search for genes to known signalling molecules: chitiooligosaccharides, or Nod factors, that control nodulation in the Rhizobia-legume interaction. PCR analysis was used to investigate the presence of the nodC gene in the cynipid gall wasp genome,h owever, no nodC-like sequencesw ere found. 2) SDS-PAGE analysis was carried out to compare inner-gall and non-gall protein signatures, demonstrating the variation between gall and non-gall tissue, and also that the protein signatures of inner-gall tissues vary between gall species. N-terminal sequencing and western blot analysis lead to the identification of a number of innergall proteins such as protein disulphide isomerase (PDI), formate dehydrogenase (FDH) and putative biotin carboxyl carrier protein (BCCP), involved in the synthesis of lipids in seeds. Analysis of the temporal and spatial expression of the putative BCCP revealed expression to be concentrated in the inner-gall cells throughout development, in all the gall species tested. 3) Cytological analysis of the inner-gall tissue was carried out throughout development of several gall species to investigate differences in their patterns of development and cytological characteristics of the inner-gall tissue, with many inner-gall cells being polytene. 4) A gall formation bioassay, to enable the activity of possible signals involved in gall formation to be tested, was developed. Rose callus tissue was used as a test tissue and the cynipid larval extract was exposed to this as a source of the active molecules. The induction of proteins in the callus after exposure to the larval extract was used as a molecular marker for activity. The polytene characteristic and the possible expression of seed proteins, suggest that seed developmental pathways may be used during gall formation.

Green roofs have many ecological benefits that address numerous modern environmental issues. Many studies have evaluated Sedums on green roofs; on the other hand, there is much interest in native plant performance on a green roof. In my study, Green Roof Blocks were planted with 3 experimental treatments: native plants only; native species plus Sedums; and Sedums only. The native species only treatment consisted of Eragrostis spectabilis, Coreopsis lanceolata, Penstemon pallidus, Penstemon hirsutus, Koeleria marcantha, Rudbeckia hirta, Aster laevis and Carex muhlenbergii. These areas were planted with one plug per native species for a total of eight plugs per Green Roof Block. Natives were interspersed between existing Sedum plantings in the native species plus Sedum planting treatment. There was again one plug per six species, but only six native plugs per block. The species in these planting areas were Bouteloua gracilis, Buchloe dactyloides, Asclepius verticillata, Bouteloua curtipendula, Geum triflorum and Sporobolus cryptandrus. All native plants were planted in the two treatments on 5/29/2013 and 6/5/2013. All plants in the study plots were irrigated weekly as needed in 2013 and 2014. On November 7 and 8, 2013, June 10 and 23, 2014, June 2015, November 2015, and April 2016 native plant survival was measured. In the plots with natives only, survival ranged from 0 to 86 percent at the end of the study. To date, Coreopsis lanceolata and Penstemon pallidus have the greatest percent survival in the natives only planting area at 86 and 45 percent respectively. In the plots with natives plus Sedums, native plant survival ranged from 0 to 70 percent at the end of the study. Survival of the four native grasses was greater than 99 percent in the first growing season. To date, the only native species remaining in the natives plus Sedums planting area is Buchloe dactyloides, with about 70 percent survival. In addition, the forb Coreopsis lanceolata has rapidly spread outside the initial planting areas, indicating that this native species not only survives on the roof, but is able to reproduce successfully.

At least 110 million landmines have been planted since the 1970s in about 70 nations, many of which remain in place today. Some risk of detection may be mitigated using currently available remote sensing techniques when vegetation is present. My study focused on using plants as phytosensors to detect buried explosives. I exposed three species representing different functional types (Cyperus esculentus (sedge), Ulmus alata (tree), Vitis labrusca (vine)) to 500 mg kg-1 of Composition B (Comp B; 60/40 mixture of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and 2,4,6-trinitrotoluene (TNT)), a commonly used explosive mixture, and measured functional traits and reflectance over a nine-week period. Cyperus esculentus was not a good indicator for the presence of explosive compounds. Comp B treatment woody species, U. alata and V. labrusca, exhibited changes in pigment content, leaf area, specific leaf area, dry leaf biomass, and canopy reflectance. The efficacy of plants as landmine detectors is species and/or functional group dependent.

The common observation that plant δ¹⁵N values are lower than those of associated soil is generally attributed to transporter-facilitated efflux of ¹⁵N-enriched N. N efflux tends to occur under specific conditions, for instance, when the external N concentration is high, when the external medium is acidic and when roots experience mechanical stress. While efflux is presumed to act as a regulator of cytoplasmic N concentrations, it is energetically costly for plants to take up N only to release it back into the rhizosphere. A link between root tissue loss (e.g. root turnover or rhizodeposition) and plant δ¹⁵N has not been suggested, although root abscission is likely to be more ubiquitous than N efflux. This thesis questions the extent to which N efflux and root abscission contribute to plant N-loss and plant δ¹⁵N values. I hypothesized that: (1) plants supplied with more N would have more negative δ¹⁵N relative to the source, and greater root abscission from a relatively larger root biomass (2) the aeration necessary for hydroponic culture can act as a mechanical stressor on roots, accentuating plant N-loss through root abscission and N efflux. Wheat was grown in sand with NO₃- supplied at five relative addition rates (RAR) and in hydroponics with three physical disturbance regimes (direct aeration, aeration constrained within a pipe and circulation of nutrient solution through sand). The δ¹⁵N of roots and shoots, as well as the plant-derived N accumulation in both growth mediums, were determined. When the N supply matched the plant N demand, as determined by the relative growth rate, there was no discrimination between plant and source δ¹⁵N. N-loss here, although negligible, was in the organic form, which implies root abscission. By contrast, when N supply exceeded plant N demand, plant δ¹⁵N values decreased (e.g. after 47 d, plant δ¹⁵N of RAR 0.075 d⁻¹ was 0.4‰ but was −4.1‰ at RAR 0.175 d⁻¹) because they lost ¹⁵N-enriched N. This N was largely inorganic and presumably lost through efflux. In disturbed hydroponic conditions (i.e. direct and pipe treatments), root 'fragments' were a major biomass- (six-fold greater than root dry weight) and N-loss (two-fold greater than plant net N uptake) pathway. Plants from all treatments lost more N within root fragments than through efflux, although the cumulative N-loss was significantly smaller from plants grown in relatively undisturbed hydroponic conditions (i.e. sand). This suggests that root abscission is likely to be an important N-loss pathway for plants and thus contributes to the global offset between plant and soil δ¹⁵N values. Moreover, efforts to improve nitrogen use efficiency of crop plants, though reduced efflux, need to take cognizance of root abscission because it is an unavoidable artefact of root growth.

In this dissertation I first examine the ability of individual plants in the field to garner localized soil nutrients. I then measure actual soil variability around perennial plants and use various statistics to quantify the scale and degree of that variability. Soil patches on opposite sides of Pseudoroegneria spicata tussocks were treated with distilled water or a nutrient solution containing N, P, or K in three field experiments. When P was augmented in the enriched soil patches, rates of P uptake increased significantly for roots from enriched patches compared with roots in control patches. Rates of ammonium and potassium uptake were apparently unchanged. When N was augmented in the enriched patches, rates of ammonium and potassium uptake increased significantly. When K was augmented in the enriched patches, no changes were seen for any of the nutrients. Plant shading was found to limit the ability of Agropyron desertorum tussocks to increase rates of nutrient uptake in enriched soil microsites. Roots of unshaded plants selectively increased phosphate uptake capacity in enriched patches by up to 73%, but shading limited this response. Enrichment of the soil patches resulted in significantly greater phosphate concentrations in roots of both shaded and unshaded plants. Nutrient heterogeneity in the soil at a native sagebrush-steppe site was quite high, with ammonium and nitrate varying by over two orders of magnitude and phosphate and potassium close to one order of magnitude within a 10x12- m area. Within 0.5x0.5-m subplots around individual plants, ammonium and nitrate varied by an average factor of 11 and 12, respectively, with less average variation for phosphate and potassium. Geostatistical semivariograms showed that soil ammonium, nitrate, phosphate, potassium, pH, and organic matter all showed detectable autocorrelation only at scales of less than 1.0 to 1.5 m. Indices of microbial activity showed no detectable autocorrelation even at the smallest measurement scale of 12.5 cm. From the degree and scale of heterogeneity encountered, I conclude that root plasticity and active foraging in a heterogeneous soil environment are likely to be important to the nutrient balance of many plants.

