Invasive plants can have significant ecological effects. Cheatgrass (Bromus tectorum) is of particular concern in North America, where its competitive nature can seriously degrade natural grasslands. This study, conducted in the White Lake Basin region of British Columbia, investigated the impact of cheatgrass on native plant diversity and the relationship between diffuse knapweed (Centaurea diffusa) and introduced grass cover. The study also analysed the association of cheatgrass with other grass species to provide insight in selecting grass seed composition for seeding after habitat disturbance. Results indicated higher native grass diversity in plots without cheatgrass and in plots containing bluebunch wheatgrass (Pseudoregneria spicata). While diffuse knapweed decreased during the study period, due to biological control, invasive grasses increased. Native grass species positively associated with cheatgrass include needle and thread grass (Hesperostipa comata), Sandberg bluegrass (Poa secunda), and sixweeks fescue (Vulpia octoflora), indicating potential for seeding in disturbed areas prone to cheatgrass.

Invasive weed species are a threat to the health and functionality of many rangeland systems. Downy brome (Bromus tectorum) is an invasive annual grass that affects the productivity of rangelands by decreasing the grazing capacity for livestock as well as altering the wildfire cycle and competing against more desirable vegetation for limited resources.In 2006, an Invasive Plant Management Plan and Environmental Assessment was approved for Dinosaur National Monument, calling for prioritization of invasive species management on high value wildlife habitat, vector areas, and for species with a high ecological impact. The Cub Creek Watershed was identified as a priority for immediate attention due to its high historical, recreational, and environmental significance.This research was another phase of an integrated effort to manage vegetation in the Cub Creek Watershed and surrounding rangelands. Field work at two locations within Dinosaur National Monument was coupled with greenhouse experiments to evaluate chemical and mechanical methods of downy brome seed reduction and control, and to evaluate the response of four weedy grasses to herbicides used in broadleaf weed management practices.

Understanding the carbon cycle of major ecosystems is important in predicting feedback responses of the terrestrial biosphere to climate change. Bromus tectorum dominated ecosystems currently cover 7% of the Great Basin and represents a major land cover type for the region. This study looked at the carbon cycle of a near monoculture field of B. tectorum in southeastern Idaho, USA. A major portion of the study was dedicated to measurement validation because of the disagreement among techniques used to measure net ecosystem exchange (NEE) of CO2 between the atmosphere and terrestrial ecosystems . NEE, net photosynthesis, and canopy and soil respiration were quantified for the B. tectorum stand using multiple methods. This allowed for comparisons among measurement techniques and permitted the calculation of a best estimate of NEE. The study found that the eddy covariance technique underestimated NEE at night for the B. tectorum stand and the magnitude of underestimation increased with increasing leaf area index of the plant canopy. Annual NEE estimated by eddy covariance for the year 2005 was over four times lower than the best estimate of -80 g C m-2 yr-1 determined by a combination of methods. Implications are that many studies currently underestimate NEE and productive systems underestimate NEE more than less productive systems.

Critical mule deer (Odocoileus hemionus) winter ranges in southeastern Utah dominated by Wyoming big sagebrush (Artemisia tridentata var. wyomingensis [Beetle and A. Young] Welsh) have developed dense cheatgrass (Bromus tectorum L.) understories. These communities are currently characterized by predominately mature to decadent stands of sagebrush with few perennial grasses and forbs. Sagebrush seedlings and perennial grasses compete for limited resources with annual grasses and forbs. To determine the affects of cheatgrass control on sagebrush growth and reproductive characteristics, imazapic (PLATEAU®, AC 263,222) herbicide was sprayed at 438.5 ml/ha with water and methylated seed oil during active fall growth of cheatgrass in 2002. Sagebrush growth and reproductive variables were measured on browsed and unbrowsed (caged) plants on sprayed and non-sprayed paired plots on 6 sites. Cheatgrass and other annual forb pretreatment cover was reduced from 23% to less than 3% the first year after the herbicide treatement and only increased to 4% the second year. Soil moisture on the treated plots was available at 15, 30, and 60 cm for several days to several weeks longer than on the control plots depending on the depth in the soil and year. Annual leader growth and flowering seedstalk length were similar on unbrowsed and browsed shrubs, but the number of seedstalks per plant was decreased by browsing. The number of sagebrush flowering seedstalks was significantly reduced by the herbicide the first year after the treatment, but recovered by the second year. The decrease in flowering seedstalks per sagebrush reduced the number of sagebrush seedlings observed the second year after the treatment (control = 81,800 seedlings/ha and treated = 16,700 seedlings/ha). Both seedstalk length (treated = 13.4 cm and control = 11.2 cm) and annual leader growth (treated = 6.2 cm and control = 5.3 cm) were greater on treated plots than control plots. Overall, imazapic can provide a window of cheatgrass and annual forb control to allow big sagebrush seedlings and perennial grasses and forbs to establish.

Bromus tectorum (cheatgrass) is an invasive annual grass that has colonized large portions of the Intermountain west. Cheatgrass stand failures have been observed throughout the invaded region, the cause of which may be related to the presence of several species of pathogenic fungi in the soil or surface litter. In this study, metagenomics was used to better understand and compare the fungal communities between sites that have and have not experienced stand failure. Samples were taken from the soil and surface litter in Winnemucca, Nevada and Skull Valley, Utah. Results show distinct fungal communities between Winnemucca and Skull Valley, as well as between soil and surface litter. In both the Winnemucca and Skull Valley surface litter, there was an elevated abundance of the endophyte Ramimonilia apicalis in samples that had experienced a stand failure. Winnemucca surface litter stand failure samples had increased abundance of the potential pathogen in the genus Comoclathris while the soils had increased abundance of the known cheatgrass pathogen Epicoccum nigrum. Skull Valley surface litter stand failure samples had increased abundance of the known cheatgrass pathogen Clarireedia capillus-albis while the soils had increased abundance of potential pathogens in the genera Olpidium and Monosporascus.

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.