Progress 09/01/22 to 08/31/23
Outputs
Target Audience:Stakeholders involved in the US onion industry are the primary audience for this project. This includes onion producers (farmers), packers, shippers, and associated stakeholders engaged in various capacities in onion production, distribution, and marketing, e.g., agronomists, crop consultants, farm managers, field workers; personnel associated with agricultural supply companies (fertilizer and pesticide dealers, irrigation supply companies, etc.), seed companies, and dealers; onion breeders (public and private); and onion storage and shipping/transport personnel and companies. Public and private research and extension specialists, undergraduate students, graduate students, and postdoctorates working with diverse aspects of onion production are also a target audience for this project. The target audiences reached during this reporting period included: Onion growers, packers, processors, and associated stakeholders in the 7 main onion-growing regions of the US; Extension professionals in the 12 onion-growing states represented in this project; Onion researchers from the US and other countries attended a session dedicated to Stop the Rot project results at the Stop the Rot Annual Team Meeting in Savannah, GA on Jan. 5-7, 2023 (25 participants); Onion stakeholders at the Southeast Fruit & Vegetable Conference in Savannah, GA on 5-7, 2023 (35 people); Growers at the Tri-County Produce Auction Meeting in New Wilmington, PA on Oct. 22, 2022 (12 people); Stakeholders at the Ephrata Agway Grower Meeting in Ephrata, PA on Dec. 13, 2022 (52 people); Onion stakeholders at the New England Vegetable and Fruit Conference, Manchester, NH on Dec. 15, 2022 (70 attendees); Onion stakeholders in Colquitt Co., GA on Jan. 24, 2023 (55 attendees); Onion stakeholders in Tattnall Co., GA on Jan. 26, 2023 (60 attendees); Onion stakeholders at the UT Onion Association Annual Meeting in Brigham City, UT on Feb. 7, 2023 (13 attendees); Onion stakeholders at the CA Garlic and Onion Research Symposium in Tulare, CA on Feb. 13, 2023 (80 attendees); Onion stakeholders at the CO Fruit & Vegetable Growers' Association Annual Meeting in Denver, CO on Feb. 21-22, 20223 (30 attendees); Onion stakeholders at a Treasure Valley, ID survey on Feb. 7, 2023 (25 attendees); Allium stakeholders at the Allium Produce Grower Update webinar on Mar. 2, 2023 (24 attendees); Onion stakeholders at the Vidalia Onion Field Day Demonstration and Training in Lyons, GA on Apr. 7, 2023 (30 attendees); Onion stakeholders at the BASF/Nunhems Onion Growers' Meeting in Kennewick, WA on Nov. 15, 2022 (50 people); Onion stakeholders at the Onion Session of the 2023 Annual Convention & Trade Show of the Pacific Northwest Vegetable Association in Kennewick, WA on Nov. 16, 2022 (250 people); Onion stakeholders at the Vegetable Spring Field Day in Uvalde, TX on May 11, 2023 (85 attendees); Onion growers at the NMSU Onion Field Day in Las Cruces, NM on June 7, 2023 (36 attendees); Onion stakeholders at the UI Parma REC Field Day in June 2023 (~50 attendees); Onion growers/stakeholders at the Muck Donut Hour weekly in August 2022 (~10 people each time); Onion stakeholders at the ID Treasure Valley Onion Field Day in August 2023 in Parma, ID (~50 people); Onion stakeholders at the WSU Onion Field Day on Aug. 31, 2023 (~80 people); The project's 14-member Stakeholder Advisory Panel represents onion farms, regional onion associations, and major vegetable seed companies (including onion breeders and plant pathologists) from across the US, with one international member. Panel members conducted further outreach to their own networks on behalf of the project. Panel members who are grower representatives include Greg Bird (President of the Michigan Onion Committee), Bob Ehn (California Garlic and Onion Research Advisory Board), Charles Hall (Executive Director of the Georgia Fruit and Vegetable Growers Association), and Michael Locati (President of the Columbia Basin Onion Research Committee. The onion seed industry is represented by Peter Rogers and Juan Carlos Brevis (Nunhems), Scott Hendricks (Bayer), and Margreet Asma (Bejo Zaden). 12 undergraduate students, 11 graduate students, and six postdoctorates have worked on research directly related to the Stop the Rot project in this reporting period. They are conducting research in Washington State, Georgia, Texas, Pennsylvania, Colorado, New Mexico, and South Africa. We used multiple channels to reach our target audience during this reporting period, including grower meetings and field days, conferences and workshops, the Alliumnet.com website, industry newsletters, and trade publications. Project team members also reached out directly to growers in each of the onion-growing regions to recruit growers for participation in the bacterial field surveys. During this reporting period, the Stop the Rot project page on the Alliumnet.com website received 7,888 page views from 4,290 visits by 3,065 users.This is a significant increase from page views in the previous reporting period. Approximately 1,110 growers, agronomists, and industry professionals were reached directly through presentations at conferences, workshops, field days, and grower meetings in this reporting period, with many others accessing recorded webinars/presentations, meeting individually with specialists on the team, etc. Most of these events were shifted back to in-person events following the COVID-19 pandemic. Communication and outreach materials and specific activities are reported in detail in the list of products. Changes/Problems: Problems affecting the work plan and budget: CO/Uchanski: Problems affecting the work plan and budget: In late 2022 the University of California sub-contract transferred $5,000 plus associated F&A (~$1,300) to the Colorado State University sub-contract due to cost savings from California and a need to additional Research Associate salary for Colorado to complete reporting in early 2023. This allowed us to complete two PDMRs from our 2022 (year 3) field work in year 4. WA/LaHue: Poor stand establishment in WA trials for irrigation and nitrogen management, so trials were abandoned for the 2022 growing season and postponed to 2023 (a year in which no trials were originally planned). Stand establishment in 2023 was acceptable and the risk of poor stand establishment was spread out by planting in two separate locations. WA/du Toit: The Project Manager, MacKay, had a severe medical emergency in Mar. 2023 that lasted a month, and then had to go on extended medical leave from early June. Sadly, MacKay had to resign as Project Manager on Oct. 1st, 2023 due to continuing medical issues. This has added significant work for the PD, du Toit, since June 1st, 2023 and has delayed aspects of the project organization and management. du Toit is seeking additional assistance to help with some aspects of the project in the no-cost extension year. Budget support: High rates of turnover in grant support staff at various institutions involved in the project has complicated the abillity to get timely documentation for tracking invoices and cost-share reporting for those subcontracts. What opportunities for training and professional development has the project provided? Graduate students: M. J. Hart. 2022. Is there an Economic Return to Reducing the Quantity of Fertilizer Applied to Onions when Growers Face Record Nitrogen Prices? University of Georgia. (M.Sc.) T. L. Waldrop. 