Browsing by Author "Trivedi, Pankaj, advisor"
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Item 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 memberThe 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.Item Open Access Biology and management of blackleg disease of potato caused by Dickeya dianthicola (ME23)(Colorado State University. Libraries, 2021) Karim, Shaista, author; Charkowski, Amy, advisor; Trivedi, Pankaj, advisor; Jahn, Courtney, committee member; Unchanski, Mark, committee memberPotato is the most commonly consumed vegetable in the United States, where people each an average of 49.2 pounds per person per year. About 80% of potatoes in the US are produced in Idaho, followed by Washington, Wisconsin, and Oregon. Potato is a vegetatively propagated crop, and progeny tubers serve as seed for cultivation the following year. Therefore, tuber-borne pathogens, such as bacteria that cause blackleg, result in serious economic losses when progeny tubers are contaminated by pathogens. Blackleg of potato is characterized by blackening of the basal part of stem and rotting of seed tubers. It is caused by Pectobacterium and Dickeya species, which are in the Pectobacteriaceae family and are collectively referred to as the soft rot Pectobacteriaceae (SRP). In 2015, multiples outbreaks of blackleg and soft rot occurred in Northeastern United Sates. This outbreak of the disease also impacted potato production all across the neighboring states, as well as other northeastern and mid-Atlantic states where Maine seed potatoes were shipped. It is most likely that prior to the Dickeya dianthicola (ME23) outbreak in the US in 2015, Dickeya was present in seed potatoes and farms in the affected states for at least a few years. However, rain in 2013 and 2014 spread the pathogen and cool temperatures caused the bacterium to remain latent in the tubers. Warm temperature in 2015 on commercial farms that used this Dickeya-infested seed resulted in significant outbreaks. The fields with outbreaks had no previous history of blackleg, the pathogen was suspected to have been present somewhere in the environment, then multiplied suddenly in response to favorable conditions, such as a heavy rain with subsequent surface pooling, and thus caused an outbreak. To prevent further spread of the disease, the primary infection source and the route of infection of the blackleg pathogen must be identified. Being able to discriminate exact subspecies of Dickeya from the others could help reduce the infection and to understand the epidemiology of the pathogen. Therefore, my research focused on development of reliable and accessible detecting tools for D. dianthicola (ME23). Unfortunately, many commercial potato varieties are susceptible to the diseases caused by SRP. Very few are tolerant, and production is compromised due to infection caused by D. dianthicola and high risk of spreading bacteria in other farms if potato seeds are infected. This led to an urgent need to screen for resistance against blackleg disease. There is insufficient information available for potato breeders on relative resistance or tolerance of commercial potato varieties to Dickeya and Pectobacterium spp. For the purpose of our work with SRP, we use the term resistance for plants that remain asymptomatic, or nearly so, after inoculation with Dickeya or Pectobacterium in typical temperature, humidity, and oxygen-level conditions. In addition, there is almost zero evidence of single gene resistance against this pathogen. Rather, disease resistance is quantitative and multigenetic, making it difficult for plant breeders to select for resistance. In addition, blackleg development is highly sensitive to multiple environmental factors including, plant age, availability of favorable environmental conditions and other bacterial pathogen present in the environment, making it difficult to screen varieties for resistance. The molecular and biochemical mechanisms underlying these quantitative resistances are also poorly understood. Therefore, are not efficiently utilized in potato breeding programs, altogether this makes it difficult to achieve true blackleg disease resistance. Nevertheless, it has been previously reported that plant resistant relies on production of small molecules such as phytoalexins or phytoanticipins associated with core resistant pathways. For example, these pathways may induce plant hormones associated with resistance, or antimicrobial peptides or enhance cell wall modifications as a physical barrier against plant pathogens. Interestingly, some accessions of the wild diploid species of potato (Solanum chacoense) are resistant to blackleg and soft rot diseases caused by SRP. My research focuses on identification of resistant lines of wild diploid potato relatives using physiological, biochemical and metabolic profile. In my work, I found that the metabolic profile of resistant stem extracts of S. chacoense consists of small molecules including phenolics, alkaloids, lipids, amino acids and organic acids, some of which may play a significant role in antimicrobial and anti-virulence properties. I found that the biochemical assays including quorum sensing (QS) and plant cell wall degrading enzymes (PCWDE) correlated with metabolites identified in metabolic profile of resistant accessions. Hence, these assays can be used as a less time consuming and easy tool for screening resistant lines against SRP. From these findings, I hypothesize that QS inhibiting molecules are responsible for triggering resistance against blackleg in S. chacoense and can be used as a potential tool in future breeding programs to achieve