Browsing by Author "Charkowski, Amy, committee member"

Now showing 1 - 5 of 5

Open Access
A microbiome approach to cultivation and management of sugar beet
(Colorado State University. Libraries, 2024) Gaylord, Margaret, author; Trivedi, Pankaj, advisor; Charkowski, Amy, committee member; Wallenstein, Matthew, committee member
The world's population is projected to reach 9.8 billion by 2050, while the urgent threat of climate change is expected to impact crop physiology and pest dynamics. Understanding, preserving and leveraging the plant-associated microbiome can result in enhanced agroecosystem functioning and disease resistance for agricultural crops, thus improving food security. Sugar beet, an economically important sugar producer in the northern hemisphere, offers insights into plant-microbiome dynamics due to its susceptibility to pathogenic microbes and its association with disease suppressive soils. Cultural and chemical management practices of sugar beet are a persistent debate due to the potential negative effects on the essential microbiome and the emergence of resistant populations. To investigate the impact of weed control strategies on the soil microbiome, we conducted a long-term field study at two locations. Using next-generation sequencing and in vitro assays, we assessed the effects of glyphosate, a mix of selective herbicides and tillage treatments on the structure and function of the soil microbiome. Furthermore, we isolated 136 bacteria from the sugar beet agroecosystem and evaluated their antagonistic abilities against key diseases of sugar beet. Through in vitro and greenhouse assays, we identified effective microbial consortia for disease reduction. Additionally, we investigated the interactions between a single antagonistic isolate and an important fungal disease of sugar beet using transcriptomic analysis to reveal underlying mechanisms for biological control and pathogen response. This comprehensive understanding of the impact of various management strategies on the microbiome provides crucial insights for future crop management and highlights the potential for exploiting beneficial microbes to enhance disease control.
Open Access
From fields to genomes: towards a comprehensive understanding of the lifestyle and evolution of Claviceps purpurea the ergot fungus
(Colorado State University. Libraries, 2020) Wyka, Stephen Andrew, author; Nalam, Vamsi, advisor; Broders, Kirk, advisor; Charkowski, Amy, committee member; Pearce, Stephen, committee member; Jahn, Courtney, committee member
Claviceps purpurea (ergot), an ascomycete and member of the family Clavicipitacea, is considered a pathogen of all grass species (family Poaecea) including economically important cereal crops which infects ovaries resulting in the development of a fungal sclerotium rather than a plant seed. Ergot infections poses significant impacts to agriculture and livestock due to various toxic alkaloids present in the sclerotia. Severe ergot poisoning in humans and livestock, ergotism, can cause corrosion/loss of extremities from gangrene, internal bleeding, diarrhea, and reduced pregnancy and abortion. Due to these serious health concerns, strict restrictions are placed on the amount of ergot contaminated grain that can be accepted for food and livestock feed. However, these toxic alkaloids are also heavily researched in the field of pharmacology and have been shown to provide some beneficial aspects in human medicine. Despite the abundance of pharmacological and agricultural research on C. purpurea researchers have been unsuccessful in identifying crop or wild grass varieties that have resistance to ergot infection, leading to critical challenges in the control of ergot disease outbreaks. Recent studies have also suggested that C. purpurea is more of a conditional defensive mutualist as opposed to a plant pathogen. Taken together, these factors demonstrate that there are still gaps of knowledge surrounding the epidemiology, lifestyle, evolution, and adaptability of this species. We implemented a comprehensive analysis into the life history of C. purpurea through a combination of field surveys, greenhouse inoculations, and deep genomic data mining to help elucidate these gaps. Field surveys were conducted to investigate the role wild grass populations surrounding cereal crop fields play in epidemiology of ergot outbreaks. Results revealed that unmanaged grasses along ditch banks, even in drought years, represent significant inoculum reservoirs of ergot, particularly when Bromus spp. are present, and should be a focal point in future research for better disease control. Greenhouse inoculations were conducted to elucidate the effects of C. purpurea infections on hosts through inoculations of a single isolate on two commercial cereal crops in a controlled setting. Our results show that the effect of C. purpurea infections can range from negative to positive, depending on infection rate, plant species, and plant tissue, but overall showed a general trend of neutral effects. However, we did observe a potential for increased root growth as infection rates increased, which could signify an interesting plant-microbe interaction that imparts a benefit, of infection, on highly rhizomatous grass hosts such as Bromus spp.. Lastly, through a collaborative effort we sequenced, assembled, and annotated 50 Claviceps genomes, representing 21 species, for a comprehensive comparison of genome architecture, plasticity, and evolution within the genera. We also conducted a detailed analysis of C. purpurea through construction of a pangenome and investigations of the recombination and positive selection landscape across the genome. Our genus-wide comparison revealed that despite having nearly identical life-strategies, these closely related species have substantially altered genomic architectures and plasticity that are likely driving genome adaptation. One key difference we observed was a shift from characteristic one-speed genomes in narrow host-range Claviceps species of sections Citrinae and Paspalorum to two-speed genomes in broader host-range lineages of sections Pusillae and Claviceps. Claviceps purpurea was observed to have a large accessory genome that is likely influenced by a large effective population size, high recombination rates, and transposable element (TE) mediated gene duplication. Due to a lack of repeat-point induced (RIP) mutation, prolific TE expansion is likely controlled by high recombination rates, which subsequently may be influencing the overall trend of purifying selection observed within the species. However, secondary metabolites genes were found to have the highest rates of positive selection on codons within genes, indicating that these genes are a primary factor affecting the diversification of the species into new ecological niches and to potentially help maintain its global distribution and broad host range.