Green roofs are an established best management practice (BMP) for storm water mitigation because of their ability to retain precipitation runoff. The purpose of this study was to quantify storm water retention of Sedum and native plant green roof systems at three substrate depths (10, 15, 20 cm). Survival of plants on green roof systems is dependent on how quickly they can establish themselves. This study also determined native and Sedum plant roof surface coverage at three green roof growth media depths (10, 15, 20 cm). A mixture of six Sedum species (S. spurium, S. sexangulare, S. album, S. Immergrunchen, S. kamtschaticum, and S. reflexum) and four native species (Sporolus cryplandrus, Boutelous curtipendula, B. gracilis , and Penstamen pallidus) were planted into the built-in-place systems (BIPs) on June 20, 2014.

There were 137 precipitation events totaling to 158.2 cm during the entire (June 20, 2014-June 30, 2015) study period and there were 87 precipitation events with a total precipitation of 108.1 cm during storm water collection (Oct. 31, 2015 until June 30, 2015). During the study period, mean storm water retention of green roof systems planted with native (>58%) and Sedum (>53%) species were identical regardless of growth media depth. Mean storm water retention in green roof systems planted with native and Sedum species in all growth media depths were greater than mean storm water retention of non-vegetated roof models (32%).

Green roof plant surface coverage plays an important role in water retention of storm water runoff. During the dormant period (January 23, 2015), roof coverage by Sedum plants was greater than roof coverage by native plants. In addition, green roof surface coverage by Sedum plants was the same regardless of depth (>89%). Green roof surface coverage of native plants in 10 cm depth achieved less coverage than native plants in 15 and 20 cm depths. These results differ from the plant-growing season (June 30, 2015). Green roof surface coverage by native plants in green roof systems with 15 and 20 cm growth media depth were identical to the roof coverage by Sedum plants in green roof systems with 10, 15, or 20 growth media depth. Green roof surface coverage by native plants in green roof systems with 10 cm growth media depth was less than the roof coverage in all green roof systems in this study.

Analysis of covariance was used to determine if green roof surface coverage by native and Sedum plants affected mean storm water retention. During the study period green roof surface coverage by native and Sedum plants did not affect storm water retention regardless of growth media depth.

This green roof research demonstrates that green roof systems planted with native plant species are effective tools for retaining storm water in the mid-western region of the United States. After 9 months, there was no difference in storm water retention between native and Sedum species planted in 10, 15, and 20 cm growth media depth. Each green roof module retained more storm water than the traditional, non-vegetated roof model. Both native and Sedum species planted on green roofs in 10, 15, and 20 cm media depth achieved more than 69 percent green roof surface coverage after nine months.

A cloud infrastructure and Android-based system were developed to enable amateurs and professionals to make use of laboratory techniques for remote plant disease detection. The system allows users to upload and analyze plant data as citizen scientists, helping to improve models for remote disease detection in horticultural settings by greatly increasing the quantity and diversity of data available for analysis by the community. Techniques used in research laboratories for remote disease detection are generally not available to home gardeners and small commercial farmers. Lab equipment is cost-prohibitive and experiments highly controlled, leading to models that are not necessarily transferable to the user’s environment. Plant producers rely on expert knowledge from training, experience, and extension service professionals to accurately and reliably diagnose and quantify plant health. Techniques for disease detection using visible and infrared imagery have been proven in research studies and can now be made available to individuals due to advancements in smartphones and low-cost thermal imaging devices. The framework presented in this paper provides an internet-accessible data pipeline for image acquisition, preprocessing, stereo rectification, disparity mapping, registration, feature extraction, and machine learning, designed to support research efforts and to make plant stress detection technology readily available to the public. A system of this kind has the potential to benefit both researchers and plant growers: producers can collectively create large labeled data sets which researchers can use to build and improve detection models, returning value to growers in the form of generalizable models that work in real-world horticultural settings. We demonstrate the components of the framework and show data from a water stress experiment on basil plants performed using the mobile app and cloud-based services.

Autophagy is a major catabolic pathway in which cell components get sequestered in a double membrane vesicle, transported to the vacuole, degraded by vacuolar hydrolases and recycled.  Through this process, cells ensure cell homeostasis and remobilise nutrients. The autophagic flux can be enhanced as an adaptive stress response, improving plants resistance against stress, reducing aging and ultimately increasing yield. However, autophagy regulation in plants remains poorly understood.  Novel plant-specific modulators can be used in a chemical genetic approach for identification of proteins involved in the autophagy pathway. Furthermore, autophagy enhancers can find their application in agriculture for improved plant fitness. Known autophagy modulators have severe off-target effects, affecting plant growth and development. A recent screening identified two potential autophagy modulators. We developed a novel method for photoaffinity labelling and pulldown assay in Arabidopsis thaliana to identify potential interactors of the modulators. The identification of autophagy-related proteins will help to further elucidate the autophagic pathway in plants. The effect of the new autophagy enhancers on plant growth and development was analysed by automated growth assays. In comparison with a currently available autophagy enhancer, treated plants showed higher viability, indicating possible further applications for the new autophagy modulators in planta.

The majority of the current production, use, and disposal of engineered nanomaterials (ENMs) occur in terrestrial environments, and consequently terrestrial ecosystems are and will increasingly be some of the largest receptors of ENMs at all stages of their life cycles. In particular, soil is predicted to be one of the major receptors of ENMs due to ENM-contaminated biosolid fertilizer and nanopesticide application to agricultural fields, runoff from landfills or ENM-bearing paints, or atmospheric deposition. Both agricultural and natural systems are at risk to ENM contamination via these release scenarios, which makes it necessary to understand the interactions between ENMs, soils, and soil organisms such as plants in order to predict their impacts in real-world scenarios. Gravity-driven vertical transport of TiO2, CeO2, and Cu(OH)2 engineered nanomaterials (ENMs) and their effects on soil pH and nutrient release were measured in three unsaturated soils. ENM transport was found to be highly limited in natural soils collected from farmland and grasslands, with the majority of particles being retained in the upper 0-3 cm of the soil profile, while greater transport depth was seen in a commercial potting soil. Physical straining appeared to be the primary mechanism of retention in natural soils as ENMs immediately formed micron-scale aggregates, which was exacerbated by coating particles with Suwannee River natural organic matter (NOM). Changes in soil pH were observed in natural soils contaminated with ENMs that were largely independent of ENM type and concentration. These changes may have been due to enhanced release of naturally present pH-altering ions (Mg2+, H+) in the soil, likely via substitution processes. This suggests ENMs will likely be highly retained near source zones in soil and may impact local communities sensitive to changes in pH or nutrient availability. Few studies have investigated the influence of environmental conditions on ENM uptake and toxicity, particularly throughout the entire plant life cycle. Here, soil-grown plants (Clarkia unguiculata, Raphanus sativus, and Triticum aestivum) were exposed until maturity to TiO2, CeO2, or Cu(OH)2 ENMs under different illumination intensities, in different soils, and with different nutrient levels. Fluorescence and gas exchange measurements were recorded throughout growth and tissue samples from mature plants were analyzed for metal content. ENM uptake was observed in all plant species, but was seen to vary significantly with ENM type, light intensity, nutrient levels, and soil type. Light intensity in particular was found to be important in controlling uptake, likely as a result of plants increasing or decreasing transpiration in response to light. Significant impacts on plant transpiration, photosynthetic rate, CO2 assimilation efficiency, water use efficiency, and other parameters related to physiological fitness were seen. The impacts were highly dependent on environmental conditions as well as ENM and soil type. Notably, many of these effects were found to be mitigated in soils with limited ENM mobility due to decreased uptake. These results show that abiotic conditions play an important role in mediating the uptake and physiological impacts of ENMs in terrestrial plants.

The short-term effects of manganese toxicity on ribulose 1,5 bisphosphate carboxylase (Rubisco) activity and concentration in tobacco chloroplasts were examined. The activity of the enzyme from both manganese-treated and control plants was determined 6, 12, 18, 24 , and 48 h after introduction of manganese (80 mg/Li. Enzyme activity was determined by monitoring rates of radioactive CO2 fixation into acid stable products. A slight stimulation of the enzyme's activity was noted in experimental plants after 18 h of exposure to manganese as compared with control plants. A decrease in the enzyme's activity in experimental plants was noted after 48 h of exposure. Visible symptoms such as chlorosis and decreased leaf size were also observed after 48 h of manganese exposure in experimental plants. Using Rocket Immunoelectrophoresis, no appreciable difference between Rubisco concentration levels of the experimental plants and the control plants was noted after 6, 12, 18, 24, and 48 h of manganese exposure indicating that the effect on Rubisco activity is a post-translational phenomenon and that Rubisco is not being degraded at an accelerated rate. Even after 7 d of exposure to high manganese concentrations, when visible symptoms such as chlorosis and necrotic lesions were very evident, the level of Rubisco in the manganese-treated plants varied little from the levels in the control plants. Manganese accumulated in the experimental plants to concentrations as high as 3282 mg,/g dry wt as determined by atomic absorption spectrophotometry. A shuttling mechanism for manganese between young and old leaves was indicated by an observed decrease in the concentration of manganese in the young leaf tissue between 12 and 18 h after treatment .