maximum resistance in our commercially grown potato varieties.Item Open Access Combined effects of warming and drying on a temperate-to-boreal forest ecotone exert additive changes on soil microbiome structure and diversity(Colorado State University. Libraries, 2020) Dean, Daniel, author; Trivedi, Pankaj, advisor; Leach, Jan E., committee member; Wrighton, Kelly, committee member; Reich, Peter B., committee memberThe soil microbial community is an important mediator of many ecosystem functions, so understanding dynamics under climate change. These responses could be more robust in transitional zones such as the temperate-to-boreal forest ecotones, which are poised to experience substantial changes under projected climate change over the next century and beyond. Because these systems are projected to move towards a warmer, drier climate, it is important to understand how the soil microbiome's structure and interactions shift under such conditions. Here, we examined the response of microbial communities to simulated warming and drought conditions using the B4WarmED (Boreal Forest Warming in an Ecotone in Danger) experiment in Minnesota, USA. B4WarmED is a fully factorial blocking experiment which uses in situ experimental 3.4°C warming and precipitation reduction to simulate the projected regional late-21st century climate. Using Shannon-Weaver Diversity and Canonical Analysis of Principled Coordinates, we found that combined warming and drying effects exerted significant effects on the diversity and structure of microbial communities after 8 years of warming, and 5 of drought treatments. Specifically, warming and drying effects appeared to combine additively, rather than exhibiting nonlinear interactive effects, at the community level. Per-taxon linear models revealed a sizeable portion of individual microbes exhibit a significant abundance response to one or both of warming and drying effects. However, co-occurrence network analysis and Dufrene-Legrende Indicator Value characterization revealed a smaller portion of bacterial sub-communities with persistent taxonomical makeup and response profiles across treatments. Within the microbial communities our analysis identified three types of taxon-specific responses to climate change stressors: resistant, opportunistic, and sensitive, with most taxa being resistant to warming and drying effects. However, our results provide strong evidence that combined warming and drought influences will impact soil microbial communities of temperate-to-boreal ecotone forests ("boreal ecotone" hereafter), with potential implications for ecosystem functioning.Item Open Access Drought impacts on the microbiome in grasslands across the Great Plains: a story of legacy effects, resistance, and resilience(Colorado State University. Libraries, 2022) Vilonen, Leena L., author; Smith, Melinda D., advisor; Trivedi, Pankaj, advisor; Cusack, Daniela, committee member; von Fischer, Joe, committee member; Zeglin, Lydia, committee memberDrought is increasing in frequency and severity across the US Great Plains as a direct result of climate change and if nothing is done to remedy climate change, drought will only continue to get worse over the next century. Thus, understanding how drought impacts natural and rangeland systems in the US will be vital to protecting these systems from negative impacts due to drought. Further, there has been a great deal of research on the aboveground response to drought, but little research on how the belowground soil community responds to drought. Lastly, some research exists on how drought impacts systems during the drought, but even less research exists on what happens after the drought. To further complicate this, the terms used to describe the period after drought are variable and inconsistent, leading to difficulty in synthesizing this literature. This dissertation aimed to re-define and make the terms used to describe the post-drought period consistent, understand how belowground communities respond after the drought has ended at one field site, and understand how microbial communities in the greenhouse respond to drought both during and after across several sites in the US Great Plains. The first chapter of this dissertation was a literature review that examined how researchers define the terms used after a drought ends and attempted to synthesize definitions for future use. The second chapter of this dissertation examined whether there were impacts leftover after a four-year drought on nutrient cycling in a mesic grassland. The third chapter examined whether there were leftover impacts from the same drought as chapter two on the microbial community. Lastly, the fourth chapter examined how microbial communities respond during and after the drought across four Great Plains sites when the microbial community was isolated from the plant community.Item Open Access Evaluating soil microbial community assembly to understand plant-soil diversity feedbacks(Colorado State University. Libraries, 2022) Hoosein, Shabana, author; Paschke, Mark W., advisor; Trivedi, Pankaj, advisor; Stromberger, Mary, committee member; Busby, Ryan R., committee member; Egan, Cameron, committee memberTo view the abstract, please see the full text of the document.Item Open Access Field population genetics of global Puccinia striiformis f. sp. tritici populations in wheat reveal a dynamic molecular battlefield(Colorado State University. Libraries, 2021) Lyon, Rebecca, author; Trivedi, Pankaj, advisor; Broders, Kirk, committee member; Pearce, Stephen, committee member; Hufbauer, Ruth, committee memberTo view the abstract, please see the full text of the document.