Browsing by Author "Vivanco, Jorge M., advisor"
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Item Open Access 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 memberReplant 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.Item Open Access 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 memberRecent 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.Item Open Access 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 memberDrought 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.Item Open Access Elucidating rhizobacterial response to autoclave disruption and crop introduction within three distinct agricultural soils(Colorado State University. Libraries, 2020) DiLegge, Michael J., author; Vivanco, Jorge M., advisor; Manter, Daniel K., committee member; Weir, Tiffany L., committee member; Minas, Ioannis S., committee memberManagement practices can affect the soil health properties of an agroecosystem, in turn effecting the resident soil microbial community. Insights toward how managerial practices effect soil microbial rearrangements are steadily being uncovered with next generation sequencing applications. This thesis covers research investigating how soilborne and plant-rhizospheric bacteria from three differential agricultural management systems are affected by applied disruption followed by the introduction of new plants to their sites. Two independent greenhouse experiments were conducted to evaluate plant-mediated bacterial rearrangements in soil following autoclave disruption. The first study utilized two soil types from a perennial peach orchard system experiencing negative effects of orchard replanting disease. Soils were sampled from a replanting disease (RD) site and a non-replanting disease (non-RD) block. Replanting disease soils were autoclaved; and peach, corn and tomato plants were grown in both autoclaved and unautoclaved RD soils, as well as non-RD soils. Bacterial phyla and their predicted functional genomics were assessed after autoclave disruption and plant growth. The second experiment was an expansion of the former, utilizing autoclave disruption and the same perennial RD soil from the former study, but with the addition of conventional and organic annual agroecosystem soils. In this experiment four crops of differing plant families (corn, beet, tomato and lettuce) were introduced to examine how soil bacterial rearrangements may be influenced by distinct crop-presence after autoclave disruption. Results showed that autoclave disruption increased plant biomass. Interestingly, the type of crop plant introduced as well as the agroecosystem soil type drove differential bacterial responses and rearrangements. These data demonstrate that both agricultural ecosystem management, paired with the family of plants grown in these ecosystems, strongly impact soil bacterial availability and rearrangement in the rhizosphere. Additionally, in agricultural sites experiencing severe long-term dysbiosis, an autoclave disruption in pair with the rotation of monocultured crops may prompt the colonization of a healthier rhizomicrobiome.Item Open Access Interactions between plants and an opportunistic human pathogen, Pseudomonas aeruginosa(Colorado State University. Libraries, 2008) Weir, Tiffany L., author; Schweizer, Herbert P., advisor; Vivanco, Jorge M., advisorPseudomonas aeruginosa is an opportunistic human pathogen that can be found living in soil, water, or saprophytically on plant tissues. It is important to understand the pathology of this organism under variable conditions because of its ability to survive in diverse environments, its role in human disease, and its use as a model organism in studies on biofilm formation, quorum-sensing, and pathogenicity. To this end, a number of unconventional model systems, including plants, nematodes, and fruit flies, have been developed to study the pathology of P. aeruginosa. In the present study, the interactions between P. aeruginosa and plants, with respect to pathogenicity, quorum-sensing, and microbial ecology are further explored. To examine what factors are important in the pathogenicity of P. aeruginosa in a plant system, compatible and incompatible cultivars of Nicotiana tabacum were infiltrated with the pathogen. Bacterial growth in planta was monitored and P. aeruginosa PAO1 gene expression was examined 24 hours after infiltration into the hosts. The data suggests that, in addition to known virulence factors, the acquisition of micronutrients such as sulfate and inorganic phosphate are also important in disease development. The results of this study also suggest that type III secretion systems may be important in P. aeruginosa's ability to infect plants, and that differences in host response, i.e. salicylic acid signaling, are determining factors in host compatibility. Another aspect of this study was to utilize the natural interactions between plant roots and soil-borne bacteria to identify root exudates that interfere with bacterial quorum sensing (QS), particularly in P. aeruginosa. Quorum sensing in P. aeruginosa controls the expression of several secreted factors that are important in virulence of the pathogen, and preventing infections by inhibition of quorum sensing is a current therapeutic target. Unfortunately, while many of the exudates appeared to have some affect on QS in general, none had strong activity against P. aeruginosa QS systems. However, one class of chemicals, triterpene saponins, was shown to be active in a lux-based QS reporter. Finally, preliminary data suggesting that root exudates can influence competitive outcomes between two soil-borne bacterial species are also presented. The interactions between bacteria are typically studied in nutrient rich medium under defined laboratory conditions. Under these conditions, P. aeruginosa outcompetes Agrobacterium tumefaciens, two bacteria that potentially compete for the same niche in the soil. However, when Arabidopsis thaliana is factored into this equation, growth of A. tumefaciens is favored. Furthermore, the negative effects of P. aeruginosa