2022. An Economic Analysis of Onion Harvesting Equipment in Georgia. University of Georgia. (M.Sc.) B. P. Bhatta. August 2023. Genetic and Genomic Studies on Diseases of Watermelon and Onion In Texas. Texas A&M. (Ph.D.) V. Ibanez, 4th year student. Dissertation title: Bacterial community associated with symptomatic and asymptomatic onion bulbs from Georgia, USA. (M.Sc.) University of Pretoria A. Grobler, 2nd year. Dissertation: Characterisation of bacteriophages of Pantoea ananatis and P. agglomerans and their potential use in managing diseases caused by these two pathogens. (M.Sc.) University of Pretoria F. Mnguni, 4th year. Thesis: Characterisation of the bacterial pathogens associated with bulb rot in the USA and South Africa. (Ph.D.) University of Pretoria BSc honours student: I. Pooa, project: Identification and pathogenicity of Enterobacter species isolated from the first and second survey of the Stop the Rot project. Universioty of Pretoria Post-Doc: Gi Yoon Shin: Comparative genomics and genetics of Pantoea onion pathogens. University of Georgia Undergraduate students: At least five undergraduate students were trained in lab techniques (preparing media, culturing bacteria, conducting PCR and gel electrophoresis) and field protocols (setting up and maintaining field plots, collecting data, evaluating onions for rot). How have the results been disseminated to communities of interest?In this reporting period, we have been actively reaching out to growers and stakeholders to: share new information and learning from the project as well as current scientific understanding of onion bacterial diseases and their management; understand growers' current state of knowledge about causes and management of bacterial diseases of onion, and identify priority concerns for growers and the onion industry regarding management of bacterial diseases. Information has been shared with growers and stakeholders through a range of communication channels, including the Alliumnet website, research summaries, extension bulletins, articles in trade publications and presentations at growers' meetings and field days. Results were also shared at professional scientific meetings (primary venues being the International Congress of Plant Pathology in August 2023, the Stop the Rot Annual Team Meeting in Jan. 2023, and many regional grower meetings). REACHING GROWERS AND ONION INDUSTRY STAKEHOLDERS: Outreach to growers and onion industry stakeholders, field representatives and extension staff has occurred through informal visits with growers during field surveys, grower meetings, field days and technical workshops. Our Stop the Rot video playlist https://www.youtube.com/playlist?list=PLajA3BBVyv1zf2obB16bNEdQPQeLW_XB_contains several videos aimed at growers and the onion industry - introduction to rot identification, in both English and Spanish; a longer video providing an overview of bacterial diseases in onion and current management options; a short video of the experimental equipment for our field trials of post-harvest disinfection treatments; a short time-lapse video of the Red Scale Necrosis (RSN) assay; and two training videos on inoculating trials and designing field experiments. Outreach and dissemination of preliminary results to onion stakeholders and the industry has been conducted through informational articles in trade publications and extension newsletters (see list of publications) and websites. Outreach to growers and industry stakeholders through the Stop the Rot Stakeholder Advisory Panel: Our 14-member Stakeholder Advisory Panel (SAP) brings a diverse range of expertise and experience to the project. The Panel includes growers, pathologists and onion breeders from onion growing regions across the US. Panel members are active in sharing information about the project to growers and onion industry stakeholders through their own regional and national networks in 12 states, and in bringing insights and information into the project from their networks. Our second annual meeting with the SAP was held on Feb. 3, 2023, by videoconference. Panel members have actively participated in our monthly project team meetings by videoconference, and they continue to receive project updates, notes from the monthly meetings and our internal project team newsletters. REACHING ACADEMIC RESEARCHERS, EXTENSION PROFESSIONALS AND GRADUATE STUDENTS The project team now includes 24 research collaborators from 12 states, representing all 7 major U.S. onion growing regions, as well as onion bacteriologist Prof. Teresa Coutinho from South Africa. We hold monthly team videoconferences to share preliminary results and experiences and discuss recent findings. These monthly meetings of 1.5 to 2 hours have facilitated research and Extension collaborations. Almost all the project collaborators are also involved in extension services and education in their regions, which makes for efficient transfer of new information and research results from the team to extension professionals and thence to growers. Technicians and graduate students from each of the regional teams also join our monthly meetings and contribute actively to the discussions, providing feedback on methods and protocols and sharing their latest results with the full team in a collegial setting. Our annual project team meeting was held in Svannah, GA, in Jan. 2023, in conjunction with the Southeast Fruit & Vegetable Conference, and the annual meeting of the W-4008 Multistate Onion Research Project. This allowed us to share and discuss research results with academic colleagues and onion stakeholders. 12 oral presentations were made. Results of Year 3 field trials in participating states have been published in peer-reviewed Plant Disease Management Reports (see list of publications). Articles have been published in scientific journals (see list of publications). Poster presentations were shared at the International Congress of Plant Pathology in Aug. 2023. What do you plan to do during the next reporting period to accomplish the goals?We received a one year no-cost extension for the grant to complete objectives that were delayed due to COVID restrictions in Year 1. Objective A: A1. Bacterial survey The regional labs will send representative strains from Season 3 to UGA to be included in the NOBSC, and will finish characterizing the strains from Seasons 1-3 that were not completed by the end of Year 4 of this project (pathogenicity testing on scales, foliage, and bulbs; and DNA sequencing for genus and potentially species identification). UGA will continue to characterize the strains received, and add results and metadata to the NOBSC database. The NOBSC dataset will be made available publicly on Alliumnet by the end of the grant. Regional labs will plan for long-term storage and back-up of their regional collections, since the NOBSC will only include a subset of strains from each regional lab. Publications on regional survey results are being developed by individual states or regions, as well as a final survey publication for the entire project, summarizing the combined survey results from all participating states over all three seasons. A2. Pathogenomic analyses, virulence factors and bacterial community analyses UGA will finish the analyses for a comparative genomics study of P. agglomerans and P. allii, and publish the results. Manuscripts for the description of novel species, including Ewingella allii, Kosakonia beeriae, and Phytobacter cepae, isolated during these surveys are in preparation. A3. Molecular diagnostic tools Woodhall will continue testing soil, seed, water, and plant samples