Bromus tectorum and other annual brome grasses have invaded many ecosystems of the western United States, and because of an annual-grass influenced alteration of the natural fire cycle on arid western range lands near monocultures are created and conditions in which the native vegetation cannot compete are established. Each year thousands of hectares become near monocultures of annual brome grasses. Pyrenophora semeniperda, a generalist seed pathogen of annual grasses, shows major potential as a possible mycoherbicide that could help in reducing the monocultures created by annual grasses. The purpose of this research was to identify the requirements for isolating cultures of P. semeniperda, search for a hypervirulent strain, and evaluate its effect in the field. The techniques for isolating the fungus have evolved and become more efficient. The first two years of working with P. semeniperda resulted in 11 isolates. During the third year of this study, we developed a single spore isolation technique that resulted in 480 additional isolates. Virulence screening resulted in detection of a range of isolate ability to kill non-dormant B. tectorum seeds. Ninety-two isolates represented a range of virulence from 0-44%. The variation in virulence was expressed mostly within populations rather than between populations. Similarly, virulence varied significantly within Internal Transcribed Spacer (ITS) genotypes and habitats but not between them. When conidial inoculum was applied in the field there was no observed difference in disease incidence between different levels of inoculum. This is thought to have been due to applying the inoculum under conditions in which most in situ seeds were infected and killed by already high field inoculum loads. While additional field trials are needed to optimize the inoculum effectiveness, the overall results of this research provide a good foundation for using P. semeniperda as a biological control for seed banks of annual brome grasses.

This thesis includes two studies: The first examined patterns of neutral genetic diversity within Bromus tectorum L. across the IMW region, and uses patterns of microsatellite (SSR) genotype distribution to make inferences about the respective roles of adaptively significant genetic variation, adaptive phenotypic plasticity, and facultative outcrossing in the ongoing invasion and recent range expansion of B. tectorum. It has been previously demonstrated that, due to extremely low outcrossing rates, it is possible to characterize individual genotypes of this species using four SSR loci. We sampled 20 individuals from each of 96 B. tectorum populations (classified by region and habitat) from throughout the IMW and used these SSR markers to characterize each individual. We found 131 four-locus SSR genotypes; however, the 14 most common genotypes collectively accounted for 79.2% of the individuals sampled. Individuals with certain SSR genotypes sorted strongly into warm or salt desert habitats (stringent habitats) and flowered earlier than individuals with genotypes from more mesic habitats, providing evidence of adaptively significant genetic variation associated with these genotypes. Other SSR genotypes were found across a wide range of habitats though they tended to be less prevalent in stringent habitats, providing evidence that adaptive phenotypic plasticity may be important for the distribution of some common genotypes. We observed very few heterozygous individuals, consistent with the highly inbreeding reproductive strategy of B. tectorum. Because specialist genotypes dominating recently invaded areas within the IMW region contained unique alleles, they are not likely to have resulted from recombination, leading us to doubt the role of facultative outcrossing as a significant mechanism facilitating the current range expansion of B. tectorum in the IMW.Previous research investigating the population and ecological genetics of Bromus tectorum L. in the North American invaded range has relied on either allozyme or microsatellite (SSR) genetic analyses, both of which have proven to have shortcomings. In order to overcome the issues associated with these other marker types, in the second study of this thesis we developed single nucleotide polymorphism (SNP) markers for B. tectorum by 1) obtaining normalized cDNA, 2) sequencing normalized cDNA using 454 sequencing, 3) aligning resultant contigs and looking for SNPs, 4) designing assays for SNP validation and genotyping using KASPar, 5) converting working KASPar assays for use with the Fluidigm EP1 platform using the 96.96 Dynamic ArrayTM IFC. Sequencing resulted in 1258041 reads, which assembled into 65486 contigs (20782 large contigs exceeding 500 base pairs). Using selection criteria of at least 10x coverage and 30% of the minor allele, 3333 putative SNPs were identified. We developed KASP assays for 255 putative SNPs, which resulted in 101 working polymorphic assays. Ninety-six assays were then successfully converted for use with KASP on the Fluidigm EP1 genotyping platform using 96.96 dynamic arrays.

Contributing to the success of Bromus tectorum in the Intermountain West may be a mechanism called apparent competition, which occurs when one species increases the pressure of a consumer on a second species. This indirect interaction has been documented only a few times in invasive plant systems, and never in a fungal pathosystem. We examined the effects of the invasive annual Bromus tectorum and predation by the seed pathogen Pyrenophora semeniperda on seedling emergence and survival for two native grasses (Pseudoroegneria spicata and Elymus elymoides), by manipulating B. tectorum densities and P. semeniperda inoculum loads in randomized plots. Identical field studies were conducted in Skull Valley, Utah (xeric site) and Sprague, Washington (mesic site). The addition of inoculum decreased emergence of native grass seedlings at both sites and increased the amount of unemerged native seeds that were killed by P. semeniperda. Higher densities of B. tectorum decreased native grass survival at the mesic site and increased survival at the xeric site probably due to the beneficial effects of B. tectorum litter on soil moisture. At both sites, there were more B. tectorum seeds found in the seed banks in plots with high B. tectorum densities than in low-density plots. This indicates an increase in available prey for P. semeniperda. There was a much lower level of infection in B. tectorum seed bank seeds at the mesic site than at the xeric site. The high level of ungerminated native seeds killed by background levels of P. semeniperda, combined with the increase in available prey for the fungus in high-density B. tectorum plots, shows that apparent competition may play a role, along with direct competition, in the success of B. tectorum. This interaction is important to consider when dealing with control of B. tectorum.

