Progress 09/01/20 to 08/31/23
Outputs
Target Audience:The target audiences that were the focus of efforts in research and extension were processing and fresh market tomato growers in California, vegetable and field crop growers, cooperative extension farm advisors, crop consultants, pest control advisors, and other agricultural professionals, as well as students and academic, industry, and government researchers in the area of plant pathology. Changes/Problems:Due to COVID-19 access restrictions, a soil chitinase biochemical assay could not be performed on soil samples collected for Objective 2a, with collaborator Dr. Tautges as was planned. However, we were able to perform other biological assays on soil samples, such as PLFA for microbial community composition and molecular identification of culturable sclerotia-associated microbes. Due to COVID-19 delays and changing restrictions, we were unable to host a workshop on co-management of soil health and plant disease and give a survey; however, workshop development was completed, with advising assistance from non-mentor collaborators. For Objective 2b, in response to a new permission granted by Director Kate Scow of the Russell Ranch Century Experiment, UC Davis, we analyzed the microbial communities associated with pathogen survival structures that were buried in field plots, rather than in pots maintained in a greenhouse. This change improved the quality of microbial data obtained from sclerotia in this experiment, by more closely mirroring environmental conditions that would be experienced in vegetable production. To compare whether sclerotia species affects mycoparasitism in soil, we also included another sclerotia-producing species, Sclerotinia sclerotiorium, for evaluation, in lieu of using Fol-infested crop residue. This change in experimental protocol was developed under advisement of the primary mentor and collaborative mentor. For Objective 3a and 3b, in-person workshops in a classroom was originally envisioned for these objective. Due to COVID concerns, project information was presented at workshops conducted virtually in cooperation with a UC Davis farm advisor. Objective 3. An in-person workshop in a classroom was originally envisioned for this objective. Due to COVID concerns, the workshop was conducted virtually in cooperation with a UC Davis farm advisor. A No-Cost Extension was granted for the project due to unforeseen circumstances that prevented timely submission of the Final Report to NIFA. What opportunities for training and professional development has the project provided?Because of opportunities for training and professional development afforded by the project, I was hired as an Assistant Professor of Plant Pathology at Clemson University. The goal for training and career development was to advance career independence of PD in cooperative extension. Objectives for training/career development were: (1) expand professional skills and competency of PD in applied plant pathology by directing an independent, integrated research and extension program, and (2) establish a transdisciplinary relationship of PD with collaborators in areas of plant pathology, soil science, soil microbiology, and sustainable agriculture. This project has provided me with ample opportunities for successful completion of training/professional development and mentorship objectives. This included monthly one-on-one research meetings with the primary mentor during the academic year. In the one-on-one meetings, I discussed progress on project goals and timelines and received advising in relation to research and extension in plant pathology. Furthermore, I met quarterly with the primary mentor to discuss professional mentorship topics, including the preparation of research statements for academic positions and curriculum vitae development. I also met with the primary mentor for biannual self-evaluations (i.e., twice during reporting period) on project completion. The primary mentor served as a resource for advising on project management, building collaborations, adjusting research plans, and recommending publication venues and meetings for communicating research findings and presenting to stakeholders. Additionally, I presented at a lab working group meeting quarterly, in order to receive feedback from the lab group. I also met with non-mentor collaborators biannually (i.e., twice during reporting period) to receive project guidance and advising on soil physiochemistry, soil microbial community analysis, and the needs of the processing tomato industry. The goal for mentorship was to provide guidance towards building the creative capacity and skillset of the PD to pursue independent lines of research. The objective for mentorship of the PD was to participate in productive and interactive mentorship under the primary mentor over the course of the proposed project. I developed my skills as an independent researcher, educator, mentor, and leader. I became a member of the steering committee for the Conference on Soilborne Plant Pathogens. I succeeded in completing project goals for this reporting period. I was a peer-reviewer for manuscripts for the journals Plant Disease and Plant and Soil. I gained professional knowledge in the analysis of microbial community datasets generated from next-generation sequencing technology. I educated growers about soil health impacts on plant pathogens through oral presentations at the 35th Annual Tomato Disease Workshop, UC ANR Virtual Healthy Soils Compost Field Day, and UC ANR Virtual