received from various states in the surveys, using the real-time PCR assays developed for more rapid testing than traditional isolations followed by DNA sequencing. A4. Phenotypic resistance screening methods Results from the phenotypic screening trials in GA and NY will be analyzed and published. Onion bulbs from the variety trial in CA are currently in storage and will be rated and tested this fall. Results of 3 seasons of cultivar field trials in WA will be combined into a journal publication, along with a paper on the phenotypic assays vs. field trials carried out in NY, CA, WA, and GA. Objective B: B1 to B6: Bulbs in storage from 2023-24 field trials in multiple states in Year 4 will be evaluated for bacterial rot, the data analyzed, and results published in Plant Disease Management Reports. A limited number of field trials will be completed in 2024-25, including irrigation and fertility trials in WA, a variety trial in UT, a pesticide trial in CA, and several cultural practice trials in GA. Results will be shared with growers and other stakeholders on Alliumnet, at grower and other professional meetings, and in various outreach materials. The field-scale risk-assessment model will be tested with more growers' fields in 2024, and using field trial data from 3-4 seasons of results, in collaboration with the WSU Decision Aid System program. Risk model results will be compared with regional-scale mapping. B7. Outreach and extension In Year 5, we will continue to direct more attention to synthesizing work from the four seasons to highlight regional and national trends in bacterial diseases and options for management. Results from field trials in Year 4 will be shared with growers, industry representatives and other interested parties at grower meetings, field days, on Alliumnet, and in trade and outreach publications. A video summarizing results of the Stop the Rot onion bacterial project has been initiated in collaboration with the WSU CAHNRS Office of Communication, to complement the highly successful 14-minute video we made at the start of the project, summarizing the situation and the gaps in knowledge. The wrap-up video will highlight key results that are readily adoptable by growers to limit losses to onion bacterial pathogens. The redesigned Alliumnet.com website will be maintained to provide a home for national onion research collaborations, including other USDA projects, the National Allium Research Conference, links to National Onion Association meetings and events, and the W-1008, W-2008, W-3008 and W-4008 onion multi-state project reports, activities, and meeting details. B8: Economic analysis Two components will be completed during the final project year. To capture the project's impact on growers' knowledge of bacterial diseases and perception of management tools to reduce economic losses, an end-line survey will be administered and analyzed. Survey results will be contrasted with the baseline survey administered in year one of the project. Economic analysis of field trials aimed at assessing the relative efficacy of alternative products (bactericides), input intensities (nitrogen), and cultural practices (undercutting, timing of topping, and length of the necks at topping) will be updated with the final year of field trial results to provide multi-year averages. Project Management and Coordination The fourth annual project team meeting is scheduled for March 5-7, 2023, in Mount Vernon, WA, and the Stakeholder Advisory Panel videoconference is scheduled for later than month.Regular monthly videoconferences for the full team, regular meetings for the co-PIs every ~3 months will continue in Year 5. The team will focus on wrapping up research projects, publishing regional research results, and compiling results into larger papers that summarize results across the entire project, e.g., 3 years of surveys across 12 states, 3-4 years of field trials on various aspects of onion bacterial disease management, risk model development and evaluation, etc.
Impacts
What was accomplished under these goals?
Objectives: A1. Bacterial disease surveys, NOBSC: In year 4, onions were surveyed in 8 states, and 1,080 bacterial strains obtained. 607 isolates were added to the National Onion Bacterial Strain Collection (NOBSC) for a total 1,872 strains from 110 genera. Metadata for strains will be available on Alliumnet.com. A2. Onion bacterial pathogenomics: Whole genome sequencing and annotation were completed for 81 P. agglomerans (Pagg) strains, and comparative genomics and phylogenetic analysis completed. 100 public genomes were added. Most Pagg strains (all onion strains) fell into 2 phlyogroups. Pagg strains encoding the HiVir gene cluster for pantaphos phytotoxin virulence factor are in phylogroup 2. The HiVir cluster is encoded on 2 extra-chromosomal plasmids. The HiVir and alt encoding plasmid from NY strain CB1 is self-transmissible, and plasmid transfer conferred virulence to Pagg strains. Phylogroup 2 strains encoding HiVir on the Pagg universal plasmid include US and SA isolates. Most Pagg onion strains carry an alt-encoding plasmid that often encode genes for Cu tolerance. A novel phosphonate cluster "HaloPhos", responsible for pathogenicity to onion in Pantoea stewartii subsp. indologenes and P. allii, was characterized, and a diagnostic assay for halE developed. Bacterial community analyses in symptomatic and asymptomatic onion bulbs were completed. A project is planned to determine changes in bacterial communities over time following inoculation of bulbs with Enterobacter ludwigii. Bacteriophages were purified from symptomatic bulbs, and 3 characterized that infect Pantoea ananatis and P. agglomerans. We will determine their efficacy for controlling these pathogens. A comparative genomics study is in progress with Rahnella strains. A3. Diagnostic tools: TaqMan PCR assays for the HiVir gene cluster, and species-specific TaqMan assays for P. agglomerans and P. ananatis were designed and evaluated. The assays were tested on bulbs inoculated with individual species and both species. A LAMP assay for P. agglomerans was designed and demonstrated at a Field Day. A4. Phenotypic onion cultivar screening methods: In GA, 51 Vidalia cultivars were screened in a field trial, and bulbs tested for scale lesions with P. ananatis. In NY, 16 cultivars in a 2022 field trial were screened with bulb scale and bulb injection assays. Data are being analyzed. In CA, a 2022 phenotypic screening cultivar trial in Kern Co. was harvested, and susceptibility compared with: 1) bulb rot at harvest from plots inoculated with Burkholderia and Pantoea, 2) severity of rot in bulbs injected with Burkholderia, and 3) a scale assay using Burkholderia. There were differences among cultivars with each assay, but results of the tests were not correlated. In Feb. 2023, a field trial was established in CA with 12 cultivars, and harvested in Aug. Onions in storage will be tested. In WA, bulbs were harvested from a 2022 trial with 12 cultivars. Timing inoculations based on cultivar maturity facilitated screening for susceptibility to bacterial infection. A phenotypic screening trial in WA used bulbs from 53 cultivars to test a bulb injection assay vs. a scale assay. There was no correlation of bulb or scale assay results with bacterial rot in storage from natural infection, and a weak correlation in results of bulb vs. scale assays. B1-B5. Onion bacterial disease management: Results from Year 3 trials were finalized after rating bulbs in storage. In Year 4, field trials of