An intrinsic link exists between soil moisture and soil nitrogen. Factors that increase or decrease soil moisture can have a profound effect on soil nitrogen cycling, which may have later repercussions in the plant community. Post-fire soil water repellency is one factor that can limit soil moisture acquisition and may indirectly affect nitrogen cycling and weed invasion in woody islands of fertility. Plots centered on burned Juniperus osteosperma trees were either left untreated or treated with a surfactant to ameliorate water repellency. Two years later, soils were excavated from the untreated and treated field plots. In the greenhouse, half of each soil type received a surfactant treatment while the other half was left untreated. Pots were seeded with either Bromus tectorum or Pseudoroegneria spicata. Analysis of field soil prior to the greenhouse trial showed that untreated, repellent soils had inorganic nitrogen levels an order of magnitude higher than wettable, surfactant-treated soils. Greenhouse pots that had received a surfactant treatment in the field and/or greenhouse had similar soil water content, plant density, and above ground biomass, which were, respectively, 55-101%, 31 to 34 -fold, and 16 to 18 -fold greater than pots without a surfactant treatment. No species effects were found. This study indicates that water repellency can reduce wetting and retention of water in the soil while promoting the retention of high levels of inorganic nitrogen. However, the effects of soil water repellency on inorganic nitrogen appeared to have a minimal effect on plant growth compared to the effect of soil water repellency on water availability.

The genus Fusarium has a wide host range and causes many different forms of plant disease. These include seed rot and seedling blight diseases of cultivated plants. The Fusarium-caused diseases of wild plants are less well-known. In this study we examined Fusarium sp. n-caused disease development on non-dormant seeds of the important rangeland weed Bromus tectorum as part of broader studies of the phenomenon of stand failure or ‘die-off’ in this annual grass. We previously isolated an undescribed species in the Fusarium tricinctum species complex from die-off soils and showed that it is pathogenic on seeds. It can cause high mortality of non-dormant B. tectorum seeds, especially under conditions of water stress, but rarely attacks dormant seeds. In this study, we used scanning electron microscopy (SEM) to investigate the mode of attack used by this pathogen. Non-dormant B. tectorum seeds (i.e., florets containing caryopses) were inoculated with isolate Skull C1 macroconidia. Seeds were then exposed to water stress conditions (-1.5MPa) for 7 d, then transferred to free water. Time lapse SEM photographs of healthy vs. infected seeds revealed that hyphae under water stress conditions grew toward and culminated their attack at the abscission layer of the floret attachment scar. A prominent infection cushion, apparent macroscopically as a white tuft of mycelium at the radicle end of the seed, developed within 48 hours after inoculation. Seeds which lacked an infection cushion completed germination upon transfer to free water, whereas seeds with an infection cushion were almost always killed. In addition, hyphae on seeds that did not initiate germination lacked directional growth and did not develop the infection cushion. This strongly suggests that the fungal attack is triggered by seed exudates released through the floret attachment scar at the initiation of germination. Images of cross-sections of infected seeds showed that the fungal hyphae first penetrated the caryposis wall, then entered the embryo, and later ramified throughout the endosperm, completely destroying the seed.

Quantification of soilborne pathogen inoculum loads is important in both agricultural and wildland settings. Quantitative Polymerase Chain Reaction (qPCR) methods using SYBR Green chemistry have been shown to be useful for quantifying fungal inoculum loads in environmental samples. The purpose of this study was to develop a method to quantify fungal pathogen inoculum loads in soil seed banks using a qPCR method with SYBR Green chemistry. The invasive annual grass Bromus tectorum was chosen for this seed bank study. There were three objectives: 1) to design target-specific primers for three fungal pathogens known to be important in Bromus tectorum seed banks, 2) to develop a procedure for measuring inoculum loads in field samples, including optimization of qPCR standard curves and protocols, for these pathogens, and 3) to perform qPCR using this methodology on a representative set of field samples to quantify pathogen DNA in seed bank soil and surface litter. The three pathogens were chosen for quantification based on their hypothesized roles in Bromus tectorum stand failure: the seed pathogen Pyrenophora semeniperda, an undescribed species of Fusarium seed rot pathogen belonging to the F. tricinctum species group (FTSG), and the newly-described causal agent of bleach blonde syndrome (Clarireedia capillus-albis). Primers designed for each pathogen were shown to be target-specific in tests against each other and 12 other fungal species cultured from B. tectorum seed banks. Subsequently developed standard curves for each pathogen had R2 values > 0.98, efficiencies between 90 and 110 percent, and generally optimal dissociation curves. Inoculum loads were expressed for each pathogen as picograms of DNA per microliter of extracted soil or surface litter. Significant differences in measured inoculum loads were found between the targeted pathogens and between soil and litter samples for each pathogen. The data provided reinforces that the SYBR Green qPCR method provides a potentially useful tool for the study of field seed and seedling diseases across a wide spectrum of both wildland and agronomic applications.