Workshop: Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers. I wrote an extension article that was distributed to growers via farm advisor newsletters (UCCE Vegetable Crops San Joaquin County, UCCE Tomato Info, and UCCE Vegetable Crops Colusa County) and a trade magazine (Progressive Crop Consultant). I presented results to a scientific audience at the American Phytopathological Society annual meeting through an interactive poster presentation (abstract published in Phytopathology) and gave oral presentations at the Conference on Soilborne Plant Pathogens and the UC Davis Department of Plant Pathology seminar series. Moreover, I co-mentored an undergraduate intern for a UC Davis Global Disease Biology practicum that was derived from research objectives. To advise my mentee, I prepared a syllabus and had regular weekly or bimonthly meetings (depending on quarter). I provided extensive direction on research objectives, materials and methods, data analysis and interpretation, and presentation preparation. I furthered my leadership skills by assisting with the coordination of a departmental seminar in winter quarter 2021 and coordinating a departmental seminar with two other postdocs and the primary mentor in spring 2021. I was also co-chair (with two other postdocs) of the UCD Department of Plant Pathology Postdocs and Professionals group, where I helped organize bimonthly meetings. Lastly, I continued to have an active role in the UCD plant disease diagnostics clinic. Due to COVID-19 restrictions, meetings and presentations were conducted virtually. Data generated from the project will support my ability to acquire external funding from federal and state agencies. How have the results been disseminated to communities of interest?As this work includes a broad host range pathogen (Sclerotium rolfsii) and a disease syndrome (Fusarium wilt) that occur in a broad range of hosts, results have broad applicability to diverse crops across the United States. Results were presented to vegetable and field crop producers in a trade magazine (Progressive Crop Consultant), three UCCE newsletters via UC ANR farm advisors (Brenna Aegerter, Amber Vinchesi-Vahl, and Gene Miyao), two workshops (Annual Tomato Disease Workshop, UC ANR Virtual Workshop: Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers), and a field day (UC ANR Virtual Healthy Soils Compost Field Day). Results were also presented to academic and agricultural professionals through an interactive poster presentation at the annual meeting of the American Phytopathological Society and via oral presentations at the Conference on Soilborne Plant Pathogens, UC Davis Department of Plant Pathology seminar series, and the UC Davis plant pathology departmental retreat. Two journal manuscripts are being prepared for submission to refereed journals. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Project objective 1a. In fall 2020 (trial 1) and 2021 (trial 2), soil was obtained at the Russell Ranch Century Experiment, UC Davis, from corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. Organic inputs consisted of poultry manure and winter cover crops. Soil was either unaltered or steam sterilized to reduce microbial activity, to establish the contribution of soil microbes to treatment effects. Dried tomato residue infested with Fol was measured for weight, placed in mesh bags, and buried in treatment soil in plastic pots. Pots were maintained at field capacity in a greenhouse. Tomato residue was removed from soil after 1 and 2 months. After rinsing, surface disinfesting, and drying each residue sample per pot, residue was weighed to compare the extent of residue decomposition between treatments. Residue was also macerated in sterilized water using a bead beater and dilution plated to estimate the density of Fol propagules per gram tissue. In concert, soil was analyzed at the end of the trial for soil physicochemical characteristics. Compared to soil with synthetic fertilizer, organic soils had higher organic matter, soil-P, and soil-K and improved soil structure. In trial 1, based on results for crop residue weight loss and fragmentation, Fol-infested tomato residue decomposed more rapidly in organic soil than in synthetic fertilizer soil. In trial 2, there was no significant difference in the decomposition of Fol-infested residue between treatments - although observed differences were consistent with the first trial. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. Survival of Fol propagules in tomato residue did not differ between treatments. Project objective 1b. In fall 2020 (trial 1) and 2021 (trial 2), soil was collected at the Russell Ranch Century Experiment from plots with long-term inputs of synthetic fertilizer (as described above) and six-year alfalfa-corn-tomato rotations. Experimental design was the same as described above. N-rich crop rotation lowered soil-K but improved soil aggregation relative to soil with synthetic fertilizer inputs. We found that that rotation with an N-rich crop was associated with higher pathogen loads in Fol-infested tomato residue, which implies that Fol survival is enhanced in an N-rich rotation regime. However, decomposition was higher in Fol-infested residue that was buried in N-rich rotation crop soil in trial 2 - which is a different result from trial 1, where there was no significant difference. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. Project objective 2a. In summer 2021, compost treatments were applied to a field plot at the UC Davis Russell Ranch facility; treatments consisted of (1) no-compost control, (2) amended with poultry manure compost, and (3) amended with green waste compost. Microplots were established within each treatment row, with or without chitin (crabmeal/feathermeal mix). Fol-infested tomato residue and Sclerotium rolfsii sclerotia were buried in each microplot per treatment. Treatment rows were planted to tomato and irrigated at 100% evapotranspiration. Sclerotia and residue were collected after 6 weeks. Infested tomato residue was processed as described in Objective 1a. Sclerotia were surface disinfested, scored for degree of fragmentation, and assayed for viability. Soil microbial community composition was compared across soil treatments using phospholipid fatty acid (PLFA) analysis and DNA sequence-based identification of culturable microbes from nonviable sclerotia. In trial 1, poultry manure compost reduced decomposition of Fol-infested tomato residue, whereas no-compost control and green waste compost soils increased decomposition of infested residue. In trial 2, the decomposition of Fol-infested tomato residue was similar among compost treatments. Sclerotia fragmentation was significantly greater in chitin-amended soils, but compost had no effect. Thus far, results suggest that chitin amendment enhances degradation of chitin-based structures. In trial 2, chitin amendment was associated with greater total microbial biomass, based on PLFA. The fungus Sarocladium kiliense was the most frequently recovered microbe from nonviable sclerotia. Project objective 2b. Amplicon-based microbial community analyses were performed on sclerotia of Sclerotium rolfsii and Sclerotinia sclerotiorum that were buried for four months in corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. Soil collected from plots were also analyzed. Genomic DNA was extracted from sclerotia and soil samples. Amplicon libraries were prepared from genomic DNA and run on MiSeq v2 Standard 500 cycle. Raw amplicon sequencing data was processed into amplicon sequence variants (ASVs) and taxonomically assigned using the dada2 pipeline in R. Using phyloseq in R, ASV datasets per treatment were filtered to include taxa were consistently present across replicates within a treatment. Effects of treatment on changes in community structure and differential abundances were analyzed using vegan and MaAsLin2 in R. Microbial communities significantly differed in composition among sclerotia species and soils. Differential abundance analysis revealed the presence of microbial genera that were more common on sclerotia in conventional versus organic management regimes. Project objective 3a. I worked with the primary mentor and non-mentor collaborators on designing a workshop presentation for stakeholders (i.e. growers, crop consultants, farm advisors, other agricultural professionals) on co-management of soil health and plant disease. Project findings from Objectives 1 and 2 were integrated into the existing body of knowledge on the effect of land-use management practices on both soil health and pathogen survival, in order to prepare educational content. Findings from the project were presented at workshops on "Tomato Disease" and "Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers." Project objective 3b. Project findings were disseminated to stakeholders in oral presentations at workshops, a field day, and publications in UC Cooperative Extension newsletters. The broad dissemination of information was achieved through presentations at a national research meeting and an university seminar series. Impacts were assessed based on number of participants at the field day and workshop. Participant response to a quiz demonstrated understanding of project principles. Workshop presentations enabled stakeholders to adapt soil management practices based on pathogen management needs. Completion of goals related to training and career development and mentorship are described in the next section
Publications
|
Progress 09/01/21 to 08/31/22
Outputs
Target Audience:The target audiences that were the focus of efforts in research and extension were processing and fresh market tomato growers in California, vegetable and field crop growers, cooperative extension farm advisors, crop consultants, pest control advisors, and other agricultural professionals, as well as students and academic, industry, and government researchers in the area of plant pathology. Changes/Problems:Objective 3. An in-person workshop in a classroom was originally envisioned for this objective. Due to COVID concerns, the workshop was conducted virtually in cooperation with a UC Davis farm advisor. A No-Cost Extension was granted for the project due to unforeseen circumstances that prevented timely submission of the Final Report to NIFA. What opportunities for training and professional development has the project provided?Because of opportunities for training and professional development afforded by the project, I was hired as an Assistant Professor of Plant Pathology at Clemson University. The goal for training and career development was to advance career independence of PD in cooperative extension. Objectives for training/career development were: (1) expand professional skills and competency of PD in applied plant pathology by directing an independent, integrated research and extension program, and (2) establish a transdisciplinary relationship of PD with collaborators in areas of plant pathology, soil science, soil microbiology, and sustainable agriculture. This project has provided me with ample opportunities for successful completion