management practices were planted to optimize management practices. Trials are in progress for irrigation (WA and CA), fertility (WA), cultural (UT, GA, NY, WA), and pesticide (CO, WA, GA, NY) practices, and postharvest application of disinfectants to bulbs (WA). Results for 2022-23 trials include: • In CA, sprinkler irrigation increased leaf blight and bulb rot, and reduced yield compared to drip irrigation. • In GA, Lifegard WP and copper reduced bulb rot but no treatment tested in CO had efficacy. A CA pesticide trial will be evaluated in 2023. In WA, Badge SC and ManKocide had limited control of bacterial leaf blight but increased yield, but had no effect on bulb rot. Chemigation increased bulb rot (large amount of water on senescing necks facilitated infection). • No differences in bacterial bulb rot were detected in a UT variety trial, to be harvested in Sep. and bulbs stored for evaluation. • In GA, more bulb rot was observed when neck length after topping was ≤1 inch vs. 2 to 3 inches. Harvesting bulbs with a chain digger vs. a straight blade undercutter resulted in less bacterial rot. In WA, rolling onion tops at onset of 'tops down' did not affect bulb rot; undercutting early increased yield and reduced bulb rot compared to undercutting at 100% tops down or no undercutting; early topping of bulbs (green/moist) reduced yield by 54% and increased bulb rot by 32-35%. • In NY, rolling onions significantly reduced bulb rot compared to onions with straight necks during windrowing. • Postharvest application of H2O2 + peroxyacetic acid or ozone to bulbs in a CO trial did not reduce bacterial bulb rot. • In NY, onions with 70% foliar bacterial infection developed only 20% bulb rot when cured with heated air for 7 days. B6. Onion bacterial disease risk modeling: A PNW bacterial disease risk model was developed using 4 risk categories: current/cumulative risk, field variables, environmental variables, and production variables. Weekly scores are plotted over the season. The model was demonstrated at farms in WA and tested on several crops in 2023. We are waiting on storage results for validation. Data from trials in Seasons 1-3 are being used to test the model. This was led by Project Manager, MacKay, who resigned in 2023 for medical reasons. PD will seek expertise to develop the model and a model app for stakeholders. Environmental factors that drive bacterial disease risk were mapped regionally to provide context for how these contribute to the risk of bacterial diseases. B7. Outreach and Extension: Year 4 outreach included 7 articles in Onion World and Vegetable and Specialty Crop News. Presentations were given at grower meetings in 7 states, attended by >780 stakeholders. B8. Economics: Economic analysis of 2 years of onion trials in NY showed that, despite record N prices, the economics of a grower's decision on how much N to apply did not change. Growers should apply amounts of N to maximize yield for the variety, soil type, location, and other aspects affecting N use. A preliminary assessment using 1 year of GA data showed larger-scale growers can increase profits by adopting a chain digger due to a decrease in bacterial bulb rot compared to a straight blade undercutter. For small-scale growers, the payback period may be too long. An analysis of economic returns to input intensity in GA (low vs. grower standard vs. high input intensity) showed the high input strategy yielded greatest per-acre economic return from reduced bacterial rot, even with high chemical prices. A survey of team members and Stakeholder Advisory Panel members assessed: (a) progress on delivering new insights and solutions for growers to reduce economic losses from onion bacterial diseases, (b) level of confidence in the solutions, and (c) need for further research and evidence. The project has made excellent or very good progress on increased awareness of bacterial pathogens of onion, and developing standardized assays for bacterial isolations and virulence screening. Field practices such as avoiding cutting necks too short (<2 inches), avoiding early topping of bulbs, and drip irrigation instead of overhead irrigation, were considered effective. PROJECT MANAGEMENT Coordination, communication, and integration across the team and with SAP members have been supported by monthly videoconferences, annual team meetings, and SAP meetings.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Khanal, M., S. Timilsina, B.P. Bhatta, K. Bophela, T. Coutinho, K. Cochran, and Khanal, M., S. Timilsina, B.P. Bhatta, K. Bophela, T. Coutinho, K. Cochran, and Malla, S. 2022. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot, isolated from Texas, USA. Int. J. Syst. Evol. Microbiol. 72:005311. https://doi.org/10.1099/ijsem.0.005311.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Davey, J., and Uchanski, M.E. 2023. Evaluation of bactericides to manage slippery skin bacterial bulb rot in onion in Colorado, 2022-2023. Plant Disease Management Reports 17:V120.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Davey, J., and Uchanski, M.E. 2023. Efficacy of disinfectants applied to onion bulbs in storage for control of slippery skin bacterial bulb rot, Fort Collins, CO, 2022-2023. Plant Disease Management Reports 17:V121.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Dutta, B., and Tyson, C. 2023. Evaluation of digging methods on post-harvest incidence of external and internal bacterial bulb in onion, Georgia, 2022. Plant Disease Management Reports 17:V006.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Dutta, B., and Tyson, C. 2023. Evaluation of harvesting methods on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2022. Plant Disease Management Reports 17:V007.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Dutta, B., and Tyson, C. 2023. Evaluation of neck-clipping length on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2022. Plant Disease Management Reports 17:V008.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Dutta, B., Donahoo, W.M., and Foster, M.J. 2023. Evaluation of bactericides and LifeGuard programs to manage internal bacterial rot of onion in Georgia, 2022. Plant Disease Management Reports 17:V009.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2023. Effects of application method and bactericides on bacterial leaf blight and bulb rot of onion, Pasco, WA, 2022-23. Plant Disease Management Reports 17:V123.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2023. Effects of bulb undercutting on bacterial leaf blight and bulb rot in an onion crop, Pasco, WA, 2022-23. Plant Disease Management Reports 17:V129.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2023. Effects of rolling tops on bacterial leaf blight and bulb rot in an onion crop, Pasco, WA, 2022-23. Plant Disease Management Reports 17:V128.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2023. Effects of time of topping on bacterial leaf blight and bulb rot in an onion crop, Pasco, WA, 2022-23. Plant Disease Management Reports 17:V125.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Nischwitz, C., and Drost, D. 2023. Evaluation of efficacy of bactericides to control slippery skin of onion in Utah, 2021. Plant Disease Management Reports 17:V152.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Manzeal Khanal, Sujan Timilsina, Bed Prakash Bhatta, Khumbuzile Bophela, Teresa Coutinho, Kimberly Cochran, and Subas Malla. 2022. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int. J. Syst. Evol. Microbiol. 2022;72:005311. DOI 10.1099/ijsem.0.005311
