Browsing by Author "Stewart, Jane E., advisor"
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Item Open Access Community structure and pathogenomics of Pinaceae-infecting Fusarium spp.(Colorado State University. Libraries, 2024) Dobbs, John, author; Stewart, Jane E., advisor; Kim, Mee-Sook, committee member; Sloan, Daniel B., committee member; Heuberger, Adam L., committee memberDue to a warming climate, the need for nursery grown conifer seedlings is continually increasing. However, several Fusarium spp. that cause pre- and post-emergent damping-off and root disease can hinder production of conifer seedlings. These soil or seed-borne Fusarium pathogens of conifers infect seedlings through the developing roots, and their similar effects on conifer hosts suggests that these pathogens may share a common evolutionary history. The shared ecological function of these Fusarium pathogens is likely associated with lineage-specific (LS) chromosomes or virulence gene(s) that are shared among these species. Identifying these potentially shared chromosomes or gene(s) and their functionality is best approached through the use of multiple 'omics technologies. Taken together, genomics, transcriptomics, proteomics, and metabolomics provide a comprehensive overview of the plant-microbial interactions at the time of Fusarium infection. This research accentuates how a combination of these technologies, such as genomics and transcriptomics, can be used to elucidate the biology of Fusarium pathogens and identify the presence of virulence-associated LS chromosomes or virulence gene(s) that facilitate the development of tools to rapidly identify and track these important pathogens. Chapter two, published in Frontiers in Plant Science, presents the observed regional effect on community structure of Fusarioid fungi collected from conifer seedlings among nurseries across the contiguous USA. The need for a global consensus to establish and maintain databases based on Fusarioid species type strains as references due to the continuing taxonomic disputes about the appropriate classification of Fusarium spp. designations was also discussed. For this reason, phylogenetic placement of the isolates was used for species identification; however, it is recognized that more research, such as whole genome sequencing, is needed to further validate the taxonomic identify of the isolates used in this study. Chapter three presents the whole genome comparisons of 17 Fusarium spp. isolates collected from conifer seedlings. Based on phylogenetic analyses of 16 conserved loci and composition of predicted genes, species were shown similar within and among Fusarium species complexes. Putative profiles of pathogenicity/virulence genes, including secreted in xylem (SIX) genes 2, 3, 9, and 14, and secondary metabolites, including the mycotoxins fumonisin and deoxynivelanol, were identified among the species complexes, but validation of expression of these genes is needed to demonstrate their functionality. Chapter four explores the mechanisms of pathogenicity and/or virulence of two understudied Fusarium spp., F. commune and F. annulatum, on conifer and non-conifer hosts and the differential gene expression in a susceptible conifer species. Further, the putative secretome profiles of Fusarium spp. within species complexes were identified, containing secreted carbohydrate-active enzymes, major facilitator supergroup transporters, apoplastic effectors, and gene products involved in secondary metabolite biosynthesis such as prolipyrone B/gibepyrone D, aurofusarin, and deoxinivelanol. Results from this study showed F. annulatum and F. commune caused disease on young conifer and non-conifer seedlings and identified putative genes associated with broad pathogenicity, and possibly indicating age-related resistance within the conifer host to certain upregulated pathogenicity genes. Due to the threat of spreading fungal pathogens from nurseries to field sites through latent infected seedlings and seed, this research highlights the need for robust early detection methods, while also providing insight into the biology of 17 Fusarium spp. that are potentially pathogenic to conifer seedlings. This research will help further develop technologies that aid managers for controlling Fusarium damping-off and root disease and mitigating the spread of novel haplotypes across regions.Item Open Access Effects of drought stress on early white pine blister rust development in limber pine(Colorado State University. Libraries, 2022) Bertram, Jonathan H., author; Stewart, Jane E., advisor; Scoettle, Anna W., advisor; Borlee, Brad, committee member; Ocheltree, Troy, committee memberClimate change and forest pathogens are expected to interact as incidences of drought increase and affect the disease triangle between hosts, pathogens, and the environment. Trees will become physiologically affected by drought stress and primary pathogens such as fungal biotrophs will experience drought stress as mediated through the host. White pine blister rust, caused by the non-native pathogen Cronartium ribicola, is a devastating fungal pathogen, and little is known about