Grant Information
| Knowledge Area | Subject of Investigation | Field of Science | Percent |
|---|---|---|---|
| 215 - Biological Control of Pests Affecting Plants | 2010 - Sugar beet | 1040 - Molecular biology | 25% |
| 212 - Pathogens and Nematodes Affecting Plants | 1114 - Peach | 1040 - Molecular biology | 15% |
| 212 - Pathogens and Nematodes Affecting Plants | 1440 - Cole crops (includes cabbage, kale, broccoli, brussels sprouts, cauliflower, kohlrabi) | 1040 - Molecular biology | 15% |
| 212 - Pathogens and Nematodes Affecting Plants | 2010 - Sugar beet | 1040 - Molecular biology | 15% |
| 215 - Biological Control of Pests Affecting Plants | 1114 - Peach | 1040 - Molecular biology | 15% |
| 215 - Biological Control of Pests Affecting Plants | 1440 - Cole crops (includes cabbage, kale, broccoli, brussels sprouts, cauliflower, kohlrabi) | 1040 - Molecular biology | 15% |
One of the long-term goals of this research is to develop new and more sustainable strategies to manage soil-borne plant pathogens. To accomplish this, we are endeavoring to understand soils that naturally inhibit plant pests and disease, termed suppressive soils. These soils hold considerable potential for managing soil-borne pathogens. Key steps in realizing this potential are to identify the causal organisms and then understand the agronomic and environmental factors that enable them to function. Armed with such knowledge, it should be possible to develop effective and sustainable pest management strategies through the application of the organisms and through agronomic practices that influence their populations. Towards this goal, the first Specific Objective of this research is to elucidate the interactions among the beneficial microorganisms, pathogens and crops that lead to the development and stability of the pathogen suppressiveness. We are currently studying soils that exhibit suppressiveness against sugarbeet cyst and root-knot nematodes. Another long-term goal of this research is to develop new and more sustainable strategies for managing replant disease. Replant disease is a disease or disorder that often occurs when crops are "replanted" in soil that had previously supported the same or similar plant species. It typically leads to reductions in plant growth, crop yields and production duration. As the causal agent(s) remain ill-defined, the second Specific Objective of this research is to identify the microorganisms that cause Prunus replant disease. Identifying the causal agents will represent a crucial step in the development of new management strategies, as this will facilitate targeted breeding programs and or the selection of targeted biological, chemical or integrated pest management strategies, thereby eliminating the need for soil fumigants such as methyl bromide. Finally, the third Specific Objective of this research is to develop new methods that enable a greater understanding of the roles microorganisms play in processes such as pathogen and replant disease. In prior research, we have developed several experimental methods, approaches, and software to facilitate a greater understanding of these phenomena. In this research, we will continue these efforts by developing new methods that will improve microbial community analyses.
Objective 1. Elucidate the interactions among the beneficial microorganisms, pathogens and crops that lead to the development and stability of the pathogen suppressiveness. Prior research examined the population dynamics of the sugarbeet cyst nematode, Heterodera schachtii, and the nematophagus fungus Dactylella oviparasitica. After two nematode generations, the population densities of H. schachtii were measured in relation to various initial infestation densities of both D. oviparasitica and H. schachtii. In general, higher initial population densities of D. oviparasitica were associated with lower final population densities of H. schachtii. We also showed that the densities of H. schachtii-associated D. oviparasitica fluctuate greatly, with rRNA gene numbers going from zero in most field-soil-collected cysts to an average of 4.24 x 108 in mature females isolated directly from root surfaces. Finally, phylogenetic analysis of rRNA genes suggested that D. oviparasitica belongs to a clade of nematophagous fungi that includes Arkansas Fungus strain L (ARF-L) and that these fungi are widely distributed. In our future research, we will expand on these findings to develop more effective decision models for sugar beet planting that are based on a thorough understanding of how the population densities of specific D. oviparasitic subtypes influence H. schachtii populations in a temporal manner. Objective 2. Identify the microorganisms that cause Prunus replant disease. Prior research has provided strong evidence that two stramenopile species and numerous bacteria are putative causal agents of Prunus replant disease in a peach orchard soil. Future research will involve performing experiments to validate these findings and to expand this line of investigation to examine other Prunus replant soils. These experiments will address the issue of causality in several ways. First, we will perform Koch's postulates experiments, where the putative causal agents are added back to soil to test their effects on plant growth parameters. Second, we will determine if stramenopile sequences are consistently associated with Prunus replant disease in a wide variety of soils and locations. Finally, we will determine if stramenopile sequences are consistently associated with Prunus replant disease in field trials. Objective 3. Develop new methods that enable a greater understanding of the roles microorganisms play in pathogen and disease associated processes. Prior research led to the development of a method termed oligonucleotide fingerprinting or rRNA genes (OFRG). This method provided the first cost-effective means to examine microbial community composition. To continue this research, we plan to develop new methods and software that enable analysis of microbial community composition with higher throughput, higher resolution and less compositional skew. We will also develop software enabling the design of more effective sequence selective PCR assays and statistical methods enabling identification of relationships among omic data that can identify non-linear relationships and is non-parametric.