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Mei Zhao, Chris Tyson, Hsiao-Chun Chen, Sujan Paudel, Ron Gitaitis, Brian Kvitko, and Bhabesh Dutta. 2022. Pseudomonas alliivorans sp. nov., a plant-pathogenic bacterium isolated from onion foliage in Georgia, USA, Systematic and Applied Microbiology 45 (1):126278. https://doi.org/10.1016/j.syapm.2021.126278.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Belo T., du Toit L., and G.T. LaHue. 2023. Reducing the risk of onion bacterial diseases through irrigation, fertility, and other cultural management strategies. Agron. J. 115:459473. http://dx.doi.org/10.1002/agj2.21301
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Belo T., du Toit L., Waters T., Derie M., Schacht B., and LaHue, G.T. 2023. Reducing the risk of onion bacterial diseases through managing irrigation frequency and final irrigation timing. Agric. Water Manag. 288:108476. https://doi.org/10.1016/j.agwat.2023.108476
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Bhatta B.P., M. Khanal, and Malla, S. 2023. Whole genome and 16S rRNA dataset of Pectobacterium carotovorum strain 21TX0081 isolated from a symptomatic onion foliage in Texas. Data Brief 46:108823.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Khanal M., B.P. Bhatta, and Malla, S. 2023. Isolation and characterization of bacteria associated with onion and first report of onion diseases caused by five bacterial pathogens in Texas, U.S.A. Plant Dis. 107:1721-1729.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Khanal M., and Malla, S. 2023. Draft genome sequence and annotation of Pseudomonas carnis strain 20TX0167 isolated from onion (Allium cepa). Microbiol. Resourc. Announc. 12(2):e01051-22. https://doi.org/10.1128/mra.01051-22.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Myers, B. Shin, G.Y., Stice, S., Agarwal, G., Gitaitis, R., Kvitko, B., and Dutta, B. 2023. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and A. fistulosum � A. cepa hybrid. Front. Microbiol. 13:1094155. doi: 10.3389/fmicb.2022.1094155.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Shin, G.Y., Dutta, B., Kvitko, B. 2023. The genetic requirements for HiVir-mediated onion necrosis by Pantoea ananatis, a necrotrophic plant pathogen. Molecular Plant-Microbe Interactions 28:381-391.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Zhao, M., Shin, G.Y., Stice, S., Coutinho, T., Gitaitis, R., Kvitko, B., and Dutta, B. 2023. A novel biosynthetic gene cluster across the Pantoea species complex is important for pathogenicity in onion. Mol. Plant Microbe Interact. https://doi.org/10.1094/MPMI-08-22-0165-R.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Zhao, M., Tyson, C., Gitaitis, R., Kvitko, B., and Dutta, B. 2022. Rouxiella badensis, a new bacterial pathogen of onion causing bulb rot. Front. Microbiol. 13:1054813.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Khanal, M., B.P. Bhatta, S. Timilsina, S. Ghimire, K. Cochran, and Malla, S. 2022. Curtobacterium allii sp. nov., the actinobacteria species causing onion bulb disease. Antonie van Leeuwenhoek 116:83-96.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
du Toit, L., Aegerter, B., Colson, G., Coutinho, T., Cramer, C., Dutta, B., Gugino, B., Hoepting, C., Kvitko, B., LaHue, G., MacKay, H., Malla, S., Nischwitz, C., Reitz, S., Shin, G., Uchanski, M., Waters, T., and Woodhall, J. 2023. Combating onion bacterial diseases with pathogenomic tools and enhanced management strategies. 12th International Congress of Plant Pathology, 21-25 Aug. 2023, Lyon, France.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2023. Susceptibility of 12 onion cultivars to bacterial leaf blight and bulb rot in Pasco, WA, 2022-23. Plant Disease Management Reports 17:V124.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Hoepting, C.A., Caldwell, S.K., and van der Heide, E.R. 2023. Effect of slow curing with artificially heated forced air via a drying wall in a box storage on bacterial bulb rot in onion, 2021. Plant Disease Management Reports 17:V141.
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Hoepting, C.A., Caldwell, S.K., and Gropp, N.K. 2023. Evaluation of rolling onions that are failing to lodge to reduce bacterial bulb rot of onion, 2022. Plant Disease Management Reports 17: V140.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Dutta, B., Zhao, M., Shin, G., du Toit, L., and Kvitko, B. 2023. A micro- and macro-perspective of bacterial pathogens affecting onion in Georgia, USA. 12th International Congress of Plant Pathology, 20-25 Aug. 2023, Lyon, France.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Mnguni, F., Shin, G.-Y., du Toit, L., Derie, M., Aegerter, B., Woodall, J., Dutta, B., Zhao, M., Hoepting, C., Gugino, B., Mazzone, J., and Coutinho, T. 2023. The diversity and pathogenicity of Rahnella species isolated from diseased onion bulbs in the United States and South Africa. International Congress of Plant Pathology, 21-25 Aug. 2023, Lyon, France.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Ibanez, V., Liakos, C., Derie, M., du Toit, L., Dutta, B., Kvitko, B., van der Waals, J., Coutinho, T.A., and Lebre, P. 2023. Metagenome analysis of bacteria present in storage onion bulbs in the USA. International Congress of Plant Pathology, 21-24 Aug. 2023, Lyon, France.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Ibanez, V., Liakos, C., Derie, M., van der Waals, J., Coutinho, T.A., and Lebre, P. 2022. Bacterial and viral inhabitants of onion bulbs in the USA. Proceedings of the 52nd Congress of the Southern African Society for Plant Pathology, Future Africa, University of Pretoria, 1 to 3 August 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Grobler, A., Theron, J., and Coutinho, T.A. 2022. Isolation and characterization of phages for potential biocontrol of Pantoea ananatis and P. agglomerans. Proceedings of the 52nd Congress of the Southern African Society for Plant Pathology, Future Africa, University of Pretoria, 1 to 3 August 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mnguni, F., Shin, G.-Y., and Coutinho, T.A. 2022. Identification and pathogenicity of Rahnella species isolated from diseased onion bulbs from the USA and South Africa. Proceedings of the 52nd Congress of the Southern African Society for Plant Pathology, Future Africa, University of Pretoria, 1 to 3 August 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gugino, B.K. 2022. Managing key diseases of onions: Stop the Rot! 2022 New England Vegetable and Fruit Conference Proceedings (pp. 3).
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Thompson, C. 2023. Major Scientific Breakthrough in Onion Research. Vegetable and Specialty Crop News, April 2023. (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Thompson, C. 2023. Downy Mildew Discovered in Vidalia Onion. Vegetable and Specialty Crop News, March 2023. (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Thompson, C. 2023. Scala Fungicide No Longer Viable Option on Botrytis for Vidalia Onion Producers. Vegetable and Specialty Crop News, February 2023. (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Thompson, C. 2023. Producers Beware: Downy Mildew Disease a Threat for Vidalia Onions. Vegetable and Specialty Crop News, February 2023. (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Hoepting, C.A. 2023. The onion rot race. August 30, 2023 Veg Edge, 19(21):7-8.
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Hoepting, C.A. 2023. Rolling onions that are dying standing up to stop the rot. August 23, 2023 Veg Edge, 19(20):6-7.