The fragmentation of natural habitat caused by anthropogenic land use changes is one of the main drivers of the current rapid loss of biodiversity. In face of this threat, ecological research needs to provide predictions of communities' responses to fragmentation as a prerequisite for the effective mitigation of further biodiversity loss. However, predictions of communities' responses to fragmentation require a thorough understanding of ecological processes, such as species dispersal and persistence. Therefore, this thesis seeks an improved understanding of community dynamics in fragmented landscapes. In order to approach this overall aim, I identified key questions on the response of plant diversity and plant functional traits to variations in species' dispersal capability, habitat fragmentation and local environmental conditions. All questions were addressed using spatially explicit simulations or statistical models. In chapter 2, I addressed scale-dependent relationships between dispersal capability and species diversity using a grid-based neutral model. I found that the ratio of survey area to landscape size is an important determinant of scale-dependent dispersal-diversity relationships. With small ratios, the model predicted increasing dispersal-diversity relationships, while decreasing dispersal-diversity relationships emerged, when the ratio approached one, i.e. when the survey area approached the landscape size. For intermediate ratios, I found a U-shaped pattern that has not been reported before. With this study, I unified and extended previous work on dispersal-diversity relationships. In chapter 3, I assessed the type of regional plant community dynamics for the study area in the Southern Judean Lowlands (SJL). For this purpose, I parameterised a multi-species incidence-function model (IFM) with vegetation data using approximate Bayesian computation (ABC). I found that the type of regional plant community dynamics in the SJL is best characterized as a set of isolated “island communities” with very low connectivity between local communities. Model predictions indicated a significant extinction debt with 33% - 60% of all species going extinct within 1000 years. In general, this study introduces a novel approach for combining a spatially explicit simulation model with field data from species-rich communities. In chapter 4, I first analysed, if plant functional traits in the SJL indicate trait convergence by habitat filtering and trait divergence by interspecific competition, as predicted by community assembly theory. Second, I assessed the interactive effects of fragmentation and the south-north precipitation gradient in the SJL on community-mean plant traits. I found clear evidence for trait convergence, but the evidence for trait divergence fundamentally depended on the chosen null-model. All community-mean traits were significantly associated with the precipitation gradient in the SJL. The trait associations with fragmentation indices (patch size and connectivity) were generally weaker, but statistically significant for all traits. Specific leaf area (SLA) and plant height were consistently associated with fragmentation indices along the precipitation gradient. In contrast, seed mass and seed number were interactively influenced by fragmentation and precipitation. In general, this study provides the first analysis of the interactive effects of climate and fragmentation on plant functional traits. Overall, I conclude that the spatially explicit perspective adopted in this thesis is crucial for a thorough understanding of plant community dynamics in fragmented landscapes. The finding of contrasting responses of local diversity to variations in dispersal capability stresses the importance of considering the diversity and composition of the metacommunity, prior to implementing conservation measures that aim at increased habitat connectivity. The model predictions derived with the IFM highlight the importance of additional natural habitat for the mitigation of future species extinctions. In general, the approach of combining a spatially explicit IFM with extensive species occupancy data provides a novel and promising tool to assess the consequences of different management scenarios. The analysis of plant functional traits in the SJL points to important knowledge gaps in community assembly theory with respect to the simultaneous consequences of habitat filtering and competition. In particular, it demonstrates the importance of investigating the synergistic consequences of fragmentation, climate change and land use change on plant communities. I suggest that the integration of plant functional traits and of species interactions into spatially explicit, dynamic simulation models offers a promising approach, which will further improve our understanding of plant communities and our ability to predict their dynamics in fragmented and changing landscapes.
Die Fragmentierung von Landschaften umfasst die Zerschneidung und den Verlust von Flächen mit natürlicher Vegetationsentwicklung und ist eine der Hauptursachen für den gegenwärtigen drastischen Verlust an Biodiversität. Diese Dissertation soll zu einem besseren Verständnis der Vegetationsdynamik in fragmentierten Landschaften beitragen. Damit verbunden ist das Ziel, Vorhersagen über die Reaktion von Pflanzengemeinschaften auf Fragmentierung zu verbessern. Diese Vorhersagen sind notwendig, um gezielte Naturschutzmaßnahmen zur Verminderung eines weiteren Verlustes an Biodiversität umsetzen zu können. In Kapitel 2 der Dissertation wird mit einem Simulationsmodell untersucht, wie sich die Ausbreitungsdistanz von Samen auf die lokale Artenzahl von Pflanzengemeinschaften auswirkt. Dabei zeigte sich, dass längere Ausbreitungsdistanzen die lokale Artenvielfalt sowohl erhöhen, als auch verringern können. Der wichtigste Einflussfaktor war dabei die Artenvielfalt der über-geordneten Pflanzengemeinschaft, in der die betrachtete lokale Gemeinschaft eingebettet war. Im dritten Kapitel wird die Konnektivität zwischen Pflanzengemeinschaften in Habitat-fragmenten, d.h. der Austausch von Arten und Individuen durch Samenausbreitung, im Unter-suchungsgebiet in Israel analysiert. Dafür wurde ein zweites räumliches Simulationsmodell mit statistischen Verfahren an Felddaten angepasst. Der Vergleich des Modells mit den Daten wies auf eine sehr geringe Konnektivität zwischen den Habitatfragmenten hin. Das Modell sagte vorher, dass innerhalb von 1000 Jahren 33% - 60% der Arten aussterben könnten. In Kapitel 4 wird zuerst analysiert, welche Prozesse die Verteilung von funktionellen Eigenschaften in Pflanzengemeinschaften bestimmen. In einem zweiten Schritt wird dann unter-sucht, wie sich funktionelle Eigenschaften von Pflanzengemeinschaften mit dem Niederschlag und der Fragmentierung im Untersuchungsgebiet in Israel verändern. Der Zusammenhang zwischen den Eigenschaften Pflanzenhöhe, sowie spezifischer Blattfläche und der Fragmentierung änderte sich nicht entlang des Niederschlagsgradienten. Im Gegensatz dazu, änderte sich der Zusammenhang zwischen der Samenmasse bzw. der Samenzahl und der Fragmentierung mit dem Niederschlag. Aus den Ergebnissen der ersten Teilstudie wird deutlich, dass Naturschutzmaßnahmen, die natürliche Habitate stärker vernetzen sollen, die Diversität, sowie die Zusammensetzung der übergeordneten Artengemeinschaft berücksichtigen müssen, um Verluste an Biodiversität zu vermeiden. Die Verknüpfung eines räumlichen Simulationsmodells mit Felddaten in der zweiten Teilstudie stellt einen neuen und vielversprechenden Ansatz für die Untersuchung der Auswirkungen verschiedener Management-Szenarien dar. Die dritte Teilstudie ist die erste Analyse der gemeinsamen Auswirkungen von Klima und Fragmentierung auf funktionelle Pflanzen-eigenschaften und zeigt die hohe Bedeutung der Untersuchung von Synergie-Effekten verschiedener Umweltfaktoren. Für zukünftige Forschung legt diese Dissertation nahe, funktionelle Eigenschaften und Konkurrenz zwischen Arten in räumlichen Simulationsmodellen zu berücksichtigen, um das Verständnis von Artengemeinschaften in fragmentierten Landschaften noch weiter zu verbessern.

Three species of fungi Sporotrichum thermophile, Botrytis cinerea and Trichoderma viride were assessed for their ability to utilize a variety of plant cell substrates (methanol extracted), Catharanthus roseus, Daucus carota, re-autoclaved C. roseus, re-autoclaved D. carota) which preliminary studies had indicated contained the necessary nutrients for fungal growth. Incubated in a suitable manner all three fungal species were able to grow on C. roseus and D. carota plant cell biomass in addition to material which had undergone methanol extraction or a re-autoclaving process to remove soluble components. Fungal biomass yields were markedly influenced by substrate, with each fungal species demonstrating a preference for particular plant cell material. Incubation conditions i.e. static or shaken and temperature also proved important. Release of glucose (i.e. values higher than Day 0) promoted by fungal breakdown of plant cell biomass was only noted with methanol extracted, re-autoclaved C. roseus and re-autoclaved D. carota material. A re-autoclaved substrate was also generally associated with high fungal C1, Cx, B-glucosidase and endo-polygalacturonase activity. In addition for each enzyme highest values were usually obtained from a particular fungal species. Buffering cultures at pH 3 or 5 further influenced enzyme activity, however in a majority of cases when flasks were unbuffered and the pH rose naturally to alkaline values higher enzyme activity was recorded. Likewise Tween 80 addition had only a limited beneficial effect. Finally filtrates containing glucose produced both from the re-autoclaving process and through fungal activity on plant cell biomass were utilized for Fusarium oxysporum, Saccharomyces cerevisiae and C. roseus plant cell culture. Although reasonable fungal biomass was obtained the use of such filtrates proved unsuitable for plant cell growth.