Target Audience
This project has four interrelated objectives listed below. The target audiences for this project are (i) scientists endeavoring to perform similar studies targeting both similar and different pathogens, (ii) scientists performing molecular based studies that would benefit from the tools we have and are developing and (iii) stakeholders that could benefit from the solutions that are developed both directly and indirectly from our research. In addition, James Borneman integrates his research findings and related concepts into his undergraduate and graduate level microbiology courses, which includes: MCBL 121L, an undergraduate microbiology laboratory course, MCBL 126, an undergraduate microbiology course in microbiomes, MCBL 211, a graduate microbial ecology course, and MCBL 226, a graduate microbiology course in microbiomes. OBJECTIVE 1. Develop Strategies to Manage Plant Parasitic Nematodes by Utilizing the Indigenous Populations of the Nematophagous Fungus Dactylella oviparasitica. OBJECTIVE 2. Develop Strategies to Manage Huanglongbing (HLB) of Citrus by Utilizing Microbiome-Based Approaches. OBJECTIVE 3. Develop Strategies to Manage Pierce's Disease of Grapes by Utilizing Microbiome-Based Approaches. We have and will continue to employ a strategy that is similar to the one described above in the Rationale section for Objective 2. To date, we have identified a fungus that when applied to grapevines can reduce disease symptoms in planta (unpublished results). OBJECTIVE 4. Develop New Methods for Molecular Microbial Ecology and Their Associated Bioinformatic Analyses. Our work under this objective has and will continue to be driven by biological questions that we have envisioned, but that can't be answered using current methods.
Changes / Problems
Nothing Reported
Training & Professional Development
James Borneman trained 1 MS student, 3 Ph.D. students and 3 undergraduate students, 1 Postdoc, and 1 Project Scientist
Dissemination Streams
Presentation: Annual Meeting of Western Regional Project W-3147 on Biological Control, October 24, 2014, Mission Inn, "Utilizing the Endophytic Phytobiome to Develop Effective and Sustainable HLB Management Strategies" Invited Presentation: 17th Annual Loma Linda University Basic Science Research Symposium, November 13, 2014. Title, "Identifying Functionally Important Bacteria By Examining Host-Associated Microorganisms." Invited Presentation: Plant Pathology and Microbiology Seminar, March 11 2015. Title, "Identifying Functionally Important Bacteria By Examining Host-Associated Microorganisms." Invited Presentation: 61st Conference on Soilborne Plant Pathogens, March 25, 2015. Title, "Improving the Sugar Beet Cropping Decision Model in the Imperial Valley." Presentation by James Borneman: Sugarbeet Work Group Meeting, February 3 2016, Holtville CA, Title: Improving Sugar Beet Economics, Productivity & Sustainability by Modifying the Cropping Decision Model. Invited Presentation by James Borneman: Foundation for Food and Agriculture Phytobiomes Meeting, May 29, 2016, Tampa Florida, Title: Managing Indigenous Populations of Dactylella oviparasitica to Suppress the Sugarbeet Cyst Nematode. Presentation by James Borneman: A Microbe-Based Strategy to Suppress the Sugarbeet Cyst Nematode. December 2, 2016. W3147 Meeting at MI in Riverside CA. Presentation by James Borneman titled "A Microbe-Based Strategy to Suppress the Sugarbeet Cyst Nematode." Annual Meeting of Western Regional Project W-3147 on Biological Control, December 2, 2016, Mission Inn. Presentation by James Borneman titled "Improving Sugar Beet Economics, Productivity & Sustainability by Modifying the Cropping Decision Model." Sugarbeet Work Group Meeting, February 8, 2017, Holtville CA. Presentation by James Borneman titled "Creating Cyst Nematode Suppressive Soils Using a Cropping Decision Model." Conference on Soilborne Plant Pathogens. Davis California, March 29, 2017. Invited presentation by James Borneman titled "Statistical Analysis of Microbiome Data When Samples Have Unequal Sequence Counts." UCR Department of Statistics, May 2, 2017. Presentation by James Borneman titled "Culture to Management - An Approach to Cultivate and Eradicate the HLB-Associated Bacterium," Citrus Research Board HLB External Review Panel Meetings in Davis on August 16, 2017. Invited Presentation by James Borneman for UCR Microbiome Datablitz. October 27, 2017. Invited Presentation by James Borneman titled, Development of Biologically Based Strategies to Control Cyst Nematodes and Huanglongbing. for BASF (Research Triangle Park, NC) October 4, 2017. Invited Presentation by James Borneman for Sugarbeet Work Group Meeting, January 31 2018, Holtville CA, Title: Improving Sugar Beet Economics, Productivity & Sustainability by Modifying the Cropping Decision Model. Invited Presentation by James Borneman titled, Indigenous Populations of Dactylella oviparasitica Suppress Nematodes in Several Regions & Crops. Joint Meeting of Conference on Soilborne Plant Pathogens and APS Pacific Division. Portland Oregon, June 27, 2018. James Borneman integrates his research findings and related concepts into his undergraduate and graduate level microbiology courses, which includes: MCBL 121L, an undergraduate microbiology laboratory course, MCBL 126, an undergraduate microbiology course in microbiomes, MCBL 211, a graduate microbial ecology course, and MCBL 226, a graduate microbiology course in microbiomes.
Next Reporting Steps
We will continue with the abovementioned research. We are also developing new strategies to manage the Huanglongbing (HLB), which is a devastating disease of citrus that is associated with an uncultured bacterium (Candidatus Liberibacter spp.), and which currently has no effective treatments. Our approaches are several including (i) using the citrus microbiome to inhibit the bacterial pathogen, (ii) using the citrus microbiome to deter feeding of the vector (Asian Citrus Psyllid) (iii) deploying the Bt toxin in phloem inhabiting bacteria (iv) and using metabolic modeling of the HLB-associated pathogen to identify peptides to kill this pathogen and that can be delivered by the CTV virus and (v) using metabolic modeling of the HLB-associated pathogen to identify the necessary reagents and conditions to cultivate the HLB-associated pathogen in vitro.