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Thompson, C. 2021. UGA Extension Encourages Copper Applications for Vidalia Onion Producers. Vegetable and Specialty Crop News, December 2022. (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Mackay, H., du Toit, L.J. and Hoepting, C. 2023. Stop the Rot Rollout of research results. Onion World. July/August 2023. https://issuu.com/columbiamediagroup/docs/ow_july-august_2023?fr=sYmUxNzQ5MDQ1MjQ
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Kvitko, B., Hoepting, C. and du Toit, L.J. 2023. Stop the Rot - Mistaken identity Onion World September/October 2023
- Type:
Other
Status:
Published
Year Published:
2023
Citation:
Hoepting, C.A. 2023. Mid-July/early bulbing signals onset of disease in onion. July 13, 2023 Veg Edge, 19(14):4-5.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Onion Storage Treatment Demonstration. Fort Collins, CO. October 24, 2022, Shad Wenta, from Wenta Nip and Sanitizing and CSU research associate, Jane Davey gave an on-farm demonstration of how to treat onion or potato crops in storage by thermo-fogging with disinfectant products to manage fungal and bacterial disease development. The presentation was given to CSUs farm manager, Sky Handyside, two undergraduate students, and two CSU research entomologists.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
du Toit, L., MacKay, H., and Kvitko, B. 2023. Objective A1. Bacterial survey and the National Onion Bacterial Survey Collection. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Kvitko, B., Shin, G.-Y., and Dutta, B. Objective A2a. Pathogenomics. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Coutinho, T., Kvitko, B., and Shin, G.-Y. 2023. Objective A2b. Microbiome analysis, Rahnella and Enterobacter identifications, and bacteriophage identifications. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Woodhall, J. 2023. Objective A3. Development of onion bacterial pathogen detection tools. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
du Toit, L., Derie, M., Waters, T., Dutta, B., Hoepting, C., Aegerter, B., Sidhu, J., and Nischwitz, C. 2023. Objective A4. Development of onion phenotyping protocols for screening for resistance to bacterial pathogens. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
LaHue, G., Aegerter, B., Belo, T., Caldwell, S., Coolong, T., Derie, M., Dutta, B., Feibert, E., Gugino, B., van der Heide, E., Hoepting, C., de Jesus, H., Mazzone, J., Murdock, M., Nault, B., Nicholson, K., Regan, K., Reitz, S., Rivera, A., Schacht, B., da Silva, A., Trenkel, I., Waters, T., Wieland, K., Wilson, R., Woodhall, J., and du Toit, L. 2023. Objectives B1 and B2. Irrigation practices and soil fertility management. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Davey, J., du Toit, L., Dutta, B., Uchanski, M., and Waters, T. 2023. Objective B3. Field evaluations of bactericides to manage onion bacterial diseases. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
du Toit, L., Derie, M., Waters, T., Dutta, B., and Hoepting, C. 2023. Objective B4. Cultural practices. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Waters, T., du Toit, L., Uchanski, M., and Davey, J. 2023. Objective B5. Postharvest disinfectant practices. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
du Toit, L., MacKay, H., and Rajagopalan, K. 2023. Objective B6. Bacterial disease risk modeling. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Hoepting, C. 2023. Objective B7. Outreach and Extension update. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Colson, G. 2023. Objective B8. Economics component. Annual team meeting, USDA NIFA SCRI Stop the Rot onion bacterial project, 5 Jan. 2023, Savannah, GA (35 people).
|
Progress 09/01/21 to 08/31/22
Outputs
Target Audience:Stakeholders involved in the US onion industry are the primary audience for this project. This includes onion producers(farmers), packers, shippers, and associated stakeholders engaged in various capacities in onion production, distribution, and marketing, e.g., agronomists, crop consultants, farm managers, field workers; personnel associated with agricultural supply companies (fertilizer and pesticide dealers, irrigation supply companies, etc.), seed companies, and dealers; onion breeders (public and private); and onion storage and shipping/transport personnel and companies. Public and private research and extension specialists, undergraduate students, graduate students, and postdoctorates working with diverse aspects of onion production are also a target audience for this project. The target audiences reached during this reporting period included: Onion growers, packers, processors, and associated stakeholders in the 7 main onion-growing regions of the US; Extension professionals in the 12 onion-growing states represented in this project; Onion researchers from the US and other countries attended a session dedicated to Stop the Rot project results at the National Allium Research Conference in Denver, CO on March 1, 2022 (93 participants); The project's 14-member Stakeholder Advisory Panel represents onion farms, regional onion associations, and major vegetable seed companies (including onion breeders and plant pathologists) from across the US, with one international member. Panel members conducted further outreach to their own networks on behalf of the project. Panel members who are grower representatives include Greg Bird (President of the Michigan Onion Committee), Bob Ehn (California Garlic and Onion Research Advisory Board), Charles Hall (Executive Director of the Georgia Fruit and Vegetable Growers Association), and Michael Locati (President of the Columbia Basin Onion Research Committee. The onion seed industry is represented by Peter Rogers and Juan Carlos Brevis (Nunhems), Scott Hendricks (Bayer), and Margreet Asma (Bejo Zaden). Ten undergraduate students, ten graduate students and four postdoctorates have worked on research directly related to the Stop the Rot project in this reporting period. They are conducting research in Washington State, Georgia, Texas, Pennsylvania, Colorado, New Mexico, and South Africa. We used multiple channels to reach our target audience during this reporting period, including grower meetings and field days, conferences and workshops, the Alliumnet.com website, industry newsletters, trade publications, and extension videos. Project team members also reached out directly to growers in each of the onion-growing regions to recruit growers for participation in the bacterial field surveys. During this reporting period, the Stop the Rot project page on the Alliumnet.com website received 7,888 page views from 4,290 visits by 3,065 users.This is a significant increase from page views in the previous reporting period. Approximately 1,100 growers, agronomists, and industry professionals were reached directly through presentations at conferences, workshops, field days, and grower meetings in this reporting period. Many of the events were shifted away from in-person to virtual format due to COVID-19 constraints across the USA and in South Africa, which made it difficult to accurately count the number of peoplewho were reached through presentations. Approximately 4,600people have viewed our series of project videos to date. Communication and outreach materials and specific activities are reported in detail in the list of products. Changes/Problems: Rising input costs and labor costs The costs of fertilizer, irrigation equipment and labor have increased sharply in this reporting period. In Oregon, Co-PI Reitz noted that input costs were greater than planned but he was able to access additional funding support from companies interested in the 2022 bactericide trials, and from the Idaho-Eastern Oregon Onion Growers Association for the 2022 irrigation and fertility trials. In Colorado, Co-PI Uchanski's labor costs were higher than planned, but we were able to transfer a small amount of surplus funds from Co-PI Aegerter's budget in California to cover the Colorado wages shortfall in 2022. Risk-based modeling: access to commercial production data Access to production data from growers and packers has been very limited as stakeholders are reluctant to share proprietary crop information in a highly competitive market. In addition, growers do not always have detailed environmental data records, particularly for soil moisture status which we hypothesize is one of the most important risk factors in bacterial disease development. This has continued to affect the ability of the team to develop and evaluate bacterial disease risk models as originally planned. In this reporting period, therefore, we have been collecting more data from our field trials in NY and UT especially, including deploying additional sensors to monitor environmental conditions in the trial plots. In the next reporting period, we will incorporate these results into a simple risk assessment tool for growers