of training/professional development and mentorship objectives. This included monthly one-on-one research meetings with the primary mentor during the academic year. In the one-on-one meetings, I discussed progress on project goals and timelines and received advising in relation to research and extension in plant pathology. Furthermore, I met quarterly with the primary mentor to discuss professional mentorship topics, including the preparation of research statements for academic positions and curriculum vitae development. I also met with the primary mentor for biannual self-evaluations (i.e., twice during reporting period) on project completion. The primary mentor served as a resource for advising on project management, building collaborations, adjusting research plans, and recommending publication venues and meetings for communicating research findings and presenting to stakeholders. Additionally, I presented at a lab working group meeting quarterly, in order to receive feedback from the lab group. I also met with non-mentor collaborators biannually (i.e., twice during reporting period) to receive project guidance and advising on soil physiochemistry, soil microbial community analysis, and the needs of the processing tomato industry. The goal for mentorship was to provide guidance towards building the creative capacity and skillset of the PD to pursue independent lines of research. The objective for mentorship of the PD was to participate in productive and interactive mentorship under the primary mentor over the course of the proposed project. I developed my skills as an independent researcher, educator, mentor, and leader. I became a member of the steering committee for the Conference on Soilborne Plant Pathogens. I succeeded in completing project goals for this reporting period. I was a peer-reviewer for manuscripts for the journals Plant Disease and Plant and Soil. I gained professional knowledge in the analysis of microbial community datasets generated from next-generation sequencing technology. I educated growers about soil health impacts on plant pathogens through an oral presentation at the UC ANR Virtual Workshop: Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers. I presented results to a scientific audience at the Conference on Soilborne Plant Pathogens and the UC Davis Department of Plant Pathology seminar series. Moreover, I co-mentored an undergraduate intern for a UC Davis Global Disease Biology practicum that was derived from research objectives. To advise my mentee, I had regular weekly or bimonthly meetings (depending on quarter). I provided extensive direction on research objectives, materials and methods, data analysis and interpretation, and presentation preparation. Data generated from the project will support my ability to acquire external funding from federal and state agencies. How have the results been disseminated to communities of interest?As this work includes broad host range pathogens (Sclerotium rolfsii and Sclerotinia sclerotiorum) and a disease syndrome (Fusarium wilt) that occur in a broad range of hosts, results have broad applicability to diverse crops across the United States. Results were presented to vegetable and field crop producers at a workshop (UC ANR Virtual Workshop: Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers). Results were also presented to academic and agricultural professionals through oral presentations at the Conference on Soilborne Plant Pathogens and the UC Davis Department of Plant Pathology seminar series. Two journal manuscripts are being prepared for submission to refereed journals. What do you plan to do during the next reporting period to accomplish the goals?The Final Report will be submitted to NIFA.
Impacts
What was accomplished under these goals?
The goal of the project plan was to enhance development and adoption of systems-based approaches for co-managing soil health and plant disease. Objectives for the integrated research and extension project were: (1) determine the impact of soil fertility management systems on pathogen persistence (research), (2) evaluate mode of pathogen survival and microbial community characteristics as pathogen risk predictors for organic amendments (research), and (3) enable producers to adapt land-use management practices to soilborne disease risk by facilitating awareness and adoption of practices that both promote soil health and suppress plant pathogens (extension). Project objective 1a. In fall 2021, soil was obtained at the Russell Ranch Century Experiment, UC Davis, from corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. Organic inputs consisted of poultry manure and winter cover crops. Soil was either unaltered or steam sterilized to reduce microbial activity, to establish the contribution of soil microbes to treatment effects. Dried tomato residue infested with Fol was measured for weight, placed in mesh bags, and buried in treatment soil in plastic pots. Pots were maintained at field capacity in a greenhouse. Tomato residue was removed from soil after 1 and 2 months. After rinsing, surface disinfesting, and drying each residue sample per pot, residue was weighed to compare the extent of residue decomposition between treatments. Residue was also macerated in sterilized water using a bead beater and dilution plated to estimate the density of Fol propagules per gram tissue. In concert, soil was analyzed at the end of the trial for soil physicochemical characteristics. Compared to soil with synthetic fertilizer, organic soils had higher organic matter, soil-P, and soil-K and improved soil structure. There was no significant difference in the decomposition of Fol-infested residue between treatments - although observed differences were consistent with the first trial. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. Survival of Fol propagules in tomato residue did not differ between treatments. This was the final trial. Project objective 1b. In fall 2021, soil was collected at the Russell Ranch Century Experiment from plots with long-term inputs of synthetic fertilizer (as described above) and six-year alfalfa-corn-tomato rotations. Experimental design was the same as described above. N-rich crop rotation lowered soil-K but improved soil aggregation relative to soil with synthetic fertilizer inputs. We found that that rotation with an N-rich crop was associated with higher pathogen loads in Fol-infested tomato residue, which implies that Fol survival is enhanced in an N-rich rotation regime. However, decomposition was higher in Fol-infested residue that was buried in N-rich rotation crop soil - which is a different result from the previous trial, where there was no significant difference. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. This was the final trial. Project objective 2a. In 2021, compost treatments were applied to a field plot at the UC Davis Russell Ranch facility; treatments consisted of (1) no-compost control, (2) amended with poultry manure compost, and (3) amended with green waste compost. Microplots were established within each treatment row, with or without chitin (crabmeal/feathermeal mix). Fol-infested tomato residue and Sclerotium rolfsii sclerotia were buried in each microplot per treatment. Treatment rows were planted to tomato and irrigated at 100% evapotranspiration. Sclerotia and residue were collected after 6 weeks. Infested tomato residue was processed as described in Objective 1a. Sclerotia were surface disinfested, scored for degree of fragmentation, and assayed for viability. Soil microbial community composition was compared across soil treatments using phospholipid fatty acid (PLFA) analysis and DNA sequence-based identification of culturable microbes from nonviable sclerotia. The decomposition of Fol-infested tomato residue was similar among compost treatments. Sclerotia fragmentation was significantly greater in chitin-amended soils, but compost had no effect. Thus far, results suggest that chitin amendment enhances degradation of chitin-based structures. Chitin amendment was associated with greater total microbial biomass, based on PLFA. The fungus Sarocladium kiliense was the most frequently recovered microbe from nonviable sclerotia. Project objective 2b. Amplicon-based microbial community analyses were performed on sclerotia of Sclerotium rolfsii and Sclerotinia sclerotiorum that were buried in corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. Soil collected from plots were also analyzed. Genomic DNA was extracted from sclerotia and soil samples. Amplicon libraries were prepared from genomic DNA and run on MiSeq v2 Standard 500 cycle. Raw amplicon sequencing data was processed into amplicon sequence variants (ASVs) and taxonomically assigned using the dada2 pipeline in R. Using phyloseq in R, ASV datasets per treatment were filtered to include taxa were consistently present across replicates within a treatment. Effects of treatment on changes in community structure and differential abundances were analyzed using vegan and MaAsLin2 in R. Microbial communities significantly differed in composition among sclerotia species and soils. Differential abundance analysis revealed the presence of microbial genera that were more common on sclerotia in conventional versus organic management regimes. Project objective 3a. Project findings from Objectives 1 and 2 were integrated into the existing body of knowledge on the effect of land-use management practices on both soil health and pathogen survival, in order to prepare educational content. Findings from the project were presented at a workshop on "Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers." Project objective 3b. Project findings were disseminated to stakeholders in oral presentations at the workshop. The broad dissemination of information was achieved through presentations at a national research meeting and an university seminar series. Impacts were assessed based on number of participants at the field day and workshop. Participant response to a quiz demonstrated understanding of project principles. The workshop presentation enabled stakeholders to adapt soil management practices based on pathogen management needs. Completion of goals related to training and career development are described in the next section
Publications
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Paugh K. R., Tautges N., Scow K., Swett C. L. 2022. How does soil health management impact survival of soilborne plant pathogens? Conference on Soilborne Plant Pathogens. Oral presentation, via Zoom.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2022
Citation:
Paugh K. R. Advancing systems-based approaches for soilborne disease management. 2022. Plant Pathology 290 Seminar Series. University of California, Davis. Invited Speaker.
- Type:
Other
Status:
Other
Year Published:
2022
Citation:
Paugh, K., Aegerter, B., Turini, T., Bagley, Z., Swett, C. L. 2022. How soil health management impacts survival of soilborne plant pathogens. UC ANR Virtual Workshop: Management of Fusarium Wilt and Other Soilborne Fungal Diseases for Organic Growers, via Zoom.