how it will perform (measured by fungal growth or disease severity) within pine hosts experiencing unusual drought. This study aimed to address some of the unknown aspects of this interaction by performing a greenhouse drought × pathogen experiment with Pinus flexilis seedlings, measuring host physiology, quantifying specific aspects of pathogen performance, and looking for interactive effects. Watering treatments consisting of well-watered, mild chronic drought, or severe acute drought were applied to 432 seedlings; after 3 months, a subset of 198 seedlings were inoculated with C. ribicola basidiospores under ideal inoculation conditions, after which watering treatments continued for a further 9 months. Specific rust performance measurements included mycelial growth via relative rust DNA quantification and ratings of disease severity by watering treatment.Item Open Access Fire-associated shifts in the soil microbiome in western conifer forests: implications for Armillaria root disease biocontrol and management(Colorado State University. Libraries, 2024) Fitz Axen, Ada J., author; Stewart, Jane E., advisor; Kim, Mee-Sook, committee member; Charkowski, Amy O., committee member; Abdo, Zaid, committee memberThe research presented in this thesis integrates the current understanding of environmental disturbances, plant associated microbiomes, and microbial biological control of fungal forest pathogens to contribute to improved disease management. In Chapter 2, I examined how fire disturbances affect soil microbial communities in areas where Armillaria root disease, caused by the pathogen Armillaria solidipes, is prevalent by documenting changes to bacterial and fungal community diversity and composition following three distinct levels of burn severity (high, low, and unburned) in a conifer forest in northern Idaho, United States. Expected reductions in bacterial community alpha diversity were observed when comparing burned communities with unburned communities; however, fungal communities showed a lack of significant change in alpha diversity in response to burn severity at the sampling time of 15-months post-fire. However, in both bacterial and fungal soil communities, compositional changes corresponding to burn severity levels were observed. Further examinations characterized similarities and differences between burn severity-associated communities and Armillaria species-associated communities to determine how these microbial changes might influence Armillaria root disease. At high-severity burn sites, colonization by A. solidipes and the associated microbial community was prevalent when compared with low-severity burn and unburned sites. In contrast, the presence and abundance of the weakly pathogenic species A. altimontana and its associated microbial community, including beneficial ectomycorrhizal fungi, appeared to be negatively impacted by high-severity burns. Further research is needed to determine which microbial taxa are critical for promoting or suppressing A. solidipes activity, yet the results from this study suggest that high-severity burns may create environments hospitable to this pathogen and thus monitoring for increased disease pressure following severe burns may be warranted. Chapter 3 focuses specifically on beneficial members of the native soil microbial community that exhibit antagonistic activity against A. solidipes. Because these native species are adapted to the environmental conditions and community interactions, they are more likely than foreign microbial species to successfully establish a stable population required for effective biological control. I isolated putative native biological control agents from soil samples collected under different burn severity conditions and tested their in vitro capabilities to inhibit the growth of A. solidipes with dual culture confrontation tests. Effective in vitro pathogen inhibition was observed with 10 microbial isolates, including five bacterial isolates from the genera Bacillus and Caballeronia and five fungal isolates from the genera Trichoderma and Mortierella. Further examination of the sites these microbes and communities originated from and their compositional changes documented in Chapter 2 revealed that the presence or abundance of our effective biological control organisms did not differ based on burn severity. Importantly, this suggests that fire disturbances may not directly influence the use of these species in management methods for Armillaria root disease in similar conifer forests. However, considering the increased presence of A. solidipes observed following a high-severity burn, there may be additional biotic or abiotic influences apart from biological control agents that are influencing the activity of A. solidipes after fire. These studies enhance our understanding of how abiotic and biotic influences interact to affect the presence of virulent soilborne forest pathogens and associated soil microbes. Considering the effects of these interactions is critical for the development of sustainable long-term management strategies that will help to preserve these ecosystems facing increasing environmental