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Browsing by Author "Vivanco, Jorge, advisor"

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    Control of Meloidogyne chitwoodi (Columbia root-knot nematode) by microbial soil inoculants in potatoes (Solanum tuberosum)
    (Colorado State University. Libraries, 2022) Gross, Gary Edward, author; Wallner, Stephen, advisor; Vivanco, Jorge, advisor; Schipanski, Meagan, committee member
    Columbia root-knot nematode (Meloidogyne chitwoodi Golden et al) is a major pest in commercial potato production in the northwestern, United States of America. M. chitwoodi infestation is widespread throughout the potato (Solanum tuberosum) growing regions of the U.S and other areas of the world. Meloidogyne spp. causes severe crop damage and economic losses in a broad range of economically important crops. Traditionally, M. chitwoodi has been controlled by the applications of chemical-based soil fumigants and nematicides. Chemical based controls have shown good effect at controlling M. chitwoodi, but due to their human toxicity, possible damage to the environment, development of nematode resistance to chemical nematicides, decreased availability of labeled chemical nematicides and the high cost of chemical nematicides there is a need for alternative methods to control M. chitwoodi. Specific soil microorganisms have been found to be antagonistic and parasitic to M. chitwoodi and other Meloidogyne spp. in potatoes and several other crops. It has also been proposed that the use of soil microorganisms that are antagonistic and parasitic to plant parasitic nematodes are an essential component to long term sustainable Integrated Nematode Management (INM). Due to the agricultural need for the development of alternative control methods of Meloidogyne spp. in crop production worldwide two commercially available microbial soil inoculant products were tested under greenhouse and open-field conditions. The two commercially available microbial soil inoculant products that were tested are NemaRoot, which contains Purpureocillium lilacinus (formally known as Paecilomyces lilacinus) and BioFit N, which contains Azotobacter chroccum, Bacillus subtilis, Bacillus megaterium, Bacillus mycoides, and Trichoderma harzianum. Previous findings have shown that Bacillus subtilis, Bacillus megaterium, Trichoderma harzianum and Purpureocillium lilacinus all have the ability to control Meloidogyne spp. to varying degrees in a number of diverse crops. The greenhouse experiments that were conducted for this research showed that NemaRoot was able to reduce M. chitwoodi root galling by 64% (P < 0.001), eggs by 74% (P < 0.001) to 91% (P < 0.001), second-stage juveniles in the substrate by 80% (P < 0.001), the reproductive factor by 67% (P < 0.001) to 80% (P < 0.001) and potato tuber damage by 77% (P < 0.001) to 82% (P < 0.001) in potatoes. The greenhouse experiments also showed that BioFit N was able to reduce M. chitwoodi root galling by 73% (P < 0.001, eggs by 81% (P < 0.001) to 97% (P < 0.001), second-stage juveniles in the substrate by 81% (P < 0.001), the reproductive factor by 82% (P < 0.001) to 87% (P < 0.001) and potato tuber damage by 78% (P < 0.001) to 78% (P < 0.001) in potatoes. The commercial open-field potato experiment showed that 2, 3 and 4 applications of BioFit N at a rate of 1.12 kg/ha per application were able to control M. chitwoodi tuber damage as well as 2 applications of Vydate (Oxamyl) at a rate of 2.2 L/ha per application. These results show that biocontrol of M. chitwoodi with microbial soil inoculants are an effective control method; especially, when used as a part of an Integrated Nematode Management (INM) strategy.
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    Development and utilization of molecular tools to understand invasion biology in Centaurea maculosa (spotted knapweed)
    (Colorado State University. Libraries, 2009) Broz, Amanda K., author; Vivanco, Jorge, advisor
    My doctoral research at Colorado State University was designed to create and utilize molecular tools to help understand ecological phenomena in the invasive weed, spotted knapweed (Centaurea maculosa Lam.). In this dissertation, I first introduce the need for research at multiple scales and the potential benefits of collectively examining molecular, physiological and ecological phenomena in an invasive plant. I then give a brief overview of the life history characteristics of spotted knapweed and report on the development and characterization of a spotted knapweed gene library. By utilizing sequence information from the gene library, I determined that both ploidy (diploid or tetraploid) and origin (native or invasive) influence expression of genes that may be important for plant defense in spotted knapweed populations. I found that spotted knapweed can differentially respond to strong or weak competitors at the level of gene expression by using existing molecular tools from a model plant coupled with sequence information from the gene library. In addition, I found that plant neighbor identity, simulated herbivory and resource availability are all important factors that influence accumulation of biomass and secondary metabolites in both spotted knapweed and a native grass species. I utilized molecular tools to demonstrate that spotted knapweed infestation alters the composition of North American soil fungal communities; however, the ecological ramifications of this observation remain undetermined. The major goal of my research was to better understand spotted knapweed invasion biology by utilizing molecular tools. I believe this approach was successful in that it led to a variety of interesting results. However, more research is required to fully link these molecular findings with ecological and physiological aspects of spotted knapweed invasion biology. It is my hope that the chapters of this dissertation highlight both the opportunities and limitations associated with using molecular tools to understand invasion biology in this system.
