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.

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.

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.

Variable mortality of Pyrenophora semeniperda--infected Bromus tectorum seeds has been referred to as a "race for survival", stating that seeds that germinate quickly are more likely to escape pathogen-caused mortality. Dormancy status is not the only variable determining outcomes within the Bromus-Pyrenophora pathosystem. Varying temperature and exposure to water may strongly influence germination outcomes of B. tectorum when in the presence of P. semeniperda. Low water potentials characteristic of semi-arid soils are often over-looked in the context of seed pathogens, and are ecologically relevant- especially for plant species that inhabit intermittently dry environments. To adequately characterize the Bromus tectorum-Pyrenophora semeniperda pathosystem, four studies were conducted to address the following questions: (1) do temperature, water potential, and dormancy status influence germination outcomes in the Bromus-Pyrenophora pathosystem, (2) do repeated wetting-drying scenarios influence germination outcomes of infected B. tectorum seeds following dehydration at low water potentials similar to those found in the field (i.e., -4 through -150 MPa), (3) can we accurately characterize the asexual life cycle of P. semeniperda on a dormant B. tectorum seed, determining when infection takes place, and what occurs during disease development in continuously hydrated conditions, and (4) how does disease development of P. semeniperda influence the B. tectorum seed embryo and endosperm. All studies were conducted using dormant and/or non-dormant B. tectorum seeds and an intermediate strain of P. semeniperda. Study one used varying temperatures (5-20°C), and five water potentials (0, -0.5, -1, -1.5, -2 MPa) (achieved using PEG 8000). Inoculated seeds were exposed to low water potentials at various temperatures for 7, 14, 21, or 28 days then re-hydrated for 28 days. In the second study, seeds were incubated at 20°C at four nominal water potentials (-4, -10, -40, or -150 MPa) following 8 or 24 hours of initial hydration. Seeds were dehydrated for 1, 7, 14, or 21 days, then re-hydrated. In study three, inoculated seeds were chemically fixed between days 0 and 21 and viewed with a scanning electron microscope. In the fourth study, infected seeds were frozen with liquid nitrogen following 3, 8, and 14 days of disease development, then cross sectioned longitudinally and laterally prior to chemical fixation. Results indicate that non-dormant seeds escape death by germinating rapidly under favorable conditions, that incubation at low water potentials greatly increases seed mortality, that -10 MPa is near the threshold for full pathogen activity, and at water potentials lower than -40 MPa, P. semeniperda may successfully survive severe dehydration if previous hydration resulting in infection has occurred. SEM images indicate that mycelia penetration occurs within 8-24 hours, and that mycelium may penetrate all opening in the seed (i.e., stomata, cracks). Development of P. semeniperda is shown to cause significant damage to the endosperm and embryo within 8 days. As starch is consumed, the endosperm collapses leaving a hollow middle. The embryo is more resilient, but gradually deforms and deteriorates.

Variable mortality of Pyrenophora semeniperda–infected Bromus tectorum seeds has been referred to as a “race for survival.” Dormant seeds are highly susceptible to P. semeniperda infection. While much is known about primary dormancy little is known about secondary dormancy in B. tectorum seeds. Dormancy status is not the only variable determining outcomes within the Bromus - Pyrenophora pathosystem. Varying temperature and intermittent hydration may strongly influence germination outcomes of B. tectorum in the presence of P. semeniperda. While it has long been assumed that B. tectorum seeds are infected by P. semeniperda in the fall it was recently suggested that seeds may be infected in the summer; however, there is little evidence to support this. To further characterize the Pyrenophora semeniperda - Bromus tectorum pathosystem two studies were conducted to address the following: (1) characterization of secondary dormancy in B. tectorum seeds and (2) summer interactions between host and pathogen after summer inoculation. Studies were conducted using dormant and/or non-dormant B. tectorum (along with B. rubens in one study) seeds and two strains of P. semeniperda. Study one used laboratory and field experiments to characterize secondary dormancy in B. tectorum seeds in terms of temperature (0.5-20°C), and water potential (-2.0-0 MPa). Data was used in repeated probit regression analysis to determine hydrothermal parameters (ψb(50), σψb, θHT) for secondary dormancy induction and loss. In the second study seeds were inoculated with one of two strains of P. semeniperda then exposed to intermittent hydration or dry storage at warm temperatures (30-60°C). After treatment seeds were rehydrated and outcomes observed. Optimum conditions for secondary dormancy induction were incubation at -1.0 MPa at 5°C. Seeds were likely to enter secondary dormancy through the cold winter months indicated by an increase or more positive ψb(50), while a decrease or more negative ψb(50) is associated with dormancy loss which is generally observed in the hot, dry summer months. When seeds were inoculated in the summer they only escaped death when summer conditions were ideal for after-ripening which allowed them to germinate rapidly under favorable autumn conditions. However, the pathogen caused high seed mortality no matter the treatment when disease progression advanced enough to inhibit seed germination. Thus this research shows that in areas with frequent summer rain storms, it would be highly advantageous to apply P. semeniperda as a biocontrol on seeds at maturity.