California grows more than 91% of fresh strawberries in the United States. Critical to this success has been management of soilborne diseases using pre-plant soil fumigation with methyl bromide. However, international regulations require a phase out of methyl bromide, soon to be completed. Reduced availability of methyl bromide has coincided with increased incidence of soilborne diseases affecting strawberry production, including Verticillium wilt, caused by Verticillium dahliae, and Black Root Rot (BRR). BRR is caused by a complex of soilborne pathogens, including Pythium ultimum, that form lesions on tertiary roots, which are critical to nutrient and water uptake. Consequently, non-chemical alternatives for sustainable management of soilborne diseases and highly productive plants are urgently needed.

Crop rotation with legumes can contribute to plant productivity and disease management by fixing nitrogen and providing a non-host interval during which the pathogen can die by natural attrition. However, rotation crops that appear to be non-hosts because they show no symptoms of disease may nevertheless support development of the pathogen and thus negate the benefit of crop rotation. One objective of this research was to evaluate systemic colonization of ten legume cover crops V. dahliae under field conditions and the extent to which plant residue supports development of V. dahliae microsclerotia (Chapter 1). This included seven cool season legumes: broad 'Windsor' bean, bell bean, field pea, hairy vetch, common vetch, purple vetch and 'Lana' woolypod vetch, and three warm season legumes: sesbania, sunn hemp and black-eyed pea. Frequency of systemic infection at ten weeks ranged from 5% (woolypod vetch) to 23% (field pea) and at the end of the trial ranged from 0% (purple vetch) to 23% (hairy vetch). The trend for mean density of microsclerotia in residue at ten weeks ranged from 0 CFU/g residue (hairy vetch) to 583 CFU/g residue (field pea) and at the end of the trial ranged from 63 CFU/g residue (broad bean) to 1096 CFU/g residue (field pea). In most cases, frequency of infection and formation of microsclerotia in plant residue was higher by the end of the trial than at ten weeks. Thus, in fields infested with V. dahliae, growers should avoid rotation with the evaluated legumes to avoid increasing soil inoculum levels.

Compost can contribute to plant productivity and disease management by improving soil structure and fertility, and providing the necessary factors to shift soils from disease conducive to suppressive. This study was undertaken to evaluate four composts that are available to California strawberry growers: manure compost, spent mushroom compost, vermicompost and yard trimmings compost. The objective was to evaluate the effect on production parameters including soil quality and fertility, and plant growth and yield. Manure and mushroom compost significantly increased soil electrical conductivity, which reached levels of 9.9±1.7dS/m and 7.3±0.8dS/m, respectively. Manure, yard trimmings and mushroom composts shifted soil pH closer to optimal levels for up to 7 months in 4 to 5 of the trials. Mushroom compost had the greatest effect on soil nitrate, with up to 32 mg/kg nitrate higher than the non-amended soil.

Another potential benefit of compost is suppression of soilborne pathogens, which can result from changes in the composition and activity of the soil microbiota. It was an objective of this study to determine if four commercially available composts influence infection of strawberry roots by V. dahliae and P. ultimum. The results showed a significant reduction in V. dahliae root infections in some compost amended soils but results were not consistent across trials. The effect of compost amendments on seedling disease caused by P. ultimum was a reduction in disease incidence by 38-43% compared to the non-amended soil.

The industry-wide shift in strawberry production generates a tremendous need for knowledge transfer and grower support. Accordingly an additional objective of this research was to solicit industry perspectives on the status of soilborne disease management. Results identified crop rotation as the most important tool in the absence of fumigation as, reported by 46% of respondents. When given a choice of thirteen management tools, crop rotation also had the highest ranking by respondents as a practice always used/recommended.

Numerous soilborne disease management tools, like crop rotation and compost, sustain high yields and reduce disease incidence, but vary in status of adoption. At a pivotal time when land is still productive but pathogens are becoming more widespread, a regional plan for maintaining pathogen-free soil has an opportunity to emerge as the foundation for a sustainable industry in the post-fumigation era. (Abstract shortened by UMI.)

The tricarboxylic acid (TCA) cycle is one of the central pathways in respiration and also plays an important role in a variety of metabolic processes including the synthesis of secondary metabolites and the provision of carbon skeletons for ammonium assimilation and amino acid biosynthesis. Effective regulation of these multiple demands on the TCA cycle is likely to be very important for plant fitness. One way that this regulation could be achieved is through metabolite channelling. This occurs when metabolites are transferred between enzyme active sites without diffusing into the bulk aqueous phase of the cell, and is known to be important in regulating demands in metabolic pathways. Although there is evidence that metabolite channelling exists in animals, there have been no attempts to investigate it in plant. The first aim of this thesis was therefore to investigate whether metabolite channelling exists in the plant TCA cycle. Isotope dilution experiments were developed to investigate metabolite channelling, and were able to show that metabolite channelling was present between certain enzymes of the TCA cycle in both S. tuberosum and A. thaliana mitochondria. The second aim of the thesis was investigate whether metabolite channelling is important in regulating the TCA cycle in plant mitochondria. The pattern of metabolite channelling did not change in mitochondria isolated from the light and the dark, or from mitochondria with increased or decreased TCA cycle rates, but it was not possible to say whether the metabolite channelling altered in a quantitative fashion. Overall the thesis provides the first direct evidence of channelling in the TCA cycle in plants, and further work should help to elucidate what role, if any, it plays.

Johnsongrass (Sorghum halepense) competition in soybeans (Glycine max) has adverse effects on soybean yields. Profitable soybean production in Kentucky and the Southeastern United States has depended upon good, cost effective johnsongrass control. Several herbicides have been developed to control johnsongrass in soybeans. Four of these recently developed compounds were imazaquin (2-[4,5-dihydro-4-methy1-4- (1-methyl-ethyl)-5-oxo-1H-imidazo1-2-y1]-3-quino1inecarboxy1ic acid), imazethapyr (+/-)-2-C4,5-dihydro-4-methy1-4-(1-methy. lethyl)-5-oxo-IH-imidazol-2-y1)-5-ethy1-3-pyridinecarboxylic acid, quizalofop 2-[4-[(6-chloro-2-quinoxalinyl) oxylphenoxyjpropaonic acid,ethyl ester, and analog of quizalofop (DPX Y6202-31). Field experiments were conducted in 1986 to evaluate (a) the effectiveness of imazaquin and imazethapyr preplant incorporated, postemergence, or in combination with pendimethalin [N-(1-ethylpropy1)-3,4-dimethy1-2.6-dinitrobenzenamine], and (b) herbicide antagonism with fluazifop[butyl(R)-2-(4-[(5- trifluoromethy 1 ) - 2-pyridinl] oxy] phenoxy] propanoate], quizalofop, sethoxydim [2-[1-(ethoxyimino)butyl] -5-(2- (rthylthio)propy1]-3-hydroxy-2-cyclohexen-l-one, fenoxaprop [(+/-)-2-[4-((6-chloro-2-benzoxa-zoly) oxy]phenoxy]propanoic acid], and DPX-Y6202-31, in combination with imazaquin, bentazon [3-(1-methylethyl)-(ih)-2,1,3, benzothiadiazin- 4(3h)-one 2,2-dioxide], acifluorfen [5-[2-chloro-4(trifluoromethyl) phenoxy]-2-nitrobenzoic acid], and chlorimuron [3-(3,4-dichloropheny1)-1-methoxy-1-methylurea and Ethyl 2--[[[[(4-chloro-6-methoxy-pyrimidin-2-yl)amino)-carbonyl] amino]sulfonyl]binzoate], for johnsongrass control in soybeans. Imazaquin was applied preplant incorporated, tankmixed with pendimethalin and imazethapyr. Imazethapyr was applied preplant incorporated and postemergence with surfactant at equal rates. DPX-Y6202-31 was applied postemergence at four different rates, and in tankmix combinations with chlorimuron, acifluorfen, bentazon, and imazaquin, with surfactant or crop oil contrate. Quizalofop was applied postemergence at tour use rates.