on the growth of A. thaliana were reduced.Item Open Access Manipulating the soil microbiome to increase plant health and productivity(Colorado State University. Libraries, 2015) Chaparro, Jacqueline Michelle, author; Vivanco, Jorge M., advisor; Leach, Jan E., committee member; Manter, Daniel K., committee member; Wallner, Stephen J., committee memberRhizosphere microbial communities offer immense benefits to plants. The rhizomicrobiome has the ability to help combat numerous biotic and abiotic stresses as well as increase plant health and productivity. In a world where the population keeps increasing at an alarming rate while food is scarce, new alternatives to feed the growing population need to be identified. The answer lies in harnessing and exploiting the beneficial interactions between plants and their rhizosphere microbiome to increase plant health and productivity. An understanding of the mechanisms that govern such interactions is essential to increase plant health and productivity. Based on this need, an analysis of the interactions between Arabidopsis thaliana and its rhizosphere microbial community was undertaken. Initial studies revealed that root exudates serve as a means of initiating, attracting, maintaining, and enhancing rhizosphere microbial community interactions. Furthermore, root exudation changes with development and leads to changes in the functional capacity and the members that make up the rhizosphere microbial community. These changes appear to occur so the plant can recruit specific functions necessary for survival. Once a framework outlining the importance of root exudation on plant-microbiome interactions was established, compounds from root exudates were added to soil, without the plant, and tested its impact on the soil microbiome. Studies revealed that these compounds when acting alone do in fact influence the soil microbiome and that distinct chemical classes have a direct influence on the soil microbial community. Most importantly, correlation analysis of microbes and the phytochemicals added to the soil revealed that phenolic compounds appear to predominantly modulate the soil microbial community. Finally, the knowledge acquired from these studies allowed development of statistical models that could predict the specific influence of root exudate compounds on the soil microbiome. Five statistical models were implemented, tested, and validated. These results identified models based on machine learning to be of great value in their ability to accurately predict the behavior of soil microbial community abundance after exposure to specific compounds. Overall, the results of this dissertation enable the ability to begin to modulate and manipulate the soil microbial community for increased plant health and productivity.Item Open Access Plant tannin interactions during Phytophthora ramorum infection(Colorado State University. Libraries, 2013) Stong, Rachel A., author; Vivanco, Jorge M., advisor; Manter, Daniel K., advisor; Holm, David G., committee member; Leach, Jan E., committee memberPhytophthora ramorum, the responsible agent of "Sudden Oak Death" and the infection of over 100 different plants has the potential to disrupt oak forests leading to devastating consequences. Resistance to P. ramorum varies by pathogen race or plant cultivar, plant species or genus, plant non-host and partial resistance. During infection, P. ramorum produces a 10 kDa elicitor protein, i.e., elicitin, that can induce plant defenses. P. ramorum uses elicitins to acquire sterols from plants since the pathogen does not synthesize sterols. Factors influencing host resistance are largely unknown, although phytochemicals, such as phenolics, are found to influence resistance to P. ramorum. Tannins, a group of polyphenolic compounds found in plant tissues are able to precipitate proteins, such as elicitins. The studies presented here investigate the possibility of an elicitin-sterol-tannin interaction in plant resistance to P. ramorum. This research includes a series of in vitro and in vivo studies of sterol and tannin interactions with P. ramorum. To explore the impact tannins may have on P. ramorum, media was treated with ground foliage, extracted tannins, or extracted sterols from three different tree types (Oregon white oak, California black oak and California bay laurel), or commercially-available sterols. Growth and sporulation of P. ramorum were higher on California bay laurel treatments as compared to the oaks. High concentrations of foliage from the oaks resulted in more rapid inhibition of P. ramorum growth and sporulation. Inhibition of P. ramorum growth and sporulation was also observed in response to plant sterols or tannins. This inhibition appears to be caused by two different mechanisms. Treatment with high concentrations of sterols reduced elicitin gene expression indicating a regulatory role. Tannins caused a decline in the amount of ELISA- detectable elicitin while there was no change seen in elicitin gene expression. All treatments showed a strong correlation between elicitin contents and P. ramorum growth and sporulation, suggesting a role for elicitin-sterol-tannin complexes in P. ramorum growth and sporulation in foliage. In a second study, several evergreen varieties of Rhododendron, Kalmia and Azalea were assessed for constitutive tannin content, sterol content and leaf susceptibility to P. ramorum. Significant differences were seen between the different species and between the two trials for tannin content. Variation of sterol content was only seen in Kalmia plants. Azalea plants showed no susceptibility to P. ramorum, while susceptibility varied between trial 1 and trial 2 for Rhododendron and Kalmia varieties. Variation of tannin and leaf susceptibility was also seen between cultivars. A positive correlation between all tannin data and lesion size suggests a relationship between tannin and P. ramorum. We propose that the formation of elicitin-sterol-tannin complexes inhibits plant defense responses allowing for greater pathogen colonization and lesion development.Item