and pathogen-related stressors. The overall goals of this research are to build upon the growing body of research examining how the soil microbiome contributes to disease development and to provide tangible results that can be incorporated by forest managers to help reduce damage caused by Armillaria root disease in fire-prone conifer forests.Item Open Access Lophodermella needle cast pathosystem: the phylogenetic relationships, host-mycobiota interactions, and molecular diagnosis of Lophodermella pathogens on Pinus(Colorado State University. Libraries, 2022) Ata, Jessa Pude, author; Stewart, Jane E., advisor; Abdo, Zaid, committee member; Kim, Mee-Sook, committee member; Mondo, Stephen J., committee member; Norton, Andrew P., committee memberThe impact of needle diseases in conifer stands has increased worldwide due to regional variations of warmer and wetter climates that spur the activity of needle pathogens. Heavy needle cast infection results in loss of growth among pine stands which can lead to losses in biomass production and decline in ecosystem goods and services. Despite this threat, a well-informed disease management strategy is lacking due to limited research on many needle pathogens that remain to have unclear taxonomy, uncharacterized fungal biology, and unknown trophic lifestyles and interactions. Thus, this research applied molecular tools to understand conifer needle pathosystems, particularly Lophodermella needle casts that have caused epidemics on Pinus contorta stands in Colorado, USA. Specifically, this research aims to analyze the phylogeny of Lophodermella species using molecular data and identify shared derived characters for taxa delimitation; investigate the interaction of the mycobiota and the P. contorta host in healthy versus diseased states; and develop molecular tools for the rapid diagnosis of Lophodermella needle cast. To achieve these objectives, this research is divided into five chapters. The first chapter gives an overview of the emerging needle diseases worldwide and the needle cast epidemics on P. contorta in Colorado caused by Lophodermella concolor and L. montivaga. It discusses current knowledge on the Lophodermella pathogens and management strategies for needle diseases. The second chapter highlights the relationship of Lophodermella species from North America (L. arcuata, L. concolor and L. montivaga) and Europe (L. sulcigena and L. conjuncta), and their potential synapomorphic characters. It also revealed a newly identified, genetically unique rhytismataceous species on Pinus flexilis that is morphologically similar to L. arcuata. The third chapter discusses the adverse impact of the diseases to needle mycobiota and the defense strategies of the P. contorta host. It further shows, for the first time, the endophytic lifestyle of Lophodermella pathogens on P. contorta. The fourth chapter details the efficiency of the PCR- based markers developed from multi-copy and single-copy gene regions to identify and detect L. concolor and L. montivaga on P. contorta, and L. arcuata and Bifusella linearis on P. flexilis. And lastly, the fifth chapter summarizes the important results of this research and discusses their potential implications on the management of emerging needle diseases. My dissertation closes with recommendations on future research that will address further questions of needle diseases caused by Lophodermella species and other pathogens.Item Open Access The role of chemical canopy sprays and irrigation methods on the incidence of the perennial canker, Cytospora plurivora in western Colorado peach orchards(Colorado State University. Libraries, 2022) Wright, Sean, author; Stewart, Jane E., advisor; Charkowski, Amy, committee member; Uchanski, Mark, committee memberCytospora plurivora is a secondary pathogen that has reached near epidemic levels in peach orchards on the western slope of Colorado. C. plurivora is responsible for Cytospora canker disease and is a limiting factor in peach production in the Grand Valley. Peach growers have limited management methods available to combat this disease, which prompted an investigation into irrigation practices as well as prophylactic chemical sprays following freeze events. In late 2020, the western slope received a freeze event that caused severe damage to peach shoots, buds, and twigs. Freeze damage provides infection courts within tree tissues that C. plurivora can infect. This freeze event prompted growers to apply prophylactic chemical sprays of Captan, lime sulfur, and lime sulfur with the addition of NuFilm. An efficacy threshold of three-months post chemical spray was determined for both Captan and lime sulfur treatments. Lime sulfur with the addition of NuFilm showed a loss of efficacy at two-months post spray. Additionally, an investigation into the movement of C. plurivora conidia under differing irrigation techniques was conducted. Both drip and micro-sprinkler treatments had positive detections for C. plurivora over the course of the study. In these studies, conidia traveled much greater distances than previously shown, traveling up to 135m from the closest canker. Understanding