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Browsing by Author "Manter, Daniel, committee member"

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    Bacteriomes of peaches and cover crops
    (Colorado State University. Libraries, 2024) Newberger, Derek R., author; Vivanco, Jorge M., advisor; Minas, Ioannis, advisor; Paschke, Mark, committee member; Manter, Daniel, committee member
    Replant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a complex of soil microorganisms combined with abiotic factors and susceptible tree genetics. Different soil disinfection techniques alleviate RS symptoms by reducing the loads of the deleterious microbiome; however, the positive effect on crop growth is temporary. Here, the current understanding of RS in orchards from a soil microbiome perspective is reviewed. The resolution to RS will require experts to outline explicit descriptions for its symptoms, determine its etiology, identify the primary phytopathogens, and fully explore sustainable treatments which alleviate RS. Two sustainable treatments of RS were selected to explore at a deeper level, soil disinfection and increasing crop diversity to observe what technique could help establish a healthy soil bacteriome. In a greenhouse study, soil disinfection via autoclave was then followed by cover cropping. It was found that soil disinfection increases plant biomass as compared to the control for only the first crop cycle while non-autoclaved soils with a history of cover cropping alleviated RS in RS-susceptible 'Lovell' peach seedlings. Although soil disinfection via autoclave was found to distinctly alter the peach soil bacteriome for the full duration of the study, this sustainable practice mimicking solarization failed to provide relief from RS for peach seedlings. Instead of long-term benefits, differential abundance comparisons displayed a loss of potentially beneficial bacteria due to soil disinfection. Paenibacillus castaneae and Bellilinea caldifistulae were beneficial bacterial species that uniquely colonized peach rhizosphere of non-autoclaved soils with a cover crop history. As a promising sustainable technique, a greater understanding of how inter-/intra-specific competition of cover crops can influence the bulk soil bacteriome was pursued. Alfalfa, brassica, and fescue were grown in 7 different plant combinations (1. alfalfa, 2. brassica, 3. fescue, 4. alfalfa-brassica, 5. alfalfa-fescue, 6. brassica-fescue, 7. alfalfa-brassica-fescue) across 3 density concentrations (low: 1–3 plants, medium: 24 plants, and high: 48 plants) for a greenhouse microcosm experiment. It was found that even in highly competitive conditions beneficial bacteria were enriched, however, there was an apparent trade-off where different plant combinations enriched distinct beneficial bacteria. As an example, even if a free-living nitrogen fixing bacteria such as an Azospirillum spp. was enriched in the bulk soil of alfalfa and brassica monocultures, it was not enriched in the bulk soil of an alfalfa-brassica plant mixture. Instead Pseudarthrobacter phenanthrenivorans, a phytohormone producer, was enriched in alfalfa-brassica plant mixtures. When zooming into the rhizosphere compartment of these microcosms, it was found that regardless of plant neighbor identity or density, a few rhizobacteria were highly correlated with a specific plant species. Meanwhile, certain plant species specific rhizobacteria were enriched only if specific conditions such as plant neighbor identity or density were met. Overall, our research found that growing diverse plant species plants prior to the re-establishment of a peach orchard could alleviate RS symptoms. Furthermore, cover crops can enrich different microbes when grown together as opposed to when grown separately. Lastly, although plants recruit a particular set of bacteria, this recruitment can shift depending on plant neighbor identity or density. Further study of cover crops may identify how they can alleviate RS in orchards worldwide.