to test in the field and provide feedback to the team. Environment-related problems Irrigation/fertility trials in Washington State during 2022 were abandoned due to poor stands from record cold and windy conditions in April after planting. The trials will be repeated in the next reporting period. Bactericide trials in Kern County, CA, were abandoned due to poor stands, and will be repeated in the next reporting period. COVID19 impacts In Idaho and Utah, the pandemic resulted in significantly increased costs and delays in the delivery of supplies associated with PCR assays and nitrile gloves, and to delays in sample analysis in fall and winter 2021. In Georgia, supply chain issues caused PI Kvitko's lab to change cryovial suppliers and formats several times. In Washington State, COVID increased travel expenses for field research, particularly during periods of intense labor needs, e.g., during harvest of field trials and when evaluating onion bulbs in storage, because of not being able to share hotel rooms. Grant administration capacity Subcontractors to Washington State University (WSU)on this project have allreported that their grant administration offices are short-staffed with high turnover. This is making it slow, if not impossible in some cases, for WSU to get the data and supporting information needed for required reporting to NIFA, such as effort certifications, and to keep subcontractor cost-share reporting up to date. Other changes Robert Sakata (CO) and Kerrick Bauman (WA) stepped down from the SAP; Mr. Sakatais no longer an active onion grower, and Mr. Bauman cited time constraints. No-cost extension request Due to delays for COVID issues, delays in receiving funding, some weather-related problems, we plan to request a one-year no-cost extension (NCE). This will allow us to complete all field trials as planned and prepare the final results for dissemination. What opportunities for training and professional development has the project provided? STUDENTS The grant has provided the opportunity for several graduate students and post-doctorates to work on different aspects of the project: Adri Grobler, MSc student at the University of Pretoria, is working on detecting bacteriophages against Pantoea species, under the supervision of Prof. Teresa Coutinho. Fanele Mnguni, PhD student at the University of Pretoria, is continuing her work under the supervision of Prof. Teresa Coutinho, on identification and comparative genomics of Rahnella species, including strains isolated from onions in Stop the Rot bacterial surveys in the US. Patience Mateka Modiba, PhD student at the University of Pretoria is working on identification and comparative genomics of Enterobacter species under the guidance of Prof. Teresa Coutinho, including strains isolated from onions in Stop the Rot bacterial surveys in the US. Tessa Belo, MS student in the Soils & Water program at the Northwestern Washington Research and Extension Center of Washington State University. Advised by collaborator LaHue and co-advised by PD du Toit. Thesis topic: Impacts of irrigation and fertilization practices on bacterial diseases in onion bulb crops in the Columbia Basin. Completed in spring 2022. Antoinette Machado, MS student at Colorado State University in January 2020, supervised by co-PI Uchanski. Thesis topic: Evaluation of bactericides and plant defense inducers to manage center rot of onion in Colorado. Completed in spring 2022. Bed Prakash Bhatta, a PhD student at Texas A&M AgriLife Research - Uvalde is being trained on isolation, culture, and inoculation of bacteria under this project. Thesis topic: Breeding for anthracnose and Fusarium wilt resistance in watermelon. Ram Neupane, Plant Pathology PhD student at Pennsylvania State University (started Spring 2021). Thesis topic will be related to bacterial diseases of onion. In Pennsylvania, three undergraduate students were involved in conducting lab and field activities associated with this project during summer 2022, from aiding in conducting the pathogenicity testing of isolates to planting, maintenance, and harvesting of field trials. Dr. Mei Zhao, postdoctorate in co-PD Dutta's program at the University of Georgia, focused on the bacterial survey, identification and characterization of bacterial isolates in GA, and greenhouse and field evaluations. Completed in spring 2022. Dr. Navdeep Singh, postdoctoral research associate at Washington State University (started Sep. 2020), primarily is working on other projects but is contributing to this work, particularly Objective B1, and will be engaged in this research until fall 2022. Dr. Gi-Yoon (Gina) Shin, postdoctorate in co-PI Kvitko's lab at the University of Georgia, is assisting with the bacterial survey, investigating the pathogenomics of Pantoea spp. that are pathogenic and non-pathogenic on onion, and identifying target regions of the genomes for developing molecular diagnostic tools for onion bacterial pathogens. At the University of Georgia, Logan Waldrop (M.A.B. student) and Morgan Hart (M.A.B. student) have been assisting PI Greg Colson with the data collection and analysis for the economics component of the project. In New Mexico, one undergraduate student assisted with bacterial surveys during the 2022 field season. TRAINING AND PROFESSIONAL DEVELOPMENT Onion bacterial inoculation workshop, June 1, 2022, online. Attended by 32 people, including team members, graduate & undergrad students from STR regional labs and South Africa. https://youtu.be/7KaRS4MnxY4 Mike Derie and Stop the Rot project director Dr. Lindsey du Toit, presented an informal work session on inoculating onion field trials with pathogenic bacterial strains, to artificially create bacterial disease in the onions. The work session was presented to team members, graduate students and post-doctorates working on the Stop the Rot project. Experimental design workshop, June 8, 2022, online, on practical guidance and basic principles for good design of field trials. Attended by 29 people, including team members, graduate & undergrad students from STR regional labs and South Africa. https://youtu.be/Las-WkZZa2Y In this informal work session, Dr. Lindsey du Toit, Project Director for the Stop the Rot project, shared best practices and lessons learned in experimental design for agricultural field trials, and statistical analysis of the results.The work session was presented to team members, graduate students and post-doctorates working on the Stop the Rot project. How have the results been disseminated to communities of interest? In this reporting period, we have been actively reaching out to growers and stakeholders to: share new information and learning from the project as well as current scientific understanding of onion bacterial diseases and their management; understand growers' current state of knowledge about causes and management of bacterial diseases of onion, and identify priority concerns for growers and the onion industry regarding management of bacterial diseases. Information has been shared with growers and stakeholders through a range of communication channels, including the Alliumnet website, research summaries, extension bulletins, articles in trade publications and presentations at growers' meetings and field days. Results were also shared at professional scientific meetings (primary venues being the American Phytopathological Society's Plant Health 2022 Conference in August 2022, and the National Allium Research Conference in March 2022). REACHING GROWERS AND ONION INDUSTRY STAKEHOLDERS: Outreach to growers and onion industry stakeholders, field representatives and extension staff has occurred through informal visits with growers during field surveys, grower meetings, field days and technical workshops. Our Stop the Rot video playlist https://www.youtube.com/playlist?list=PLajA3BBVyv1zf2obB16bNEdQPQeLW_XB_contains several videos aimed at growers and the onion industry - introduction to rot identification, in both English and Spanish; a longer video providing an overview of bacterial diseases in onion and current management options; a short video of the experimental equipment for our field trials of post-harvest disinfection treatments; a short time-lapse video of the Red Scale Necrosis (RSN) assay; and two training videos on inoculating trials and designing field experiments. Outreach and dissemination of preliminary results to onion stakeholders and the industry has been conducted through a number of informational articles in trade publications and extension newsletters (see list of publications) and websites/online alerts. Outreach to growers and industry stakeholders through the Stop the Rot Stakeholder Advisory Panel:Our 14-member Stakeholder Advisory Panel (SAP) brings a diverse range of expertise and experience to the project. The Panel includes growers, pathologists and onion breeders from onion growing regions across the US. Panel members are