how chemical canopy sprays and different watering practices affect the incidence of Cytospora canker disease will assist in preserving the peach industry on the western slope of Colorado.Item Open Access Time series analysis of limber pine (Pinus flexilis) health in the U.S. Rocky Mountains in response to white pine blister rust (Cronartium ribicola) and bark beetles(Colorado State University. Libraries, 2018) Leddy, K. A., author; Stewart, Jane E., advisor; Abdo, Zaid, committee member; Sloan, Dan, committee member; Schoettle, Anna, committee member; Liber, Howard, committee memberFrom 2004-2007, 106 permanent limber pine monitoring plots were established and measured throughout the U.S. Rocky Mountains (MT, WY, CO) to characterize health trends in response to white pine blister rust (WPBR) and bark beetles (including mountain pine beetle, "MPB", and Ips spp., "Ips") over time. These plots were subsequently measured in 2011-2013 and again in 2016-17 to form a time series analysis of limber pine health. Data were gathered on 8,206 monumented trees (4,176 limber pine) and included measurements on various stand, ground cover, and landscape characteristics over the three time intervals. The overall percentage of live trees infected with WPBR was 29.4% in 2004-07 and 25.7% in 2016-17, with incidence decreasing in parts of Wyoming (Pole Mountain, Laramie Peak), increasing in southern Colorado (Sangre de Cristo Mountains), and stable in other subregions. However, of limber pines that were healthy during the first measurement, 22.2% were declining/dying and 21.1% had died by the end of the study period due to WPBR and/or bark beetle damages. Due to this, it is likely that new WPBR infections are occurring as the large number of live, infected trees dying during the survey may have masked newly infected trees in incidence calculations. In heavily WPBR-infected areas such as Pole Mountain, Wyoming, 65% of live trees were infected (in 2004-07), and of trees that began the study as healthy, 23% were declining or dying and 38% had died by the end of the study period (2016-17). Additionally, WPBR severity increased significantly from the beginning of the study with 4 previously uninfected sites gaining WPBR infections, 29 sites advancing to 'moderately infected' and 5 sites becoming 'heavily infected'. The overall average number of cankers per tree (3.5) was stable, but the number of infected limber pine with a canker in the lower 1/3 of the stem (18%) increased significantly (+4.2%, P = 0.001). When examining all limber pine in the study, 8%, 3% and 3% were killed by MPB/Ips., WPBR, and combined effects of these agents, respectively. Of the 887 live, but declining or dying limber pine, 52% had WPBR infections and 38% had damage from twig beetles (Pityophthorus spp., Pityogenes spp.) in 2016-17. Though all sites had ≥ 20% limber pine composition, 34% of sites had no limber pine regeneration and 7% had no regeneration of any tree species over the entirety of the study period. The results of this time series indicate that limber pine populations in the U.S. Rocky Mountains are declining due to effects from WPBR and MPB/Ips. Long-term surveys capture the effects of these damage agents on native tree populations and provide critical guidance for future management and restoration of these ecologically valuable species. Limber pine is at risk due to the various biotic and abiotic agents threatening their health. Thus, future directions involve restorative management practices for highly impacted areas where limber pine is a climax species and proactive management for healthy limber stands to promote resilience to likely damage agents. In highly impacted areas (WPBR incidence, mortality, or bark beetle damage on >50% of trees and low limber pine density and regeneration), where limber pine co-exists with other tree species, it may be favorable to allow the natural succession of other tree species to become dominant. However in xeric, harsh sites where limber pine is a climax species, these highly impacted areas are at-risk for losing all tree cover and should be considered for protective and restorative planting strategies. As natural resistance to WPBR occurs on the landscape, genetic screening and protection of mature limber pine carrying either complete or partial resistance to the pathogen should be pursued to preserve this genetic diversity. A priority should be to protect resistant against bark beetles and fire using established management practices. Additionally, seed-sourcing from resistant trees can allow for resistant progeny to be out-planted into high priority areas, thus buffering stands at risk for high WPBR mortality. Moreover management plans that promote diversification of age and diameter classes within stands can provide resilience against pest and pathogen attacks, as bark beetles vary in diameter preference and WPBR infections tend to cause higher mortality in smaller diameter trees. Lastly in healthy limber pine stands, proactive management of pest impacts to promote stand resilience is recommended as in Schoettle & Sniezko (2007) in order to preserve these healthy populations.