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    Effect of phosphorus fertilization on rhizosphere microbiome of crops
    (Colorado State University. Libraries, 2019) Pantigoso Guevara, Hugo A., author; Vivanco, Jorge M., advisor; Manter, Daniel, committee member; Minas, Ioannis, committee member; Fonte, Steven, committee member
    Recent studies in plant-microbe interactions have revealed the importance of the rhizosphere microbiome in agriculture. However, little is known about the impact of fertilization on the rhizosphere and its associated microbial communities. This thesis investigates whether phosphorus (P) fertilizer has led to a shift in bacterial community composition and functions in both cultivated and non-cultivated plants. Two independent greenhouse experiments were conducted to evaluate P impacts. The first study explored the effects of low (0 and 50 kg ha-1) and higher P levels (101 and 192 kg ha-1) of triple super phosphate (0-45-0) amendments on soil microbial community composition associated with the rhizosphere of blueberry plants. The abundance of soil bacteria with phosphatase genes was also tested. The second experiment used a gradient of domesticated potato plants (modern cultivars, landrace and wild) to evaluate the effect of P addition on plant biomass and bacterial communities associated with the potato rhizosphere. Further, the study aimed to detect the most abundant microbial taxa, shared and unique, across six genotypes of Solanum genera. Four tuber-bearing and two non-tuber bearing potatoes were used in this study. Tuber-bearing included Solanum tuberosum subsp. tuberosum (a direct progenitor of modern potatoes) and the potato cultivars 'Red Norland', 'Yukon Gold' and 'Russet Burbank'. The non-tuber bearing potatoes included Solanum bulbocastanum and Solanum tuberosum subsp. tuberosum. Plants were grown in soils collected from an agricultural field where cover crops were previously cultivated. Three levels of phosphorus were applied (0, 67, 133 kg ha-1) during the experiment. Rhizosphere soil was collected and analyzed by amplicon sequencing targeting 16S rRNA gene. Our results showed that potato genotype is the main driver of microbial community composition, followed by fertilizer level. Non-tuber bearing potatoes were different from tuber-bearing potatoes and showed a higher degree of dissimilarity in microbial taxa compared to others. Additionally, a shift in bacterial abundance within the community was observed in response to high P levels. Xanthomonadacea and Alteromonadacea were the two families consistently increase or decrease (respectively) in response to incremental P levels. Interestingly, the latter was only present in non-cultivated potato plants, this family could be an important microbial member that has been lost with cultivation.
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    Effects of plant-selected rhizobacterial communities on the drought resistance of tomato plants
    (Colorado State University. Libraries, 2021) Monohon, Samantha J., author; Vivanco, Jorge M., advisor; Manter, Daniel, committee member; Wrighton, Kelly, committee member
    Drought stress has had devastating effects for vegetable growers world-wide, leading to much recent research focusing on the development of drought-resilient crops. The importance of the rhizosphere microbiome in plant performance under drought stress is under development, including the use of beneficial inoculations of PGPR and transplanting of microbial communities. However, further research is needed to fully understand plants' innate abilities in mediating rhizobacterial recruitment to benefit plant resistance to drought stress. Here, two greenhouse studies were performed to determine the efficacy of conditioned soils containing plant-selected rhizobacterial communities as a means to increase drought resilience of host plants. Soils were autoclaved to lower microbial complexity and ensure the greatest plant influence over soil rhizobacterial recruitment. Tomato plants were grown in soils, autoclaved and control, to assess microbial recruitment under a gradient of water treatments: well-watered, moderate drought and severe drought. Autoclaved soils revealed a potential amplification of plant-selective influence over microbial community assemblage for drought-specific bacteria. Inoculants derived from this study were used to observe the impacts of microbial history on a plant's ability to tolerate contemporary drought stress conditions. Microbial history was shown to have a significant effect on microbial community composition and plant performance under drought conditions. To further apply the conditioned effects of microbial communities on tomato plants under severe drought stress, a multi-generational study was performed to amplify plant-selected microbial communities from soils previously exposed to severe drought treatment. Effects of soil conditioning and microbial history suggested the presence of bacteria, conditioned over generations of plant-selection, involved in microbially-mediated plant growth restriction of tomatoes as a drought avoidance strategy. In summary, prior exposure of plants and microbial communities to drought stress may provide beneficial traits for host plants under contemporary drought conditions.
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    Estimation of capsaicinoid compounds and other nutritionally important compounds in Colorado grown pepper cultivars
    (Colorado State University. Libraries, 2021) Hamed, Mansor, author; Jayanty, Sastry S., advisor; Wallner, Stephen, committee member; Bartolo, Michael, committee member; Stone, Martha, committee member; Manter, Daniel, committee member
    To view the abstract, please see the full text of the document.
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    Minimizing the storage losses of potatoes under different storage treatments
    (Colorado State University. Libraries, 2021) Emargi, Esam, author; Jayanty, Sastry S., advisor; Wallner, Stephen, advisor; Stone, Martha, committee member; Manter, Daniel, committee member
    To view the abstract, please see the full text of the document.
