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Browsing by Author "Stewart, Jane E., committee member"

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    A survey of foliar fungal endophyte communities of Rocky Mountain bristlecone pine populations in the Colorado Rocky Mountains
    (Colorado State University. Libraries, 2017) Albertson, Alyssa, author; Bedinger, Patricia, advisor; Kassenbrock, C. Kenneth, advisor; Stewart, Jane E., committee member; Schoettle, Anna W., committee member
    Rocky Mountain bristlecone pine (Pinus aristata) is an exceptionally long-lived charismatic tree species found at high elevations in the southern Rocky Mountains of Colorado, New Mexico, and Arizona (Fryer, 2004). This species has recently come under threat from the disease white pine blister rust (WPBR). White pine blister rust is caused by the pathogenic fungus Cronartium ribicola, which was inadvertently introduced into North America from Europe in the early 1900's, and has since spread widely with devastating impacts (Burns et al., 2008). In North America, WPBR is largely lethal to five-needle pine species. In Colorado, WPBR has been found in stands of Rocky Mountain bristlecone pine and limber pine (Pinus flexilis), and efforts have been made to identify trees with increased resistance to the disease. The USDA Forest Service Rocky Mountain Research Station has identified specific trees that harbor some level of heritable resistance to WPBR, versus those appearing fully susceptible (Schoettle, 2004; Schoettle et al., 2012; Schoettle et al., 2014). Essentially all plants in the wild harbor endophytic bacteria and fungi, which are defined as co-existing in plant tissues without causing evidence of disease, and it is increasingly appreciated that endophytes can alter plant responses to both biotic and abiotic stresses (Rodriguez et al., 2008). It has been reported that fungal endophytes can enhance resistance to blister rust in western white pine (Pinus monticola) (Ganley et al., 2008). The endophytic fungi of Rocky Mountain bristlecone pines have not been previously studied. We used two techniques to survey the endophytic fungal communities present in wild populations of resistant and susceptible bristlecone pines. The first technique was to isolate endophytic fungi by culturing surface-sterilized pine needles. The second technique was to extract DNA from the pine needles, and use PCR amplification of fungal-specific sequences, followed by high-throughput Next Generation sequencing (NGS) to identify and quantify fungi present, regardless of whether or not they could be cultured. By culture we recovered 259 fungal isolates that were placed into 81 morphological groups, whereas the NGS returned 42,003 useable DNA sequences that were grouped into 791 operational taxonomic units (OTUs). The two techniques used in this study had significant overlap; most of the cultured fungi were also identified in the NGS data set. The high throughput sequencing data also revealed differences between the endophyte populations of trees previously inferred to have or lack resistance to white pine blister rust at each location. Further research will be needed to understand whether endophytes may modify, slow, or even prevent infection by the pathogen C. ribicola.
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    Impacts of cropping system and nutrient management on soil health and soil-borne pathogens in smallholder systems of western Kenya
    (Colorado State University. Libraries, 2024) Mutai, Joyce Chelangat, author; Fonte, Steven J., advisor; Vanek, Steven, advisor; Stewart, Jane E., committee member; Schipanski, Meagan E., committee member
    Crop production in smallholder farms is often limited by low soil fertility and the presence of soil-borne pathogens. Both challenges are associated with limited nutrient inputs, low rotational diversity, as well as small land holdings and the associated need for continuous cultivation in many smallholder systems. This dissertation explores the varied ways in which cropping systems and nutrient management strategies influence key soil health parameters and relationships with key soil-borne pathogens. Additionally, this research tests a suite of soil health bioassays to facilitate farmers' understanding of soil-borne pathogen status on their farms. I utilized a mix of observational research, short-term on-farm experiments, and long-term cropping system trials to understand: 1) the potential of simplified soil pathogen tests (for Fusarium, Pythium, and plant parasitic nematodes (PPN)) to provide insight on soil pathogen pressure, 2) the impact of dis- tinct nutrient management strategies (organic vs. synthetic inputs) on key soil health parameters and associated soil-borne pathogens, and 3) effects of cropping system (mono-cropping vs. more complex systems) on key soil health parameters and soilborne pathogens. To address these objectives, I first validated a suite of simplified soil bioassays to screen for PPN (e.g., Meloidogyne, Pratylenchus) and other