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Aspergillus section Flavi species are important causal agents of aflatoxin contamination in crops including maize, groundnuts, cottonseed, and tree nuts. These species co-occur in agricultural fields where they compete for nutrients and space and contaminate crops with aflatoxins. Aflatoxin contamination of food and feed impacts the health of humans and animals causing liver damage, stunting in children, immune suppression, and death. There is a need to understand the interactions of aflatoxin-producing species and the role of abiotic and biotic factors in modulating competition between fungi in Aspergillus section Flavi. Furthermore, interactions between atoxigenic strains of Aspergillus, aflatoxin-producing fungi, environmental parameters, and crop hosts need to be studied in detail in order to optimize the aflatoxin biocontrol technology for diverse cropping systems. Thus, the overall goal of this dissertation research was to characterize the impacts of competition between Aspergillus section Flavi species on aflatoxin contamination in crops. The first objective (Chapter 2) was to quantify the influence of temperature on interactions among species of Aspergillus section Flavi. Competition experiments between highly aflatoxigenic S-type species, A. aflatoxiformans (AA) and the unnamed taxon known as the Lethal Aflatoxicosis Fungus (LAF), and L-type species, A. flavus L morphotype (AF) and A. parasiticus (AP), were conducted on maize kernels at 25°C and 30°C. Sporulation by L-type isolates was reduced during competition with S-type fungi at 30°C, while relative quantities of conidia produced by S-type species either increased or did not change during competition. Results indicate that both species interactions and temperature can shape population structure of Aspergillus section Flavi. The second objective (Chapter 3) was to characterize the influence of crop host on outcomes of competition between AF, AP, AA, and LAF during infection and colonization of maize and

Symbiotic microbial communities can be found in all plant species in all major terrestrial ecosystems including wild, horticultural, agricultural and residential garden settings. Microorganisms such as some bacteria and fungi that colonize the interior of a plant tissue without causing apparent disease – endophytes -- can be acquired through horizontal transmission or via vertical inheritance. Studies have shown that endophytes inhabit all tissue types of host plants and play vital roles in plant health and productivity, providing tolerance against biotic and abiotic stresses. However, the diversity of endophytes occurring in different plant tissues such as leaves, stems and seeds, and the factors that influence the endophytic diversity in those tissues is not well known. The knowledge gap is especially large for semi-arid areas such as Arizona, where endophytes may be especially important for plant survival under environmental stress.In the first part of this study, I evaluated colonization of three different types of crop seeds by soilborne fungi under different agricultural, residential and wild grassland settings in central and southern Arizona, USA. I found that fungal colonization differed among plant varieties, even when placed into the same soil. Seeds recruited distinct fungal communities in different locations, and fungal communities differed among agricultural, residential, and grassland settings. Variation in fungal communities was consistent with variation in soil chemistry. This work provides a case study regarding the diversity of fungal endophytes that can infect seeds in Arizona soils and highlights the prevalence of certain taxa, such as Fusarium and Alternaria, that are especially common and may be beneficial for plants, despite their reputations more broadly as undesirable pathogens or producers of mycotoxins. In the second part of this study, I provide a first perspective on endophytic biodiversity associated with common plants in a residential

Roots serve both to anchor plants in the soil, and to help plants acquire water and nutrients. Plants have to optimize the growth of their root system, as roots cost energy to expand and maintain. This is accomplished through short and long distance signaling pathways that connect environmental conditions of the roots and available energy in shoots. XIP1/CEPR1 and CEPR2 are two Leucine-Rich Repeat Receptor-Like Kinase that are important for root growth responses to differing nitrogen levels in the environment. While previous results implicated these two receptors in signaling from roots to shoots, here I have shown that they are part of a short-range pathway within roots that controls lateral root initiation. Furthermore, through the use of genetic tests I have connected a group of physically-interacting proteins to XIP1/CEPR1 and CEPR2-related phenotypes. I have shown that these receptors and interacting proteins play roles in controlling early growth, flowering time, silique maturation, and lateral root initiation, emergence and elongation.

With increasing global populations and demand for energy, greater strain is placed on the limited supply of fossil derived fuels, which in turn drives the need for development of alternative energy sources. The discovery of biophotolysis in Chlamydomonas reinhardtii and the development of a spectral-selective photosystem I activating/photosystem II deactivating light (PSI-light) method provides a promising platform for commercial hydrogen production systems. The PSI-light method allows electrons to pass through the photosynthetic electron transport chain while reducing radiation available for photosynthetic oxygen evolution that inactivates hydrogenase. Exploring the physiology of photohydrogen production using the PSI-light method can provide insight on how to optimize conditions for maximum hydrogen production. Through the use of photosynthetic mutant strains of C. reinhardtii, it was possible to suppress photosynthetic oxygen evolution further than using photosystem I light alone to extend photohydrogen production longevity and total yield. A preliminary investigation of an iterating light treatment revealed that longevity and yield could be increased further by providing a period of darkness to allow cells to consume evolved oxygen and resynthesize hydrogenase. Work with these mutants provided understanding that a balance of radiation was required to provide electrons to hydrogenase while limiting oxygen evolution, and that when no light was provided, fermentation of stored starch was the major contributor of electrons to hydrogen production. To determine the role of starch during hydrogen production, wild type cells were exposed to different media and light treatments and monitored for starch consumption and hydrogen production. The results indicated that starch was required for hydrogen production in the dark, but for photohydrogen production, starch likely played a minor role in contributing electrons to hydrogenase. The experiments also showed the importance