Green roofs are living rooftops that have been around for centuries. Green roofs serve many purposes including food production, insulation of buildings, and reducing the urban heat island effect. More and more research is being done to utilize unused space on top of buildings for a better community. Food shortage is one of the biggest problems in the United States and across the world. Due to increased population and a decrease of resources, fresh food is becoming more difficult to obtain. Fresh produce intake increases in communities as the amount of available produce within 100 meters of their residence increases (Bodor et al., 2007). Urban agriculture could help mitigate the shortage of healthy food by getting the community involved to produce their own food. Local food production results in less cost and less spoilage of food due to decreased transportation and increased quality of produce. My study was designed to demonstrate that vegetables can be produced successfully on a green roof in three different growth media. The growth media blends evaluated were 100% compost, 50% green roof media and 50% compost, and 100% green roof media. Vegetables were grown in Filtrexx^® GardenSoxx ^®. Vegetables were planted over two growing seasons from 2015 to 2016. The results from my study demonstrated that carrots and lettuce are viable crops on a rooftop garden using the studied system. In the one harvest of Buttercrunch lettuce, there was no significant difference in lettuce biomass produced between the three different growth media blends used. The first growing season with Short ‘n Sweet carrots, showed no significant difference in carrot biomass produced between the three growth media blends. In the second growing season, started July 2016, the results of the carrot biomass harvest varied between the growth media blends. Carrots grown in the 50% compost and 50% green roof media blend had the most biomass when compared with carrot biomass from the 100% compost blend. I have demonstrated that Short ‘n Sweet carrots and Buttercrunch lettuce can be grown in GardenSoxx^® on a rooftop garden in three different growth media blends.

The processes by which plant spatial patterns are formed, and the effects of those patterns on plant community dynamics, remain important areas of research in plant ecology. Plant spatial pattern formation has been linked to many ecological processes that act to structure plant communities at different spatiotemporal scales. Past studies of pattern formation are common, but recent methodological advances in data collection and analysis have permitted researchers to conduct more advanced observational studies of pattern formation in space and time. While studies of the effects of plant spatial patterns were formally rare, they have increased in the last decade as new types of experiments and analysis have been developed to better understand the myriad effects of plant patterns on community dynamics. My dissertation research examined both the causes and consequences of plant spatial patterns in the context of natural and experimental Great Basin semi-arid plant communities. In both cases, I implemented novel methodologies for data collection, experimental design, and data analysis in an attempt to address current gaps in knowledge related to the processes by which plant spatial patterns are formed, as well as the effect of plant spatial patterns on community dynamics. The results inform both basic and applied plant ecology, and set the stage for further research on the causes and consequences of plant spatial patterns in semi-arid plant communities.

Over the past century, changes in farming practices have resulted in an enormous increase in agricultural productivity. Substantial gains in crop yields were due to several factors, including the use of nitrogen fertilizers and pesticides (Youngquist, 1999). These chemicals are primarily derived from fossil fuels, such as petroleum and natural gas. Considering these are both finite resources, there is a need to develop alternative technologies that boost crop productivity in a sustainable way. Recent studies have proposed the use of endophytes to promote plant growth and increase yields. One specific endophyte, Enterobacter sp. 638, has been shown to enhance plant growth in a variety of hosts. E. 638 produces plant hormones which result in increased biomass (Taghavi et al., 2011). This study measures the effects of inoculation with E. 638 on growth and gene expression in tomato (Solanum lycopersicum ). Two factors, inoculation and stress, were examined for their effects on time to flower, time to first produce fruit and first ripening event, as well as total mass of fruit and vegetative tissue. Stressed conditions were simulated by growing tomato plants in small (19 L) pots in a greenhouse, while unstressed plants were placed outside in larger (∼57 L) pots to minimize restriction of root growth and maintain a more natural environment.

Furthermore, this study used qPCR to measure the relative expression of genes involved in auxin transport, cytokinin signaling, ethylene signaling and cell wall expansion in tomato roots. The effects of inoculation on gene expression between control and exposed plants were compared. The results of this study may have major implications to agriculture by reducing cost and reliance on petroleum based chemicals, as well as to the field of plant physiology. Understanding how plants respond to inoculation with E. 638 may lead to a better understanding of plant responses to external stimuli.

Carinata (Brassica carinata A. Braun), a non-food oilseed crop and an alternative bio-jet fuel feedstock, has received attention for its potential as a low-input option for production in the semi-arid regions of the Northern Great Plains of USA. The crop has a lower N fertilizer requirement as compared to the other oilseeds, suggesting less negative impact on soils and GHGs emissions. Carinata is a new crop to South Dakota (SD), thus, the best management practices have yet to be developed. In addition, no sufficient research to address the impact of growing carinata on soils and GHG emissions has been reported. The objectives of the study were to: (i) evaluate the response of seed yield and agronomic traits for carinata to N and S fertilizer rates, and (ii) evaluate the impact of growing carinata with different rates of N and S fertilizers on select soil properties and GHG emissions. Field experiments were conducted in 2017 and 2018 to assess the response of carinata to four N rates (56, 84, 112 and 140 kg N ha^–1) and three S rates (0, 22 and 45 kg S ha^–1) and) at Brookings, SD under conventional tillage. Increasing N fertilizer rate significantly increased plant height, branching, lodging severity, number of pods plant^–1 but significantly decreased seed oil concentration. Increasing S fertilizer rate significantly increased plant height, branching, agronomic traits, seed yield, and seed oil concentration. This study showed that the economically optimal N rate was 85 kg N ha^–1 and the economically optimal S rate was 36 kg S ha^–1. Application of N fertilizer had minimal impact on soil parameters; N fertilizer increased soil EC, soil organic carbon (SOC), stable carbon, labile N, soil K, and soil P. Sulfur fertilizer decreased soil EC, SOC, labile N, and soil inorganic N content but increased extractable S content. Results from GHG emissions showed that, in addition to soil temperature and moisture conditions, N fertilizer increased CO₂¬ and N₂O emissions, whereas, S fertilizer application did not affect emissions. Methane fluxes fluctuated due to the impact of soil temperature and moisture.

Findings from this study suggested that carinata has low nutrient requirements compared to the traditional crops grown in SD, and optimum N and S requirements for this crop were developed. This study also suggested that, in general, carinata has minimal impacts on soils and GHG emissions, however, a long-term monitoring of soils and GHG fluxes under different rotations, soils and environmental conditions can be beneficial in understanding the impacts associated with carinata production.

Glyphosate-resistant Palmer amaranth (Amaranthus palmeri [S.] Wats) is an economically troublesome weed to southeastern United States soybean (Glycine max [L.] Merr.) growers. Palmer amaranth is troublesome due to its evolution of resistance to multiple herbicide modes of action, competiveness, and prolific seed production. Greenhouse studies were conducted at the Delta Research and Extension Center in Stoneville, MS to evaluate different rates of 2,4-dichlorophenoxyacetic acid (2,4-D) for control of Palmer amaranth. Field experiments were conducted at the Delta Research and Extension Center in Stoneville, MS in 2013 and 2014 to evaluate Palmer amaranth emergence using a cultural practice and a residual herbicide. Field experiments were also conducted at the Delta Research and Extension Center in Stoneville, MS in 2013 and 2014 to evaluate Palmer amaranth control with applications of glyphosate, glufosinate, and 2,4-D alone and in mixtures.

Terrestrial and oceanic biomass carbon sinks help reduce anthropogenic CO₂ emissions and mitigate the long-term effect of increasing atmospheric CO₂. Woody plants have large carbon pools because of their long residence time, however N availability can negatively impact tree responses to elevated CO₂. Seasonal cycling of internal N in trees is a component that contributes to fitness especially in N limited environments. It involves resorption from senescing leaves of deciduous trees and storage as vegetative storage proteins (VSP) in perennial organs. Populus is a model organism for tree biology that efficiently recycles N. Bark storage proteins (BSP) are the most abundant VSP that serves as seasonal N reserves. Here I show how poplar growth is influenced by N availability and how growth is influenced by shoot competition for stored N reserves. I also provide data that indicates that auxin mediates BSP catabolism during renewed shoot growth. Understanding the components of N accumulation, remobilization and utilization can provide insights leading to increasing N use efficiency (NUE) of perennial plants.

Auxin is a crucial plant hormone that shapes and directs plant growth. Indole-3-acetic acid (IAA) is the predominant auxin in nature. Auxin regulates cell expansion and cell division in a dose dependent way. Therefore, plants evolved an extremely complex yet highly coordinated network to maintain auxin homeostasis, including IAA biosynthesis, transport, conjugation and oxidation. Among these, the least known process is IAA oxidation. Discovering how IAA is terminated is very important in completing the whole picture of IAA homeostatic regulation. By partial purification of IAA oxidases from Arabidopsis , we detected IAA oxidation activity from both microsomal fractions and soluble fractions. We first investigated the protein in microsomal fraction and identified one oxidase named as ACC oxidase 2 (ACO2), an ethylene synthetase that belongs to 2-oxoglutarate and iron (II) [2OG(Fe)] dependent dioxygenase family. In vitro enzyme assays with IAA showed that ACO2 could catabolize IAA and that the product had the same retention time as indole-3-carbinal (ICA), an decarboxylative IAA oxidation product. The same enzyme assay with the ACO2 homologues ACO3 was conducted, and ACO3 showed similar activity. An ACO2 loss-of-function allele showed ethylene related phenotypes, including longer hypocotyls and reduced apical hook angle in etiolated seedlings, and delayed bolting. Further, null aco2 mutants also showed reduced phototropic bending, a typical auxin related phenotype. These results indicate that ACO2 might be involved in both ethylene and auxin signaling.