Following its introduction to North America in the late nineteenth century, Bromus tectorum L., an inbreeding invasive winter annual grass, has become dominant on millions of hectares of sagebrush steppe habitat throughout Intermountain Western North America. It appears that within the last 30-40 years, B. tectorum has expanded its range southward into the Mojave Desert and also into more climatically extreme salt desert environments. Previous research using microsatellite markers and experimental studies has suggested that lineages found in desert habitats are genetically distinct from those found in the sagebrush-steppe habitat and possess suites of traits that pre-adapt them to these environments. To provide additional support for our hypothesis that desert habitat-specific haplotypes dominate and are widely distributed across warm and salt desert habitats, we genotyped approximately 20 individuals from each of 39 B. tectorum populations from these habitats and adjacent sagebrush steppe habitats using 71 single nucleotide polymorphic (SNP) markers. Our data clearly demonstrate that populations throughout the Mojave Desert region, as well as in salt desert habitats further north, are dominated by a small number of closely related SNP haplotypes that belong to the desert clade. In contrast, populations from adjacent environments are largely dominated by haplotypes of the common clade, which is widely distributed throughout the North American sagebrush steppe. Populations across all habitats were usually dominated by 1-2 SNP haplotypes. This suggests that inbreeding B. tectorum lineages can often maintain their genetic integrity. It also explains the strong association between marker fingerprints and suites of adaptive traits in this species.

The seedling-infecting pathogen Ustilago bullata Berk. is a naturally occurring biological control agent for cheatgrass (Bromus tectorum L.). The effects of temperature and nutrients on pathogen teliospore germination behavior and the effects of temperature on host seed germination were examined. The effects of temperature on sporidial proliferation, host infection in a temperature-controlled environment and in a field setting for eight populations were investigated. The infection success of Ustilago bullata on Bromus tectorum in cultivated fields as a function of seeding date, inoculation method, inoculum density, supplemental watering, and litter was also investigated. Teliospores germinated faster on potato dextrose agar than on water agar. Teliospores germinated slowly at temperatures far from the optimum of 15 and 20 C. There were among population variations in teliospore germination and sporidial proliferation, but differences among populations were much more pronounced at temperatures below 15 C. Infection also decreased and varied far from the optimum with almost no infection at 2.5 C in a controlled-environment and in the field for the December-planted seeds. Warmer early fall rather than the colder late fall was suitable for successful infection. This agreed with both laboratory and controlled-environment experiments. Intratetrad mating was observed with teliospores at 2.5 C. Teliospore germination tracked seed germination closely with teliospore germination rate exceeding the host seed germination rate over the range of 10 to 25 C where both were measured. Below 10 C, teliospore germination rate fell below host seed germination. This phenomenon was associated with lower infection percentages, suggesting that teliospore germination needed to be ahead of the seed for maximum infection. Inoculum density was positively correlated with infection rate. Litter significantly increased infection, while supplemental watering significantly increased plant establishment. Since teliospores from different populations showed similar germination patterns at temperatures typical of autumn seedbeds in the Intermountain West, it may not be necessary to use locally-adapted pathogen populations in biological control program. A biocontrol program is most likely to be effective under a scenario where autumn precipitation permits emergence of most of the host seed bank as a fall cohort.

There has been a global decline of specialist species observed in recent decades due to the impacts of climate change, invasive species, and habitat loss. Habitat loss and degradation may lead to a mismatch between habitat attractiveness and actual quality, otherwise known as an ecological trap. Ecological traps occur when an organism is constrained by its evolutionary past to select for cues that no longer accurately predict habitat quality. Specialist species are more susceptible to ecological traps due to greater reliance on and fidelity to historic sites and resources. The burrowing owl (Athene cunicularia), a specialist bird species adapted to open ecosystems, has declined throughout its extent. Anthropogenic activity has drastically and rapidly altered burrowing owl native habitat, exposing their habitat to disturbances such as cheatgrass (Bromus tectorum) invasion. The presence of cheatgrass is known to impact the biota of a region and understanding those impacts is becoming increasingly important. The purpose of this study was to quantify the impact of cheatgrass on burrowing owl populations. By assessing how cheatgrass influences the resource selection, nesting success, and food habits of burrowing owls, we provided information that can be utilized to make more informed decisions on how to conserve burrowing owls and their critical nesting habitat. In addition, this information can provide insight into the risk of ecological traps occurring to all specialist species experiencing degradation of their native habitat.