Open Access Primary and secondary metabolism in Centaurea maculosa and their potential roles in invasion biology(Colorado State University. Libraries, 2008) Broeckling, Corey D., author; Vivanco, Jorge M., advisorCentaurea maculosa is plant species native to Eurasia which has become invasive in North America, in part through allelopathic behavior. Allelopathy remains a highly debated subject, and a more firm understanding is necessary. C. maculosa is reported to secrete catechin as an allelochemical that is toxic to North American native plants. In this dissertation, a novel colorimetric assay for use in detection of catechin from soils is described and validated. This assay is highly sensitive, selective, and fast, which should allow for more detailed measures of catechin under field conditions, and ultimately a better understanding of the variation in catechin accumulation. To increase the depth of understanding of catechin biosynthesis, I report the cloning and characterization of C. maculosa dihydroflavonol reductase (CmDFR), a gene very likely to be necessary for catechin biosynthesis. To expand our view of metabolism beyond catechin, metabolome analysis is applied to field collected plant material, and demonstrate that the physiology of C. maculosa varies with the surrounding plant community -- plants growing in patches with high C. maculosa density tend to be accumulate higher levels of secondary metabolites than plants growing in the company of few conspecifics. Finally, the results of a study that clarifies the role of root exudates in structuring the soil fungal community are presented in the context of invasion biology.Item Open Access 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 memberDeficient 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.Item Open Access Root-rhizosphere interactions and modifications(Colorado State University. Libraries, 2016) Lapsansky, Erin Rebecca, author; Vivanco, Jorge M., advisor; Stromberger, Mary, committee member; Pilon-Smits, Elizabeth, committee member; Wallner, Stephen, committee memberThe interactions between the plant and rhizosphere are complex, but recent research is elucidating more about a diverse array of relationships. In response to the growing demand for natural or plant produced pesticides and herbicides, a novel method for the identification of bioactive root exudates was developed utilizing the hypothesis that exudate compounds changing in relative abundance over plant development were likely bioactive. Research investigated this hypothesis on Arabidopsis grown in vitro and then in maize grown under greenhouse conditions. Four compounds were identified as bioactive, modifying plant growth, supporting this novel method of bioactive compound identification. In a second study, it was hypothesized that Plant Growth Promoting Rhizobacteria (PGPR) could be used to induce specific changes to Root System Architecture (RSA) which could impart growth benefits in specific environmental conditions. In vitro, three bacterial strains displayed the ability to modify RSA, and in a greenhouse study with nutrient deficiency, one strain was able to impart growth benefit to Arabidospsis. Both bioactive root exudates and PGPR demonstrated the potential to create desired root morphology, suggesting that root systems could be optimized to overcome environmental limitations such as drought or nutrient deficiency. Finally, a review focusing on a novel interpretation of the relationship between plants and the rhizosphere, discusses how the plant primes the rhizosphere to support and protect its offspring.Item Open Access Study of bioactive proteins in the roots and root exudates of model plants(Colorado State University. Libraries, 2007) De-la-Peña, Clelia, author; Vivanco, Jorge M., advisorThe plant root system serves many roles, including anchorage and uptake of nutrients and water. The ability of roots to release a wide range of organic and inorganic compounds into the rhizosphere to communicate with roots of other plants and other organisms has been the focus of recent studies. Among the compounds released into the rhizosphere, proteins comprise an important amount of energy secreted by roots but have not been studied in detail. In the present study, I conducted a proteomic and enzymatic analysis of Arabidopsis thaliana root exudation across a developmental gradient to track the changes that occur in the root-secreted proteins at different plant developmental stages. Further, I found that the secretion of proteins (including pathogenesis-related [PR] proteins, myrosinases, and enzymes related to protein refolding) was qualitatively and quantitatively related to the growth stage of the plant. For instance, the intensity and activity of PR proteins such as chitinases were higher at peak flowering times than at any other time during Arabidopsis development. I also studied the root secretion of proteins by two model plants (Medicago sativa and A. thaliana) during their interaction with the symbiont of one of these specks (Sinorhizobium meliloti) and with an opportunistic pathogen of A. thaliana (Pseudomonas syringae pv. tomato DC3000). I found that the early interactions between M.sativa and S. meliloti induced exudation of enzymes such as acid chitinases, thaumatin proteins, PR10 and PR1 proteins. However, these proteins were not induced when M. saliva was inoculated with P. syringae DC3000. In addition, I found that P. syringae DC3000 could differentially induce the secretion of proteins related to defense in A. thaliana, whereas S. meliloti did not provoke the same response. The final study of my dissertation focused on the activity of ribosome-inactivating proteins (RIPS, PC 3.2.2.22) in Arabidopsis thaliana. Based on amino acid sequencing, it was determined that the purified RIP had homology to the mature form of a pectin methylesterase (PME, At1g11580); this purified protein showed PME activity. Further the A. thaliana full-length and mature PMF forms were cloned into the expression vector PQE30 and both constructs were expressed in Escherichia coli.