We also investigated the soluble IAA oxidases, AtDAO1 (DAO1) and AtDAO2 (DAO2). In vitro enzyme assays showed that both recombinant DAO1 and DAO2 have IAA oxidation activity and the product is the non-decarboxylated 2-oxindole-3-acetic acid (oxIAA), the major IAA metabolite observed under normal growth conditions. Analysis of the loss-of-function null allele dao1-1 showed that DAO1 is the predominant IAA oxidase and is responsible for 95% of oxIAA production in Arabidopsis seedlings. Dysregulation of IAA oxidation altered the IAA metabolism profile and causes accumulation of other IAA conjugates and a series of morphological alteration, including elongation of organs, increased lateral roots and delayed sepal opening. Investigation of expression patterns shows that DAO1 is a cytosolic protein that widely expressed throughout the plant, especially in the root tip, the pericycle of root, the cotyledon, and the sepal, highly correlating to the phenotypes of dao1-1. These results suggest that IAA oxidation plays an important role in IAA homeostasis during the whole life of Arabidopsis.

Palmer amaranth is a growing concern in the United States. Previously thought to only be able to occupy the southern United States, this plant can now be found throughout the northern states as well. Infestations of Palmer amaranth can now be found in South Dakota and is raising many concerns. Palmer amaranth is characterized by large growth and can be highly competitive with many important crops. Soybean is an important crop in South Dakota, as well as the rest of the world, and has not escaped the detrimental aspects of an infestation of Palmer amaranth. The objectives of this study were to determine the possible impacts Palmer amaranth South Dakota.

Surveys were given to applicators and producers from many counties in South Dakota to gauge public awareness of Palmer amaranth and determine other possible infestations of Palmer amaranth. These surveys were made available at commercial applicator recertification classes throughout South Dakota and the Soy 100 meeting in Brookings, SD.

Growth rates and plant volume and biomass of Palmer amaranth from several seed source locations and local ascensions of common waterhemp and redroot pigweed were examined and compared in eastern South Dakota. Growth studies were conducted near Aurora, SD over two years using three planting dates from mid-May to late-June. Plant volume was measured every 10 to 20 days until harvest beginning in late-July. At harvest, plants were oven-dried and biomass was recorded.

Efficacy of several herbicide treatments were recorded on Palmer amaranth seedlings. Pre- and post-emergence treatments were conducted on Palmer amaranth planted in either sand or potting mix. Post-emergence treatments were applied at the three- to four-leaf stage. Visual ratings of plants were conducted 21 days after treatment.

Soybean yield loss due to Palmer amaranth was determined near Corsica, SD. Palmer amaranth in square meter plots were counted and harvested for biomass when soybeans reached R7 to R8. Plots containing two rows of soybeans were harvested several weeks later and yield loss was determined.

Survey results indicated that more needs to be done to provide information to the public based on respondents’ ability to correctly identify Palmer amaranth, common waterhemp, and redroot pigweed seedlings and mature plants. Several respondents also indicated possible infestations of Palmer amaranth. Not all counties in South Dakota were represented by the study.

Palmer amaranth had greater growth and biomass than either common waterhemp or redroot pigweed. Final volume of Palmer amaranth was greater at lower densities. Growth rates between sampling dates varied among planting dates, which resulted in similarities in final volume among planting dates. Common waterhemp and redroot pigweed shared similar plant volumes and biomass, however, plants in 2015 were larger, possibly due to climatic differences between years.

Herbicides tested that offered the best control of Palmer amaranth was a pre-emergence application of S-metolachlor and a post-emergence application of either dicamba or glufosinate. Glyphosate only provided partial control and mesotrione provided variable control. Atrazine had the little control as a pre- or post-emergence treatment. Thifensulfuron had no control of Palmer amaranth.

Soybean yield loss in 2016 determined an incremental loss of 9% at one Palmer amaranth m^–2. Maximum yield loss of 45% was seen at 15 plants m^–2, however, yield losses at densities slightly lower and higher caused a 35% maximum yield loss prediction. Yield loss in 2017 was variable due to outside factors and a relationship between yield loss and Palmer amaranth density or biomass could not be determined.

As crop land decreases and population increases, soil quality is becoming a concern. Utilizing cover crops in cropping systems could improve soil quality. This study examined 16 treatments of single-species cover crops, cover crop mixes, and two control treatments on a silt-loam soil, in a corn ( Zea mays L.) - soybean (Glycine max L. Merr.) crop rotation under no-tillage, to determine their effect on soil physical properties. Cover crop biomass differed (p<0.10) among treatments and produced a maximum of 15.6 Mg ha^-1 of biomass in the crimson clover treatment. Water infiltration rates increased as much as 282% in the complete-mix treatment compared to the fallow control. Differences in infiltration rates due to cover crop species were shown in two-years. However, these results suggest that it may take more time for cover crops to affect change in bulk density and aggregate stability.

Increases in photosynthetic rates (A), biomass production and grain yield have been measured across a range of C₃ plants under elevated atmospheric [CO₂] ('eCO₂'). However, decreases in the nutritional status of many C₃ plants growing at eCO₂ often occur concurrently with these increases. Several mechanisms have been proposed for these eCO₂-induced decreases, such as dilution effects due to enhanced carbohydrate production, down-regulation of photosynthesis, reduced root development, and decreased transpiration-driven mass flow delivery of nutrients. Reduced mass flow at eCO₂ is generally accepted as one cause for altered nutrient status in C₃ plants. However, eCO₂-induced reductions in mass flow remain understudied in C₄ plants, even though they account for about 18% of the total global net primary productivity and represent a large food source globally (e.g. maize and sorghum). This thesis investigated how mass flow reductions affect the nutrient status of wheat (C₃) and maize (C₄) plants. Reduced mass flow in both maize and wheat plants was induced with eCO₂ and by varying leaf-to-air vapour pressure deficits (VPD). I hypothesised that reduced mass flow at eCO₂ and at low VPD will negatively affect nutrient status in both the C₃ (wheat) and the C₄ (maize) species. In the first experiment, maize and wheat plants were grown at 400 and 800 ppm [CO₂], in three well-watered soils, ranging from sandy to clayey, with and without fertilisation. In the second experiment, plants were grown at three VPD levels, namely 1.613 kPa, 0.773 kPa and 0.350 kPa, in well-watered soil and sand. In the latter experiment, to demonstrate the importance of mass flow, plants grown in sand were supplied nutrients in such a way that they had to rely exclusively on mass flow or diffusive processes (i.e. limited interception) for nutrient delivery to their rhizosphere. eCO₂ stimulated A on average by 22% in maize and by 50% in wheat, while stomatal conductance (ɡₛ) and cumulative water loss (CWL) were respectively decreased by 35% and 31% in maize, and by 26% and 37% in wheat. eCO₂ reduced mass flow delivery of most nutrients on average by 32% in maize, and by 38% in wheat. The hypothesis that eCO₂-induced reductions in mass flow negatively affect nutrient status in maize 33 and wheat was however not supported. This was attributed to the well-watered conditions of the soils, which may have allowed for other processes (e.g. diffusion) to make up for the mass flow reductions. From 0.773 kPa to 0.350 kPa VPD, CWL was decreased on average by 14% and 20% in the maize and wheat plants, respectively. A and ɡₛ were little affected by VPD, but plants of both species always accumulated more biomass at 0.773 kPa. Consequently, there was little evidence to suggest that VPD-induced reductions in mass flow negatively affect nutrient status in maize and wheat. Reduced CWL may have impeded root-to-shoot transport of ions and reduced dry biomass accumulation in the maize and wheat plants at 0.350 kPa (-40% and -22% on average respectively, relative to 0.773 kPa plants). Tissue [NPK] was also decreased (-13%, -41% and -47% respectively) in the 0.350 kPa VPD sand wheat plants, while increases in the proportion of finer roots may have alleviated effects of reduced CWL on tissue [NPK] in the C₄ species. The findings from both experiments imply a decrease in the importance of mass flow for the delivery of nutrients to the rhizosphere under well-watered conditions. However, reductions in mass flow to a similar extent in both species at eCO₂ and low VPD - measured in the present study - suggest that under conditions of low water and nutrient availability, tissue nutrient concentrations could be negatively affected when transpiration is reduced.