We used demographic methods to address one of the main challenges facing ecological science: forecasting the effect of climate change on plant communities. Ecological forecasts will be crucial to inform long-term planning in wildland management and demographic methods are ideal to quantify changes in plant abundance. We carried out our research in the sagebrush steppe, one of the most extensive plant ecosystems of Western North America. Our research intended to inform ecological forecasts on an exotic invader, cheatgrass (Bromus tectorum). Moreover, we investigated the general question asking: to what degree competition among plants influences the outcome of ecological forecasts on the effect of climate change? We carried out two field experiments to test the hypothesis that warming will increase cheatgrass abundance in the sagebrush steppe. This hypothesis was strongly supported by both experiments. Warming increased cheatgrass abundance regardless of elevation, neighboring vegetation or cheatgrass genotype. Moreover, we found cheatgrass was hindered by snow cover. Therefore, warming increases cheatgrass growth directly by increasing temperature, and indirectly by decreasing or removing snow cover. In our last experiment, we tested whether forecasts of climate change effects on rare species can ignore competition from neighbors. This should occur because rare species should have little niche overlap with other species. The lower the niche overlap, the less competition with other species. To test this hypothesis, we used a long-term data set from an Idaho sagebrush steppe. We built population models that reproduced the dynamics of the system by simulating climate and competition. Model simulations supported our hypothesis: rare species have little niche overlap and little competitive interactions with neighbor species.

No description available.

The landscapes of the Great Basin and Mojave Deserts are changing due to plant invasion. Highly flammable invasive grasses increase the size and frequency of fire causing a cascade of effects through the plant and animal communities. One of the most influential animal groups in desert systems is small mammals. We sought to learn how small mammals are impacted by fire and how their influence on the plant community differs between burned and unburned habitat. Small mammals did not have higher rates of mortality as a direct result of a controlled burn. In the Great Basin, there were short-term reductions in abundance, richness, and diversity of the small mammal community in burned plots. In the Mojave, species richness and diversity increased in burned plots shortly after fire and no abundance differences were detected. These results correspond with our prediction based on the dominant small mammal species at each site. Small mammals are primarily granivores; however, they also have strong impacts on the plant community via folivory. We tested for small mammal impacts on seedling survival in burned and unburned habitat. Small mammal access, burned vs. unburned habitat, and plant species were all important determinants of survival. Small mammals greatly reduced survival at both sites in burned and unburned habitat and often had a stronger impact in unburned than burned plots. Accounting for small mammal folivory may be a crucial step in successful post-fire rehabilitation. Finally, we used seed trays to test how small mammals influence the persistence of seed on the landscape. Small mammals reduced persistence of an invasive and native plant species in the Great Basin in 2012, yet a year later when small mammal abundance was reduced, no small mammal effect was observed. In the Mojave, persistence was reduced for the majority of species both years of the study. Small mammals did not appear to avoid seed of invasive plant species as we had predicted and may be important consumers reducing the reproductive potential of these invaders. If small mammals do prefer non-native seedlings over natives and are also consuming non-native seed, they may be greatly reducing the presence of non-natives both on the unburned landscape as well as after fire. Non-native consumption by small mammals could aid in the biotic resistance of these desert ecosystems. This research further enforces the important role that small mammals play as consumers, dispersers, and regulators of the plant community.

After-ripening, the process of seed dormancy loss in dry storage is associated with a decrease in the mean base water potential, one of the parameters of hydrothermal time. The rate of change of the mean base water potential is assumed to be a linear function of temperature above a specific base temperature and as a result can be described by a thermal after-ripening (TAR) time model, an extension of hydrothermal modelling. The thermal requirement for after-ripening is the thermal time necessary for the modelling base water potential of the seed to shift from its original value to its final value. In order to include the effects of water potential on the rate of dormancy loss, a hydrothermal after-ripening (HTAR) time model was developed. Laboratory and field studies were conducted using seeds of Bromus tectorum. These studies identified four important ranges of water potential that influence the rate of dormancy loss. The ranges are identified as follows: seeds experiencing soil water potentials seeds experiencing soil water potentials <-400 MPa do not after-ripen, between -400 MPa and -150 MPa seeds after-ripen as a function of temperature (T) and water potential (Ψ), seeds experiencing water potentials >-150 MPa after-ripen as a linear function of temperature, and somewhere above -40 MPa seeds are too wet to after-ripen. These ranges suggest that specific reaction thresholds associated with non-fully imbibed seeds also apply to the process of after-ripening. The HTAR model for B. tectorum seeds generally improved predictions of dormancy loss in the field under soil conditions that were too dry for TAR alone. Reduced after-ripening rate under extremely dry conditions is ecologically relevant in explaining how seeds may prolong dormancy under high soil temperature conditions.