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    Nitrogen fertilizer impacts on soil microbiome and tomato plant development
    (Colorado State University. Libraries, 2023) Rohrbaugh, Carley, author; Vivanco, Jorge, advisor; Delgado, Jorge, committee member; Fonte, Steven, committee member; Manter, Daniel, committee member
    Nitrogen (N) fertilization largely supports agricultural production. Urea is a common N amendment used in agriculture and when overapplied it has negative consequences in the environment due to its highly labile and reactive form. Alternative fertilizers, such as controlled release fertilizers (CRF) have been designed to diminish the harmful effects of applied N. This thesis investigates and makes comparisons regarding N fertilizer types and their effects on microbial community composition and plant development. Both research questions were addressed by growing tomato (Solanum lycopersicum 'Rutgers') plants as the test crop, which serve as a good model crop for indoor greenhouse production and were grown to the vegetative stage in both studies covered in this thesis. The fertilizer types considered are urea, a quick releasing form of N fertilizer and Environmentally Smart Nitrogen (ESN), a controlled release fertilizer. The soil used in these studies was from a low N plot (5.2 mg/L NO3) from the Agricultural Research, Development and Education Center (ARDEC) in Fort Collins, Colorado. The first research question addressed in Chapter 2 examines how different types of N fertilizers compare under different soil conditions and fertilizer rates. Altering the soil microbiome through sterilization (via autoclave processing) allows us to understand how urea and a controlled release fertilizer compare in their impact on microbial community composition and N assimilation by a tomato crop. It was found in this study that the use of ESN promoted plant performance and enhanced soil nitrate concentration. The soil microbiome findings from this first experiment showed that high rates of nitrogen fertilization led to higher relative abundances of nitrifying bacteria species. The second research question addressed in Chapter 3 follows a developmental study to track how N fertilizer impacts tomato plant performance, rhizosphere microbiome assembly, and plant nutrient uptake by sampling weekly for eight weeks. It was found in this study that ESN enhanced nitrogen use efficiency and plant nitrogen uptake. The soil microbiome results indicated a shift in community structure at the middle stage of the rhizosphere development. By studying the plant growth and rhizosphere microbiome response to urea and a controlled release fertilizer applied soil, we can improve our understanding on N release rates and bacteria that are responsive to these agents. This is the first research to our knowledge examining N fertilization's impact on rhizosphere development during early to vegetative growth using, especially using a weekly sampling resolution.
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    Role of rhizosphere bacteria and root exudates on the assimilation of phosphorus
    (Colorado State University. Libraries, 2022) Pantigoso Guevara, Hugo A., author; Vivanco, Jorge M., advisor; Fonte, Steven, committee member; Davis, Jessica, committee member; Manter, Daniel, committee member
    Deficient phosphorus (P) bioavailability in soils is a major challenge for sustainable food production as effective strategies to access unavailable P are limited. Solubilizing-bacteria and root exudate metabolites that solubilize P are promising approaches to increase available P for plants. We hypothesized that compounds in root exudates could elicit the P-solubilization activity of bacteria. To test this hypothesis, the root exudates of Arabidopsis grown in vitro under sufficient and deficient P conditions were characterized using GC-MS. We tested the ability of previously screened root exudates to solubilize plant-unavailable P in vitro. In parallel, potential P-solubilizing bacteria were isolated from the rhizosphere of wild potatoes using conventional microbiology techniques. The bacteria strains were tested, both individually and in consortia, for their ability to solubilize organic (phytin) and inorganic (calcium) P sources in vitro and in planta. Lastly, selected root exudate compounds were incubated together with P-solubilizing bacteria, and bacterial growth, P solubilization activity, and plant growth were evaluated. Our results demonstrate that malic, nicotinic, and 3-hydroxypropionic acids improved solubilization of P as compared to a control. Likewise, the bacterial strains E. cloacae, P. pseudoalcaligenes, and B. thuringiensis enhanced plant growth and P content with additions of plant-unavailable P. Furthermore, we found that threonine and 4-hydroxybutyric acid elicit P solubilization in all bacteria, under both organic and inorganic sources, independent of bacterial growth. Subsequent exogenous application of threonine to soils improved plant root growth, enhanced nitrogen and phosphorus content in roots and increased available levels of potassium, calcium, and magnesium in soils. Altogether, our findings expand on the function of exuded specialized compounds and suggest approaches to effectively recover residual P from soil, improving crop growth and nutrition.