- Type:
Other
Status:
Other
Year Published:
2021
Citation:
Calderon A., Paugh K. R., Swett C. L. 2021. The Effect of Soil Management on Microbial Antagonists of Plant Pathogens in Soil. UC Davis Global Disease Biology Undergraduate Practicum Report.
|
Progress 09/01/20 to 08/31/21
Outputs
Target Audience:The target audiences that were reached by efforts in extension and outreach were processing and fresh market tomato growers in California, vegetable and field crop growers, cooperative extension farm advisors, crop consultants, pest control advisors, and other agricultural professionals, as well as academic, industry, and government researchers in the area of plant pathology. Changes/Problems:Due to COVID-19 access restrictions, a soil chitinase biochemical assay could not be performed on soil samples collected for Objective 2a, with collaborator Dr. Tautges as was planned. However, we were able to perform other biological assays on soil samples, such as PLFA for microbial community composition and molecular identification of culturable sclerotia-associated microbes. Due to COVID-19 delays and changing restrictions, we were unable to host a workshop on co-management of soil health and plant disease and give a survey; however, workshop development was completed, with advising assistance from non-mentor collaborators. The workshop will be conducted virtually in the next reporting period, to prevent any further delay due to changing COVID-19 restrictions. Otherwise, there were minimal disruptions to project objectives due to COVID-19. For Objective 2b, in response to a new permission granted by Director Kate Scow of the Russell Ranch Century Experiment, UC Davis, we will be conducting microbial community analyses on pathogen survival structures that were buried in field plots, rather than in pots maintained in a greenhouse. This change should improve the quality of microbial data obtained from sclerotia in this experiment, by more closely mirroring environmental conditions that would be experienced in row crop production. To compare whether sclerotia species affects mycoparasitism in soil, we also included another sclerotia-producing species, Sclerotinia sclerotiorium, for evaluation, in lieu of using Fol-infested crop residue. This change in experimental protocol was developed under advisement of the primary mentor Cassandra Swett and collaborator Amisha Poret-Peterson. No major shortcomings are anticipated for the next funding period. What opportunities for training and professional development has the project provided?This project has provided me ample opportunities for training and professional development. Progress towards training/professional development and mentorship objectives included monthly one-on-one research meetings with the primary mentor during the academic year - which were typically 2 hours or longer. In the one-on-one meetings, I discussed progress on project goals and timelines and received advising in relation to research and extension in plant pathology. Furthermore, we met quarterly to discuss professional mentorship topics, including the preparation of research statements for academic positions and curriculum vitae development. I also met with the primary mentor for biannual self-evaluations (i.e., twice during reporting period) on project completion. The primary mentor served as a resource for advising on project management, building collaborations, adjusting research plans, and recommending publication venues and meetings for communicating research findings and presenting to stakeholders. Additionally, I presented at a lab working group meeting quarterly, in order to receive feedback from the lab group. I also met with non-mentor collaborators biannually (i.e., twice during reporting period) to receive project guidance and advising on soil physiochemistry, soil microbial community analysis, and the needs of the processing tomato industry. I developed my skills as an independent researcher, educator, mentor, and leader. I succeeded in completing project goals for this reporting period. I gained professional knowledge in the design and implementation of an experiment involving DNA amplicon-based microbial community analysis. I educated growers about soil health impacts on plant pathogens through oral presentations at the 35th Annual Tomato Disease Workshop and UC ANR Virtual Healthy Soils Compost Field Day. I wrote an extension article that was distributed to growers via farm advisor newsletters (UCCE Vegetable Crops San Joaquin County, UCCE Tomato Info, and UCCE Vegetable Crops Colusa County) and a trade magazine (Progressive Crop Consultant). I presented results to a scientific audience at the American Phytopathological Society annual meeting through an interactive poster presentation (abstract published in Phytopathology) and orally presented at the UC Davis Plant Pathology Research Retreat. Moreover, I mentored one intern for three quarters. To advise my mentee, I prepared a syllabus and had regular weekly or bimonthly meetings (depending on quarter) about the internship project. I provided extensive direction on research objectives, materials and methods, data