Common integrated vegetation management (IVM) practices including herbicide and mowing applications on right-of-ways and forages were evaluated on green antelopehorn populations near Starkville, MS. Live stems in each plot were counted prior to treatment application and approximately one year after treatment (YAT). Analysis of the stem counts 1YAT indicated aminopyralid+metsulfuron, imazapyr, picloram+2,4-D, maximum rates of triclopyr ester or choline, glyphosate, imazapyr+aminocyclopyrachlor+metsulfuron reduced the number of green antelopehorn stems compared to the untreated. Aminocyclopyrachlor, aminocyclopyrachlor+chlorsulfuron, aminopyralid, aminopyralid+2,4-D, dicamba+2,4-D, foramsulfuron+iodosulfuron+thiencarbazone, fluroxypyr, hexazinone, metsulfuron, metsulfuron+chlorsulfuron, nicosulfuron+metsulfuron, sulfometuron, sulfosulfuron or low rates of triclopyr did not reduce the stem count 1YAT when compared to the untreated. Mowing timing and frequencies applications were initiated May through July and evaluated through August. Mowing early in the season increased milkweed stems one month after treatment versus late season mowings. Majority of milkweed plants developed mature seed pods and senesced by early August.

In arid and semi-arid ecosystems, dominant tree species create dramatic mosaics of plant islands of fertility and relatively barren plant interspaces that exert immense pressure on ecosystem processes and offers an ideal opportunity to explore the impact of bacterial communities. We evaluated potential links between soil respiration and N mineralization, and community co-occurrence networks and predicted gene function across three tree island microsites (i.e., beneath tree canopies, at the canopy edge, and in interspaces) in a replicated field experiment in thirty-eight woodlands sites in the Great Basin Desert in UT, USA. Additionally, we potentially intensified the effects of tree islands by creating a treatment where whole trees were shredded and the resulting fine woody debris (FWD) was deposited onto the soil surface and measured a suite of characteristics relating to the metabolic functional state of communities (i.e., microbial efficiency as the microbial quotient, C substrate quality, biomass, and dissolved organic C) to improve our interpretation of potential links between function and structure. We found that tree islands were the predominant driver, creating highly complex and connected assemblies of bacterial populations and easily discernable differences in abundance and composition of predicted functional genes. Specifically, communities directly beneath Juniperus and Pinus canopies were comprised of at least 5.2-times more connections between bacterial taxa than present in networks from interspace and edge. Using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) to predict the gene expression, differences in the functional potential mirrored shifts in network complexity. Tree island communities expressed 236 genes with many related to the degradation of polyaromatic or polycyclic compounds, while interspace communities expressed only 66 genes associated with the decomposition of more labile C substrates. We observed a robust tree island microsite effect on all ecosystem processes, with soil respiration rates increasing 12% and N mineralization decreasing 29% in canopy than interspace soils demonstrating that a more recalcitrant substrate from a sole C source provided high amounts of low quality of DOC and lead to a decrease in metabolic efficiency, but ultimately selected for a specific community assembly. Alternatively, communities at the edge of canopies, experiencing both tree island and interspace soil conditions generated similar levels of soil respiration as canopy soils regardless of not selecting for a highly connected community and/or specific genes suggesting that a diverse composition of labile and recalcitrant C substrates from multiple sources (e.g., trees, perennial grasses, annual grasses, and forbs) potentially elevates function by promoting the activity of a wide range of taxa. Our results identify that tree islands exert enough pressure to create distinct interactions between bacteria and alter gene expression resulting in changes in ecosystem function, but the link between structure and function is mediated through the diversity and quality of C substrates.

Chenopodium L. is a relatively under-studied genus that includes the cultivated seed crop quinoa (Chenopodium quinoa Willd.). Quinoa is an allotetraploid (2n=4x=36, AABB genomes) that is cultivated by subsistence farmers and commercial growers in the Andean regions of South America. Approximately 60% of a quinoa seed is starch, a glucose polymer that is an important carbohydrate energy source in the human diet. Seed starch is normally comprised of amylose and amylopectin in a 1:3 ratio, but starches with different amylose:amylopectin ratios have different properties and potential uses. The accumulation of the amylose fraction of starch is controlled by a single dominant gene in quinoa, GBSSI. We report the sequencing and characterization of the GBSSI gene in 18 accessions of Chenopodium, including Andean quinoa and the related Mesoamerican chenopod grain species, C. berlandieri subsp. nuttalliae Saff. Two distinct homoeologs (GBSSIa and GBSSIb) were identified in the tetraploid accessions, and 19 different alleles were identified, including three null mutants – one in an accession of quinoa and two in a waxy landrace of C. berlandieri subsp. nuttalliae, referred to as ‘H02’. Expression analysis of the null mutants revealed that GBSSIa and GBSSIb were both strongly expressed late in quinoa and C. berlandieri subsp. nuttalliae seed development. Starch phenotyping indicated that ‘H02’ produced no amylose, likely due to its having two mutated copies of GBSSI. GBSSI sequences were used to analyze the phylogenetic relationships between quinoa and other members of the Chenopodium genus. This study and the discovery of Chenopodium GBSSI null-mutants will assist in the development of new Chenopodium crops with novel starches.

An integrated management approach for jointed goatgrass control was investigated at two farms in northern Utah using three tillage regimes and tree herbicides. The tillage regimes included no tillage, conservation tillage, and conventional tillage. Each regime was composed of different tillage practices common in the Intermountain West. A preemergence herbicide, clomazone, and two postergance herbicides, 2, 4-D and glyphosate, were investigated. Greenhouse studies were also conducted to investigate clomazone efficacy and depth of planting of winter wheat and jointed goatgrass. Differential sensitivity to clomazone between jointed goatgrass and winter wheat did not occur in the greenhouse for the rates tested. A treatment of 0.11 kg ai ha-1 clomazone reduced wheat and jointed goatgrass fresh weights similarly by 49 and 63% respectively. Jointed goatgrass did not germinate below 6.4 cm and emergence was initially reduced at the 2.5 cm soil depth. Winter wheat emergence was not lowered until the seed was planted 5.0 cm deep or deeper and continued to 8.9 cm deep.

Legumes contribute significantly to sustainable agriculture because of their high protein content. This intrinsic nitrogen is the product of a mutualistic association between their roots, and a group of soil bacteria, collectively known as rhizobia. The rhizobium-legume symbiosis is a complex developmental process that involves rhizobial entry and differentiation, coupled in space and time, with the development of a root organ (the nodule) and is subject to modulation by environmental factors. Salt stress is a strong negative regulator of rhizobium-legume symbiosis, but despite its agricultural impact, the mechanism of salt regulation of rhizobium-legume symbiosis is poorly understood. This dissertation addresses this issue with focus on early rhizobium-legume signaling and maturation of nodules, using the model legume Medicago truncatula. The rhizobium-legume symbiosis is initiated with a molecular dialogue between the symbiotic partners, followed by the entry of rhizobia inside the host. These processes are under tight genetic regulation and involve the symbiotic induction of several host genes. I used a candidate gene-approach to locate the temporal intersection of salt and rhizobium-legume signaling and found that the ionic component of salinity hyperinduces Early Nodulin 11 (ENOD11) and ERF Required for Nodulation 1 (ERN1). I also found that the hyperinduction of ENOD11 requires two symbiotic rhizobial signals- Nod factors (NF) and succinoglycan and the host transcription factor Nodulation Signaling Pathway 2 (NSP2). In order to explore the possibility of an extensive transcriptional re-programming during rhizobium-legume signaling in the presence of salinity, I profiled the host root transcriptome and discovered strong transcriptional upregulation by salt, of several host genes associated with NF perception, rhizobial infection and ubiquitination. Curiously, I found that the hyperinduction of these genes correlate with an inhibition of rhizobial entry into the host. These findings highlight that early rhizobium-legume signaling and rhizobial colonization of the host are under tight transcriptional regulation of the host. Despite the early inhibition of infection, few nodules develop under salt stress. However, these nodules are morphologically abnormal, indicating that salinity must interfere with nodule maturation, a prerequisite for nitrogen fixation. Consistent with the theme of early symbiotic signaling, I found host genes involved during the early stages of nodule differentiation to remain highly expressed in nodules that developed under salt stress, suggesting a delay in maturation. This inference was further corroborated when I found that genes associated with the later stages of nodule development and nitrogen fixation showed decreased expression in the presence of salt. Additionally, I observed that this developmental shift of nodules under salinity was associated with differential accumulation of osmolytes, such as, proline betaine and homostachydrine in the salt-stressed nodules. Together, my work provides a mechanistic understanding of the intersection between nodulation and salt signaling, a question of major agricultural impact.