key soilborne pathogens (Pythium and Fusarium) against formal laboratory methods. I collected soils across eleven on-farm trials in western Kenya (66 plots total), examining the impact organic vs. synthetic nutrient inputs on bean production. The soil nematode bioassays involved counting lesions on soybean roots and galls on lettuce roots and were strongly correlated with the abundance of gall forming, root-knot nematodes (Meloidogyne) and root lesion nematodes (Pratylenchus) recovered in laboratory-based extractions. Effectiveness of a Fusarium bioassay, involving the counting of lesions on buried soybean stem, was validated via DNA sequencing to identify Fusarium taxa and a pathogenicity test of cultured Fusarium strains. Finally, a Pythium soil bioassay using selective media clearly showed presence of the pathogen, with seed rotting and colonies observed. When examining nutrient management impacts on nematode communities, soils amended with manure had fewer PPN and considerably more bacterivores and fungivores compared to soils amended with synthetic N and P. Similarly, Pythium presence was lower in soils amended with manure, and higher levels of Fusarium in the same plots, likely due to the ability of various Fusarium taxa to exist as a saprophyte. Our findings suggested that relatively simple bioassays can be used to help farmers assess soilborne pathogens with minimal costs, thus enabling them to make informed decisions on soil health and pathogen management. In a second study, I used an exploratory approach to examine common cropping systems in western Kenya smallholders including: maize monocultures, maize-legume intercrops, maize in rotation with legumes and vegetables, and horticultural systems based on perennial crops and vegetable production. I sampled 35 farms to understand the impact of cropping system diversity and associated nutrient management on the abundance of Fusarium pathogens and LN. I found that organic inputs led to fewer lesion-causing nematodes compared to the inorganic inputs system, but an inverse relationship with Fusarium pressure was observed. Permanganate oxidizable C (POXC), particular organic matter (POM), total C, and soil pH were highly correlated with each other and negatively associated with LN pressure, while POM was positively correlated with Fusarium pressure. In a third study, I leveraged a long-term (18-year) field trial in western Kenya, testing cropping systems representative of smallholder farms. The long-term trial evaluates three cropping systems: 1) continuous maize monocrop, 2) maize in rotation with the woody legume, Tephrosia (T. candida), and 3) maize intercropping with soybean, and two nutrient management strategies: 1) application of farmyard manure (vs. not), and retention or removal plant residue, with all plots receiving regular fertilizer inputs. I sampled soil from 40 plots and measured soil physical (texture, POM), aggregate stability, bulk density), chemical (pH, total C, available P, POXC), and biological (Fusarium, Pythium, RKN, LN) properties. Results indicated that long-term manure significantly improved soil properties including pH, POXC, POM, total C, and soil aggregation. Moreover, manure significantly reduced Pythium and RKN pressure. Soil pH and POXC were associated with Pythium and RKN, such that plots with low pH and POXC levels had high abundance of these soilborne pathogens. Fusarium abundance on the other hand, was higher with manure and associated variables (aggregation, POXC, total C). In a fourth study, I utilized a long-term trial (45 years) in Kabete, central Kenya focused on integrated soil fertility management in continuous maize-bean rotation and the resulting impacts on soil characteristics was well-suited to this goal. I examined the effects of dry manure application, maize stover management (incorporated vs. removed), and synthetic fertilizers (N and P applied vs. no application) in a full-factorial experiment on a range of soil physical, chemical, and biological properties. Results indicated that application of organic inputs, especially manure, greatly improved soil organic matter (SOM) pools, soil pH, aggregate stability, and decreased bulk density, compared to synthetic fertilizers. At the same time, manure significantly reduced Pythium and LN pressure, while plant residues reduced RKN and Pythium considerably. In summary, the simplified soil pathogen bioassays and soil health analyses considered in this dissertation offer a powerful set of tools to help smallholder farmers and the local research or extension organizations that they work with to monitor and anticipate soil related challenges in their fields, thus supporting agricultural livelihoods and resilience. Additionally, these findings suggest that continuous mining of nutrients and minimal returns of organic matter (i.e. removal of crop residues and no manure application) appears to drive the decline of important soil health properties (pH, POXC, POM, aggregation, and total C), with important implications for soil-borne pathogens.