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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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    Soil bacterial influence on alfalfa growth and health
    (Colorado State University. Libraries, 2013) Sheflin, Amy M., author; Vivanco, Jorge, advisor; Weir, Tiffany, committee member; Badri, Dayakar, committee member; Manter, Dan, committee member; Paschke, Mark, committee member
    Soil microbial communities have demonstrated enormous potential for promotion of plant health and productivity. In particular, the diversity of the soil community may play an important role for increased plant growth. However, previous research has focused on soil fungal diversity and neglected the role that diversity of soil bacteria may play in influencing plant growth. Therefore, a greenhouse study was conducted to determine if soil bacterial community structure influences alfalfa productivity. Prior to setup, nine soils with varying physico-chemical and microbiological profiles were chemically and biologically characterized. Soil physico-chemical factors for experimental soils were quantified via standard methods of soil nutrient testing. In addition, soil microbiology was characterized using 454 pyrosequencing to determine soil diversity indices and taxonomic classification of the soil bacterial community. These microbial communities were extracted into soil suspensions and transplanted to alfalfa plants growing in a sterile substrate. Filtered (soil microorganisms removed) and non-filtered (soil microorganisms retained) soil suspensions were applied to separate soil chemical and microbiological effects. Alfalfa plants were grown in a greenhouse for 60 days post germination; then roots and shoots were harvested, dried and weighed. This experimental setup was used to answer two distinct research questions. In the first study, alfalfa biomass was correlated with both soil physico-chemical and bacterial measures to determine which soil factors influenced plant productivity. For four soils, a biologically inactive (filtered) extract included unidentified chemical factors that had a negative effect on plant biomass production. However, in two of these cases inclusion of soil microbes counteracted this negative effect and restored plant growth to a level equal to the non-amended control. Among bacterial classes, the relative abundance of Deltaproteobacteria in soils was significantly correlated with plant productivity. Correlations between plant productivity and soil bacterial richness, diversity and evenness were marginally significant and more highly correlated than soil physico-chemical factors. Results suggest that soil microbiology can compensate for negative effects on plant growth due to soil chemistry, potentially due to microbial remediation of organic soil chemical residues such as herbicides. Also, in this study, relative abundance of specific bacterial taxa was more highly correlated than bacterial diversity indices with improved plant productivity. Many species of bacteria, referred to collectively as plant growth promoting rhizobacteria (PGPR), are known to be particularly beneficial to plant health and yield. However, inconsistency in establishment of PGPR inoculants has limited their practical use in the field. While PGPR inoculation failures have been partially attributed to competition with the indigenous soil community, studies focusing on the role that indigenous soil bacteria play on the establishment of PGPR inoculants are rare. Soil bacterial diversity is known to prevent establishment of fungal pathogens and may inhibit PGPR establishment as well. Therefore a second study was conducted using four of the nine original experimental soils, which were selected to represent the largest variety of US locale and management types from collected soils. Including four soils allowed for expansion beyond previous bacterial diversity research, which utilized only one soil type, while simultaneously including inoculation treatments of two different organisms. The same experimental setup was utilized except that either a PGPR (Pseudomonas putida) or a pathogenic microorganism (Phytophthora medicaginis) was introduced for comparison to non-amended controls. Subsequently, effects on alfalfa biomass production and disease were measured. In addition, PGPR colonization by P. putida KT2440 was quantified using qPCR via detection of the gfp gene carried on the KT2440 plasmid. Results from the second study showed increases in alfalfa productivity with added PGPR were significantly larger in soils with higher soil microbial diversity. However, no differences in PGPR root colonization were observed among non-filtered treatment groups. These results suggest that the increased effectiveness of the PGPR in high diversity communities was due to increased effectiveness of other beneficial soil microorganisms. Indeed, several native PGPR and N cycling species were correlated with shoot biomass increases when adding PGPR. Conversely, disease incidence and severity caused by "P. medicaginis" was not significantly associated with soil bacterial diversity. These results emphasize the role of soil microbial community composition and its functional relationship with the invading organism in predicting effects of an introduced PGPR inoculant or soil pathogen. In conclusion, both soil chemical and biological qualities were evaluated to lend confidence that observed effects on alfalfa biomass and microbial invasion were due to biological rather than chemical influences. Soil bacteria were found to influence plant productivity by counteracting other soil factors with negative effects on plant growth. In addition, soil community diversity played a less consequential role in these experiments than the specific taxonomical and functional bacterial members. Furthermore, soil bacterial diversity significantly improved the beneficial effects of PGPR inoculants, but was not shown to significantly reduce disease incidence or severity.