The elucidation of the binding of marijuana’s psychoactive compound, (-)-D9- tetrahydrocannabinol (THC), to specific membrane receptors, in the early 1990s, led to the identification of endogenous arachidonate-based lipids that activate cannabinoid receptors in mammals. While the metabolic and signaling pathway for these 20 carbon N-acylethanolamines (NAE) and their derivatives has been well characterized in mammals, thus far, only 12-18 carbon NAEs have been identified in plants and their metabolic pathway has been partly characterized. In plants, NAEs have been shown to modulate a number of physiological processes, including seed and seedling development and ability to respond to stress; however, the mechanisms by which they function remain to be elucidated. Our recent identification of a 20C NAE (arachidonylethanolamide) in moss provided us with an exciting possibility to identify receptor-mediated endocannabinoid signaling responses in plants that is akin to mammals. In this seminar, I will provide insights into the past, present and future aspects of plant endocannabinoid research.

Next-generation sequencing (NGS) has revolutionized the field of genetics by providing a means for fast and relatively affordable sequencing. With the advancement of NGS, whole- genome sequencing (WGS) has become more commonplace. However, sequencing an entire genome is still not cost effective or even beneficial in all cases. In studies that do not require a whole-genome survey, WGS yields lower sequencing depth and sequencing of uninformative loci. Targeted sequencing utilizes the speed and low cost of NGS while providing deeper coverage for desired loci. This thesis applies targeted sequencing to the genomes of two different, non-model plants, Artemisia tridentate (sagebrush) and Lupinus luteus (yellow lupine). We first targeted the transcriptomes of three species of sagebrush (Artemisia) using RNA-seq. By targeting the transcriptome of sagebrush we have built a resource of transcripts previously unmatched in sagebrush and identify transcripts related to terpenes. Terpenes are of growing interest in sagebrush because of their ability to identify certain species of sagebrush and because they play a role in the feeding habits of the threatened sage-grouse. Lastly, using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. Second, we targeted the flanking loci of recognition sites of two endorestriction enzymes in genome of L. luteus genome through genotyping-by-sequencing (GBS). GBS of yellow lupine provided enough single-nucleotide polymorphic loci for the construction of a genetic map of yellow lupine. Additionally we compare GBS strategies for plant species without a reference genome sequence.

The world's population is expected to grow from 6 billion to about 10 billion by 2050. The greatest population increase is expected to occur in Africa, Latin America, and Asia. To feed a world with huge increases in population and to sustain the well-being of humans, a large increase in food production must be achieved. The projected increase in food production must be accomplished on the existing cultivated areas because the expansion of new land is limited by environmental concerns, urbanization and increasing water scarcity. Different compounds have been developed for the "immunization" of plants against several pathogens. These compounds induce systemic acquired resistance (SAR) in plants, leading to broad-based, long-lasting resistance to a wide range of pathogens. The salicylic acid binding protein 2 (SABP 2) has been identified as a key enzyme in the salicylic acid mediated pathogen resistance pathway, converting methyl salicylate (MeSA) to salicylic acid (SA), a key compound responsible for SAR . S-methyl benzo [1, 2, 3,] thiadiazole-7-carbothiate (BTH) was the first commercial compound used for plant immunization. We have synthesized and characterized some new salicylic acid derivatives [methyl-2-(2-hydroxy benzoyl thio) acetate and derivatives], and we have studied the in-vitro activity with SABP2 of BTH by HPLC analysis.

"The cuticle is the outermost defensive barrier in land plants, onstituting a shield that protects against both biotic and abiotic stresses. It is comprised by a group of organic solvent soluble lipids that are commonly referred to as waxes and the plant polyester cutin. "

This work consists of four sections: (1) the adsorption behavior of bovine serum albumin (BSA) by three types of oxide nanoparticles (NPs), TiO 2 (50 ± 5 nm), SiO2 (30 ± 5nm), and Al 2O3 (150 ± 5 nm for &agr; type and 60 ± 5 nm for γ type) in deionized water; (2) phosphate adsorption on these oxide NPs and bulkparticles (BPs); (3) influence of phosphate ions on BSA adsorption; and (4) BSA desorption from oxide NPs in phosphate solution. BPs were also used for comparison with NPs. For BSA adsorption in deionized water, the adsorption maxima on oxide particles are controlled by the surface area and hydrogen content, while the adsorption process is primarily induced by electrostatic interaction, hydrophobic interaction, and ligand exchange between BSA and oxide surfaces. With increasing of hydrogen content, the BSA adsorption mechanism switches from a mainly hydrophobic interaction to hydrogen bonding and ligand exchange. Calculations based on surface area and BSA size, suggest that a multilayer of BSA covers &agr;-Al2O3, but only a single layer surrounds the other oxide particle surfaces. BPs lead to greater conformational change of BSA molecules after their adsorption on the surfaces of oxide particles, although NPs adsorbed more BSA than BPs by weight. For phosphate, the adsorption process is mainly governed by the surface charge of the oxides. Strong electrostatic repulsion can prevent the adsorption of phosphate ions on an oxide surface. Meanwhile, a good linear relationship was observed between surface-normalized BSA adsorption maxima and surface charge of the oxides. For the influence of phosphate ions on BSA adsorption, BSA adsorption is suppressed by phosphate ions, while BSA molecules have no influence on phosphate adsorption. The competition between BSA molecules and phosphate ions is regulated by electrostatic interaction, the hydrogen content of the oxides and oxide surface area (especially micropore surface area). The difference of influence between hydrophobic and hydrophilic interactions on BSA adsorption reduces with the increase of phosphate concentration. Moreover, quantification was employed to calculate the displacing amount of phosphate ions to BSA molecules in competition. The displacing amount of phosphate ions is regulated by micropore surface area, and shows a good linearity with the hydrogen content. For BSA desorption, the BSA desorption hysteresis is observed for SiO2 NPs due to the high aggregation of this type of NPs. The aggregation of NPs can entrap BSA molecules in the closed interstitial spaces, leading to the BSA desorption hysteresis. For &agr;-Al2O 3 and γ-Al2O3 NPs, the hysteresis is observed only at low BSA concentration due to the influence of BSA molecules and electrostatic repulsion to the suspension of NPs. For TiO2 NPs, no significant hysteresis is observed because of their low aggregation and strong electrostatic repulsion. Phosphate adsorbed amounts remain unchanged within the adsorption and two-cycle desorption, indicating the entrapped BSA molecules may not bond to the oxide NPs.

This dissertation examined the response to termination of CO2 enrichment of a forest ecosystem exposed to long-term elevated atmospheric CO2 condition, and aimed at investigating responses and their underlying mechanisms of two important factors of carbon cycle in the ecosystem, stomatal conductance and soil respiration. Because the contribution of understory vegetation to the entire ecosystem grew with time, we first investigated the effect of elevated CO2 on understory vegetation. Potential growth enhancing effect of elevated CO2 were not observed, and light seemed to be a limiting factor. Secondly, we examined the importance of aerodynamic conductance to determine canopy conductance, and found that its effect can be negligible. Responses of stomatal conductance and soil respiration were assessed using Bayesian state space model. In two years after the termination of CO2 enrichment, stomatal conductance in formerly elevated CO2 returned to ambient level, while soil respiration became smaller than ambient level and did not recovered to ambient in two years.

Dissertation

The sooty blotch and flyspeck (SBFS) complex causes blemishes on apples in humid, temperate growing regions worldwide. In contrast to flyspeck etiology, the many species of fungi causing sooty blotch (SB) have not been well studied. The first set of objectives in this study was to use PCR to identify SB species isolated from apples and selected reservoir hosts in the northeastern United States, and to identify patterns of species distribution on hosts and among sites. Results indicated that Geastrumia polystigmatis was the predominant species on apples, whereas Peltaster species were more common on reservoir hosts. Species distribution varied among sites. Phylogenetic analysis of 54 G. polystigmatis isolates revealed little genetic variability in the ITS region. The second set of objectives involved investigating the response of G. polystigmatis to changes in nutrition, temperature, heat stress, and relative humidity, and in vitro responses of G. polystigmatis and Peltaster fructicola to fungicides commonly used in orchards. Observation of growth on half-strength potato dextrose agar, malt extract agar, and 2% water agar revealed that mycelial growth of G. polystigmatis was thicker and more melanized in the presence of readily available carbohydrates. Temperature range experiments demonstrated that the optimum temperature for growth was approximately 24ºC. The fungus was able to survive exposure to 32ºC for at least one week, 37ºC for at least 48 hours, and 42ºC for at least 8 hours. Growth was optimum at 99-100% relative humidity. Isolates of P. fructicola were very sensitive to thiophanate-methyl, mancozeb, cyprodinil, penthiopyrad, fenbuconazole, and trifloxystrobin. Isolates of G. polystigmatis were sensitive to thiophanate-methyl and cyprodinil, but significantly less sensitive to all other fungicides than P. fructicola. The addition of salicylhydroxamic acid to trifloxystrobin significantly reduced growth of P. fructicola, but not that of G. polystigmatis. This study represents the first in-depth investigation into the identity of species causing SB in the Northeast, the basic biology of G. polystigmatis, and the fungicide sensitivities of G. polystigmatis and P. fructicola.