analysis and interpretation, and presentation preparation. I furthered my leadership skills by assisting with a departmental seminar in winter quarter 2021 and coordinating a departmental seminar with two other postdocs and the primary mentor in spring 2021. I was also co-chair (with two other postdocs) of the UCD Department of Plant Pathology Postdocs and Professionals group, where I helped organize bimonthly meetings. Lastly, I continued to have an active role in the UCD plant disease diagnostics clinic. Due to COVID-19 restrictions, meetings and presentations were conducted virtually. How have the results been disseminated to communities of interest?As this work includes a broad host range pathogen (Sclerotium rolfsii) and a disease syndrome (Fusarium wilt) that occurs in a broad range of hosts, results have broad applicability to diverse crops across the United States. Results were presented to vegetable and field crop producers in a trade magazine (Progressive Crop Consultant), three UCCE newsletters via UC ANR farm advisors (Brenna Aegerter, Amber Vinchesi-Vahl, and Gene Miyao), a workshop (Annual Tomato Disease Workshop), and a field day (UC ANR Virtual Healthy Soils Compost Field Day). Results were also presented to academic and agricultural professionals through an interactive poster presentation at the annual meeting of the American Phytopathological Society and an oral presentation at the UC Davis plant pathology departmental retreat. A journal manuscript is in progress. What do you plan to do during the next reporting period to accomplish the goals?Project objectives will be completed in the next reporting period. For Objectives 1a and b, each respective trial will be repeated once. For Objective 2a, the field trial will be repeated once, with compost amendments being additive to those applied in the earlier year. For Objective 2b, genomic DNA will be extracted from sclerotia and soil samples. For bacterial and fungal community analysis, amplicon libraries of 16S rRNA and ITS, respectively, will each be run per lane on the MiSeq v2 Standard 500 cycle. Raw amplicon sequencing data will be processed into amplicon sequence variants (ASVs) and taxonomically assigned using the dada2 pipeline in R. Using phyloseq in R, ASV datasets per treatment will be filtered to include taxa which are consistently present across replicates within a treatment. Effects of treatment on changes in community structure and differential abundances will be analyzed via deseq2 for each amplicon dataset. For Objectives 3a and b, I will implement a workshop for stakeholders on the co-management of soil health and plant disease in the upcoming reporting period. I will present findings in extension publication(s) and at least one field day and one extension meeting. Impacts will be assessed based on number of participants and reported changes in production practices in an annual survey. I will also update my online profile on ResearchGate with project information.
Impacts
What was accomplished under these goals?
Objective 1a: In fall 2020, soil was obtained at the Russell Ranch Century Experiment, UC Davis, from corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. Organic inputs consisted of poultry manure and winter cover crops. Soil was either unaltered or steam sterilized to reduce microbial activity, to establish the contribution of soil microbes to treatment effects. Dried tomato residue infested with Fol was measured for weight, placed in mesh bags, and buried in treatment soil in plastic pots. Pots were maintained at field capacity in a greenhouse. Tomato residue was removed from soil after 1 and 2 months. After rinsing, surface disinfesting, and drying each residue sample per pot, residue was weighed to compare the extent of residue decomposition between treatments. Residue was also macerated in sterilized water using a bead beater and dilution plated to estimate the density of Fol propagules per gram tissue. In concert, soil was analyzed at the end of the trial for soil physicochemical characteristics. Compared to soil with synthetic fertilizer, organic soils had higher organic matter, soil-P, and soil-K and improved soil structure. Based on results for crop residue weight loss and fragmentation, Fol-infested tomato residue decomposed more rapidly in organic soil than in synthetic fertilizer soil. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. Survival of Fol propagules in tomato residue did not differ between treatments. This trial was performed once, thus far. Objective 1b: In fall 2020, soil was collected at the Russell Ranch Century Experiment from plots with long-term inputs of synthetic fertilizer (as described above) and six-year alfalfa-corn-tomato rotations. Experimental design was the same as described above. N-rich crop rotation lowered soil-K but improved soil aggregation relative to soil with synthetic fertilizer inputs. We found that that rotation with an N-rich crop was associated with higher pathogen loads in Fol-infested tomato residue, which implies that Fol survival is enhanced in an N-rich rotation regime. There was no significant difference in decomposition of infested tomato