The greenhouse industry is interested in light emitting diodes (LEDs) as a light source supplement to solar light to improve plant growth and development. Before LEDs can be adopted as supplemental light for greenhouse crops, plant responses to LED spectral quality need to be investigated. Tomato and cucumber seedlings were grown under different supplemental blue and red photon flux ratios (B:R ratios) under high (16-19 mol m⁻² d⁻¹) and low (5-9 mol m⁻² d⁻¹) solar daily light integrals (DLIs). The supplemental daily light integral was 3.6 mol m⁻² d⁻¹. A treatment without supplemental light served as a control. Both tomato and cucumber seedlings had increased growth rate and improved morphology when grown under the supplemental LED light compared to the control. However, no significant differences were observed for any growth and morphological parameters measured in this study between the different B:R ratios for both cucumber and tomato transplants under high DLI conditions. Cucumber seedlings showed a tendency to decrease dry mass, leaf number and leaf area under low DLI conditions with increasing B:R ratio. Tomato seedlings did not show any differences between the different B:R ratios under low DLI conditions. Seedlings growth and morphology under supplemental LED light were compared to those under supplemental high pressure sodium (HPS) light. Cucumber seedlings under supplemental HPS light had greater shoot dry mass than those under the supplemental red LED light. Tomato shoot dry mass showed no differences between the HPS and red LED supplemental light treatments. Cucumber seedlings were also grown under supplemental LED pulsed lighting and supplemental LED continuous lighting. Cucumber seedlings showed no differences in shoot dry mass and net photosynthetic rate between the treatments. Collectively, these studies concluded that red LED is preferred for supplemental lighting and the increase of blue light does not offer any benefits unless the efficiency of blu

Pterocarpan phytoalexins are antimicrobial compounds produced by legumes when challenged by biotic stresses. Most legumes produce pterocarpan phytoalexins with (-)-stereochemistry but pea (Pisum sativum L.) produces as its major phytoalexin (+)-pisatin. Pea also occasionally produces a minor amount of (-)-maackiain as a pterocarpan phytoalexin, and studies on the biosyntheses of (+)-pisatin and (-)-maackiain have shown that up to (-)-7,2'-dihydroxy-4',5'-methylenedioxyisoflavanone [(-)-sophorol] and 7,2'-dihydroxy-4',5'-methyl-enedioxyisoflavanol [(-)-DMDI]they have common intermediates with (-)-DMDI being where the two pathways diverge. The final step in (+)-pisatin biosynthesis is the methylation of (+)-6a-hydroxymaackiain [(+)-6a-HMK] by 6a-hydroxymaackiain methyltransferase (HMM2) but the steps from (-)-DMDI to (+)-6a-HMK are unknown.The shifting of the stereochemistry from (-)-DMDI to (+)-6a-HMK has been proposed to involve the achiral isoflavene, 7, 2'-dihydroxy-4', 5'-methylene-dioxyisoflav-3-ene (DMDIF). In this dissertation, I have shown that cis-(-)-DMDI is the enzymatic product of (-)-sophorol, and is the precursor of DMDIF which is produced by the dehydration activity of "isoflavene synthase" (IFVS). IFVS activity was not observed in elicited tissues of alfalfa, chickpea, beans, pepper, and broccoli, plants that do not produce (+) pterocarpans. Partial purification of IFVS demonstrated that it is either large in size or tightly complexed with other proteins. The SDS-PAGE of the 29-fold purified product revealed 12 major bands that aggregated into 3 bands in the non-denaturing PAGE. IFVS activity was in band 3 which co-migrated with marker proteins of>100 kDa in size. Proteins identified from LC-MS/MS peptide sequences of the proteins in band 3, when compared to three protein databases, did not identify any proteins with an enzymatic activity expected for IFVS. A disease resistance-response protein (a dirigent-like protein) and two protein-binding protein

Analysis of complex traits like plant specialized metabolism is a difficult task in non-model systems as plant specialized metabolism is controlled by a number of factors such as environment, genotype, age, and tissue. To help address this problem, we have taken a bioinformatic approach that involves sequencing select tissues that are enrichedfor the biosynthesis of specialized metabolites. Using this approach, we have sequenced multiple tissues from a variety of species and compared them against one another. This comparative approach has allowed us to identify some of the genes responsible for the biochemical differences in and between species as well as genes that may be involved in control of specialized tissue development or metabolism. This dissertation begins with a brief introduction of plant metabolism, and pays special attention to historical and present views of plant metabolism, the importance of specialized metabolism, its evolution, and why it is advantageous to study specialized metabolism from specialized tissues like glandular trichomes and rhizomes. To this end, I detail our production and comparisons of glandular trichomes of several Solanum species using next-generation 454 sequencing. I also extensively review the underground stems, or rhizomes, of Viridiplantae. Discussions of our production and comparison of rhizome EST libraries from Zingiber officinale, Curcuma longa, and several Sorghum species are also made. My efforts to lay the groundwork that will hopefully permit functional analysis of interesting genes identified through our sequence comparisons of glandular trichome or rhizome EST libraries, in non-model systems are also discussed.