Open Access
Management strategies for Cytospora plurivora: the role of canopy sprays in western Colorado peach orchards
(Colorado State University. Libraries, 2024) Greenberger, Jilly Sal, author; Stewart, Jane E., advisor; Tonnessen, Bradley W., committee member; Charkowski, Amy, committee member; Uchanski, Mark, committee member
Cytospora spp. are globally distributed pathogens on more than 120 species of woody plants, in both agricultural and natural systems. In Colorado, Cytospora canker, primarily caused by the fungal pathogen Cytospora plurivora, is one of the most destructive diseases affecting peach trees (Prunus persica), a key specialty crop with significant economic and cultural importance. The resulting yield loss and financial strain on peach growers threaten the survival of the industry and options for management are limited. No resistant varieties have been identified and no fungicides are currently registered for use on Cytospora canker in Colorado. Chemical management focuses on prevention of new infections on wounded tissue: the infection court for C. plurivora. Fungicides applied directly to pruning wounds have proven effective but are impractical for many growers due to the extensive labor required. Additionally, these spot treatments have not been evaluated for efficacy on wounds on main scaffold branches or trunks, which are critical infection sites. Canopy sprays, facilitated by air-blast sprayers, could be a more cost-effective option for Cytospora canker control, with the potential to target entire tree scaffolds. Air blast sprayers are currently used by growers to manage other diseases and pests, as well as for nutrient applications; however, their efficacy on canker pathogens is not well understood. This study aims to explore the utility of canopy sprays with air blast sprayers for management of C. plurivora in organic and conventional peach orchards, and to determine best practices for achieving optimum coverage of bark on scaffold branches. Field trials were conducted in organic and conventional orchards, located at the CSU Agricultural Experiment stations in western Colorado, to assess both spray coverage and fungicide efficacy. Field trials to assess air-blast spray coverage were conducted in the spring and summer of 2023 to explore the effect of season of application and fan use on bark coverage. Water Sensitive Paper (WSP) cards were placed at three heights on each tree, sprayed with water, and analyzed with ImageJ software (Rasband, 1997) to determine the percent coverage of cards. Higher percent coverage was observed in the spring on bare trees, likely due to foliage blocking cards in summer trials. Fan use had variable effects on coverage within and between orchard planting blocks. Issues with uniformity in coverage were observed in all orchard blocks, with top cards receiving the lowest coverage in almost all cases. Fungicide field trials were conducted in the fall of 2023 and spring of 2024. An Organic Materials Review Institute (OMRI) listed fungicide, lime sulfur (Lime-Sulfur Solution™, NovaSource), was tested in the organic orchard and a conventional fungicide, captan (Captan 4L, Drexel Chemical Company, Memphis, TN), tested in the conventional orchards. Trees were wounded and inoculated with mycelial plugs of C. plurivora at the bottom of primary scaffold branches, on mid-scaffold branches, and on top branches. Resulting lesions were measured several months post-inoculation to assess disease development. Fungicide efficacy was evaluated by comparing lesion area (mm2) of treated and untreated trees. In fall fungicide trials, minimal lesion growth was observed overall, and treatments with lime sulfur and captan showed no efficacy in any orchard planting block. In the spring fungicide trials, treatment with lime sulfur significantly decreased lesion size in the organic orchard: on middle branches by 58% and top branches by 87%. Results of captan treatments were inconclusive but warrant future studies. No efficacy was observed in one planting block in the conventional orchard, but in the planting block with more mature trees, captan treatment was associated with a 147% decrease in lesion size. The results of this study suggest that air blast sprayers may be an effective tool for C. plurivora management, but future studies are needed to confirm the extent of their efficacy. Fall canopy sprays may not be effective or necessary, while summer sprays may have limited efficacy due to low coverage on foliated trees. Efficacy was observed with spring application of lime sulfur at 3%, supporting its use in canopy sprays. Efficacy of captan applications could not be confirmed or rejected due to inconsistency of results. The rate used in this study, 3.5 liters/hectare, may be insufficient, as had been found previously. Midrate applications (7 liters/hectare) of captan should be tested in future studies. Overall, efficacy was limited, highlighting the importance of integrated pest management strategies and the need for continued research on alternatives to chemical control.
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 member
Cytospora 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.
Open Access
Understanding the disease ecology of the corn bacterial leaf streak pathogen Xanthomonas vasicola pv. vasculorum
(Colorado State University. Libraries, 2019) Ortiz Castro, Mary Carmen, author; Leach, Jan, advisor; Broders, Kirk, advisor; Charkowski, Amy, committee member; Schipanski, Meagan, committee member
Bacterial leaf streak, caused by Xanthomonas vasicola pv. vasculorum (Xvv), is an emerging disease of corn in North and South America. Based on the combined $52.4 billion value of the corn industry, early reports of Xvv disease severity, and lack of management methods, this emerging pathogen represents an economic threat to corn production in the United States. The primary goal of this research is to provide a basic understanding of the infection ecology and survival of the corn bacterial leaf streak pathogen. Through genetic transformations of the bacteria with fluorescent proteins and confocal microscopy, we were able to show the localization of the bacteria within plant leaves. In addition, we found that there is a significant interaction between Xvv isolates and two corn varieties. By evaluating the bacterial fitness across representative isolates of Xvv, we showed that 22°C is the optimal temperature for bacterial growth in culture. We also evaluated the interaction of Xvv with the endophyte Pantoea ananatis and found that the presence of the endophyte significantly decreases Xvv's disease response. Finally, through litter studies at multiple locations, we demonstrated that infected residue left on the surface of the soil harbored significantly greater quantities of Xvv than infected residue buried 10 cm below the surface. These findings will be useful to understand the bacterial leaf streak disease cycle and aid in the development of management strategies that may limit the distribution of Xvv within corn fields and prevent its spread to other corn producing regions.