residue in N-rich crop soil compared to synthetic fertilizer soil. This effect on Fol-infested tomato residue was lost in sterilized soil, suggesting a biotic origin for observed differences. This trial was performed once, thus far. Objective 2a: In summer 2021, compost treatments were applied to a field plot at the UC Davis Russell Ranch facility; treatments consisted of (1) no-compost control, (2) amended with poultry manure compost, and (3) amended with green waste compost. Microplots were established within each treatment row, with or without chitin (crabmeal/feathermeal mix). Fol-infested tomato residue and Sclerotium rolfsii sclerotia were buried in each microplot per treatment. Treatment rows were planted to tomato and irrigated at 100% evapotranspiration. Sclerotia and residue were collected after 6 weeks. Infested tomato residue were processed as described in Objective 1a. Sclerotia were surface disinfested, scored for degree of fragmentation, and assayed for viability. Soil microbial community composition was compared across soil treatments using phospholipid fatty acid (PLFA) analysis and DNA sequence-based identification of culturable microbes from nonviable sclerotia. Poultry manure compost reduced decomposition of Fol-infested tomato residue, whereas no-compost control and green waste compost soils resulted in the greatest breakdown of infested residue. Sclerotia fragmentation was significantly greater in chitin-amended soils, but compost had no significant effect. Thus far, results suggest that type of compost amendment influences survival of plant-based but not chitin-based survival structures, and that chitin amendment enhances degradation of chitin-based structures. In addition, PLFA analysis showed lower abundance of AMF fungi in chitin-amended soils. The fungus Sarocladium kiliense was the most frequently recovered microbe from nonviable sclerotia. Objective 2b: In fall 2020, sclerotia of Sclerotium rolfsii and Sclerotinia sclerotiorum were buried in corn/tomato plots managed with either synthetic or organic fertilizer inputs since 1994. A mesh bag with sclerotia (one bag per species) was buried in each of six sites per treatment plot. The trial was spatially replicated, with three field plots per soil health management treatment. Bulk soil samples were collected from each site on the day of burial. After three months, mesh bags and soil samples were collected from each site per plot. Sclerotia were rinsed, surface sterilized, and stored in 2mL tubes. A subset of sclerotia per site was transferred to nutrient media in Petri dishes to evaluate viability. For microbial community analysis, soil samples and the remaining subset of sclerotia per site were flash frozen and stored at -80°C. A protocol for genomic DNA extraction from sclerotia and soil samples was optimized for yield and purity. Objective 3a: I worked with the primary mentor and non-mentor collaborators on designing a workshop for stakeholders (i.e. growers, crop consultants, farm advisors, other agricultural professionals) on co-management of soil health and plant disease. Project findings from Objectives 1 and 2 were integrated into the existing body of knowledge on the effect of land-use management practices on both soil health and pathogen survival, in order to prepare educational content. Objective 3b: Project findings were disseminated to stakeholders in oral presentations at a field day and workshop and in publications in UC Cooperative Extension newsletters. The broad dissemination of information was achieved through presentations at a national research meeting and by publishing in a trade journal. Impacts was assessed based on number of participants at the field day and workshop.
Publications
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Paugh, K. and Swett, C. 2020. Fusarium wilt newsletter, October 2020: Fusarium wilt of tomato. UCCE Vegetable Crops in San Joaquin County.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Paugh, K. R., Tautges, N, Scow, K., and Swett, C. L. 2020. Co-managing soil health and plant disease: Effects of soil health practices on persistence of plant pathogens with differing modes of survival. (Abstr.) Phytopathology, 110(12S):S2.143.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Paugh, K. and Swett, C. 2020. Fusarium wilt of tomato, caused by Fusarium oxysporum f. sp. lycopersici race 3 - a soil-borne killer. UCCE Tomato Info (November 2020).
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Paugh, K. and Swett, C. 2021. Fusarium wilt of tomato, caused by Fusarium oxysporum f. sp. lycopersici race 3 - a soil-borne killer. UCCE Vegetable Crops Newsletter - March, 2021, Colusa County.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Paugh K. R., Tautges N., Scow K., Swett C. L. 2020. Soil health and soilborne disease management. 35th Annual Tomato Disease Workshop (virtual). (Oral presentation)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Paugh, K. R. 2021. Impact of soil health practices on survival of soilborne plant pathogens. UC ANR Virtual Healthy Soils Compost Field Day. (Oral presentation)
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