Salinity usually reduces plant growth in terms of height and biomass, but can increase secondary metabolite production. This frequently reported observation in guayule (Parthenium argentatum Gray, Asteraceae) was investigated for possible mechanisms.Osmotic and specific ion effects of four chloride salts (CaCl2, MgCl2, KCl, and NaCl) on leaf anatomical and plant physiological parameters were studied. One-year-old plants of guayule line AZ 2 were grown under two salt concentrations (750 ppm and 1500 ppm) for each salt type (plus a control) in sand culture (semi-hydroponic) for eight weeks under controlled greenhouse conditions in Tucson, Arizona.Growth in height decreased with increasing salt concentration. Shoot dry weight, rubber, and resin contents, however, showed no significant differences between treatments, indicating no effect from either salt concentration or salt type. There was a trend for increasing rubber content with increasing salt concentration, although not statistically significant. At the same time, net CO2 gas exchange rates decreased significantly with increasing salinity.With increasing salt concentration, guayule showed osmotic effects in terms of height, indicating a lower hydraulic conductivity. Although plants of higher salt concentrations utilized significantly less water, they had the same shoot dry weights, rubber, and resin contents. Salt-stressed plants therefore achieved higher water use efficiencies. The diurnal net CO2 gas exchange rates were significantly reduced with increasing salinity; the nocturnal net CO2 gas exchange rates showed no significant difference between the treatments.Anatomically, it was found that the stomata were raised or elevated above the epidermis, and supported by upwardly curving cells. When guayule was grown under salt treatments, the trichomes were found to include deposits of material. Trichomes might act as a detoxification repository for excess ions. Although the physiological significance of raised sto

Guayule (Parthenium argentatum Gray) is a rubber producing plant native to the Chihuahuan Desert, which is currently being investigated as a source of hypoallergenic latex. Current efforts are focusing on increasing latex/rubber production in the plant by either manipulating the rubber biosynthetic pathway, altering agronomic practices to take advantage of environmental conditions that increase rubber synthesis, or both. Field and greenhouse studies were conducted to more fully understand the effect of genetic and environmental manipulation on rubber production in guayule. Three guayule breeding lines were transformed in order to increase the availability of the initiators of rubber synthesis. The tissue-culture-derived transgenic plants and their seed-generated progeny were grown in separate field experiments. Transformation with the genes for the initiators of rubber synthesis did not increase rubber concentration or yield. Height and width had high heritability estimates in the transgenic progeny and were the traits most correlated with rubber yield, while rubber concentration was poorly correlated with height and width. Greenhouse studies were conducted to understand why water stress and low night temperatures increase rubber concentration. Water stress increased the contribution of the stems to the total rubber in the plant and increased the bark to wood ratio of the stem. Most rubber is accumulated in the stems and these two effects of water stress contributed to the increased rubber concentration in water-stressed plants. Low night temperature reduced plant growth without a decrease in carbon exchange. Allocation of carbon fixation products to rubber synthesis rather than growth, contribute to the high rubber production under low night temperatures. Contributions from both breeders and agronomists are needed to further improve guayule rubber/latex yield.

Guayule (Parthenium argentatum Gray) is a natural rubber producing plant presently being commercialized for production in arid and semi-arid regions of the world. Inconsistent seed (achenes) quality and the lack of methods to discriminate between good and bad seed lots are significant problems, allowing commercial stands to be established only by transplants, rather than by more cost effective direct-seeding. The objective of this study was to investigate why guayule seed and seed lots vary significantly in quality. The laboratory and greenhouse experiments involved separation of seed based on physical attributes (diameter, color and weight) and the confirmation of internal structures (embryo and endosperm) by x-ray analysis. The effect of different conditioning treatments on seed lots was also tested. Separation of seed by size (diameter) was shown to be less efficient than separation by color. Color was the most effective means of separating heavier and darker (opaque-black and gray color grades) seed, and these seed were confirmed to be filled, containing internal structures by x-ray analysis. Germination percentage and rate were greater for seed with these characteristics than for yellow and bright-black seed, which are lighter and predominately partially filled or unfilled. Conditioning treatments used for guayule seed older than two years had no effect on seed germination and emergence percentage or rate. However, differences in germination and emergence were found among lines, therefore, differences among seed lots appear to be due to variation in the number of filled seed. The quality of seed lots was significantly improved when seed were separated based on color first, then by weight. The separation of good quality seed (filled) from poor quality seed (unfilled) is crucial to lower the costs of stand establishment by direct seeding. Therefore, the quality of seed lots can be improved significantly (higher proportion of filled seed) by separating first by co