active in sharing information about the project to growers and onion industry stakeholders through their own regional and national networks in 12 states, and in bringing insights and information into the project from their networks. Our second annual meeting with the SAP was held on March 25, 2022, by videoconference. Panel members have actively participated in our monthly project team meetings by videoconference, and they continue to receive project updates, notes from the monthly meetings and our internal project team newsletters. Several panel members have also participated in team work sessions as subject matter experts. REACHING ACADEMIC RESEARCHERS, EXTENSION PROFESSIONALS AND GRADUATE STUDENTS The project team now includes 24 research collaborators from 12 states, representing all 7 major U.S. onion growing regions, as well as onion bacteriologist Prof. Teresa Coutinho from South Africa. We hold monthly team videoconferences to share preliminary results and experiences and discuss recent findings. These monthly meetings of 1.5 to 2 hours have facilitated research and Extension collaborations. Almost all the project collaborators are also involved in extension services and education in their regions, which makes for efficient transfer of new information and research results from the team to extension professionals and thence to growers. Technicians and graduate students from each of the regional teams also join our monthly meetings and contribute actively to the discussions, providing feedback on methods and protocols and sharing their latest results with the full team in a collegial setting. Our annual project team meeting was held in Denver, CO, in March 2022, in conjunction with the National Allium Research Conference, the annual meeting of the W-4008 Multistate Onion Research Project, and the annual conference of the Colorado Fruit and Vegetable Growers Association. This allowed us to share and discuss research results with a large number of academic colleagues and onion stakeholders, both in person and online. Eighteen oral and 8 poster presentations were made at the National Allium Research Conference in Denver, CO, February 28, 2022. The results of Year 2 field trials in participating states have been published in 12 peer-reviewed Plant Disease Management Reports (see list of publications). Three articles have been published in scientific journals (see list of publications). Four poster presentations were shared at Plant Health 2022, the annual conference of the American Phytopathological Society. Posters were presented by team members at the International Conference on Plant Pathogenic Bacteria, Italy, July 2022, and at the conference of the Soil Science Society of America in April 2022. What do you plan to do during the next reporting period to accomplish the goals? OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial surveys In the next reporting period, we will complete pathogenicity testing and genus identification for bacterial strains isolated from onion crops during Years 1, 2 and 3. Regional labs will again send both representative pathogenic isolates and non-pathogenic isolates to UGA to represent the diversity found in each region. Strains sent to UGA will be identified to species using MLSA schemes, and tested for pathogenicity on onion. Metadata and results will be added to the NOBSC database and made available publicly on Alliumnet. Regional labs will plan for long-term storage and back-up of their regional collections, since the NOBSC will only include strains that are in the national collection. A2. Pathogenomic analyses, virulence factors & bacterial community analyses Additional strains sent to UGA for the NOBSC will be subjected to whole genome sequencing and examined to identify putative virulence factors associated with the ability to cause diseases on onion, in order to validate the virulence factors identified in the first 3 years of this project and for testing the molecular diagnostic tools being developed for onion-pathogenic strains of Pantoea spp. Results of the bacterial community analyses from asymptomatic and symptomatic bulbs collected from a field in each of GA and WA will help assess potential interactions among complex microflora associated with asymptomatic and symptomatic onion bulbs. A3. Molecular diagnostic tools PCR assays designed to differentiate pathogenic vs. non-pathogenic isolates of P. ananatis and P. agglomerans will be tested in Year 4 with seed, soil, water, foliar, and bulb samples sent to Woodhall's lab at the Univ. of Idaho. The PCR protocols will be modified as needed to optimize the species-specific and pathogenicity-specific assays. A4. Phenotypic resistance screening methods In Year 4, we will evaluate the suitability of the modified scale vs bulb assays for use in screening onion cultivars for resistance to bacterial pathogens. Results will be compared for the bulb vs. scale assay comparison completed in CA, WA, and NY in 2022, and compared with results from cultivar field trials in each state. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT In Year 4, the focus will be on outreach and dissemination of knowledge gained in the previous three years of field trials. A limited number of field trials will be completed, including repeated irrigation and fertility trials in WA and pesticide trials in CA that had to be abandoned in Year 3 due to very poor stand counts. We will focus on completing the data analysis of all Year 3 trials once bulbs in storage have been rated in Feb.-Mar. 2023, and publishing the results to share with growers and other stakeholders on Alliumnet, at meetings, and in various outreach materials. We plan to synthesize the trial results to highlight regional and national patterns and conclusions that should help growers make appropriate decisions about disease management options. We plan to refine a risk-based approach to decision support for growers, based on the trial results, and will be asking growers in different regions to test the prototype risk model in their onion crops in 2023. ECONOMIC ASSESSMENTS The potential for adoption of management recommendations based on results of these trials will be assessed annually by the SAP and stakeholders with economist Colson. Economic analyses will be developed from the results of various trials based on inputs (expenses) and outputs (marketable yield). This will include: Drafting academic articles reporting survey findings. Assisting the Extension team and grant leadership to incorporate findings from field trials into the Alliumnet website and outreach materials. Working with team members as field trial data become available to translate findings into cost-benefit and risk-based analyses. OUTREACH AND EXTENSION In Year 4, we will direct more attention to synthesizing work from the first 3 seasons to highlight regional and national trends and patterns in bacterial diseases as well as options for management. Results from Year 3 work will be shared in research summaries, on Alliumnet.com, in project newsletters, trade publications, regional websites, and presentations at growers' meetings and field days. Plans are underway to develop more videos, "quick guides", highlights of annual project results, training and extension materials, and an interactive map of the USA with bacterial disease survey results. The newly redesigned Alliumnet.com website will be maintained to provide a home for national onion research collaborations, including USDA projects, National Allium Research Conference information and proceedings, links to National Onion Association meetings and events, and the W-1008, W-2008, W-3008 and W-4008 onion multi-state project reports, activities, and meeting details. PROJECT MANAGEMENT AND COORDINATION The third annual project team meeting is scheduled for January 5-7, 2023, in Savannah, GA, and the Stakeholder Advisory Panel videoconference is scheduled for February 3, 2023. Regular monthly videoconferences for the full team, regular meetings for the co-PIs every 2-3 months, and weekly meetings of the PD and Project Manager will continue in Year 4.
Impacts
What was accomplished under these goals?
OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial disease surveys, NOBSC Onion foliage and bulbs were surveyed in 12 states. In Years 1 and 2, 116 bacterial genera were isolated from >4,800 samples of symptomatic onion leaves and bulbs, the 5 most prevalent being Pantoea, Pseudomonas, Burkholderia, Enterobacter, and Bacillus. The distribution and pathogenicity of genera varied across regions. 1,265 strains (pathogenic and non-pathogenic) are now in the National Onion Bacterial Strain Collection (NOBSC), to represent diversity in the regions surveyed. These are identified to species and tested for pathogenicity on onion. NOBSC metadata will be available publicly on Alliumnet.com. A2. Onion bacterial pathogenomics Bacterial community analyses in symptomatic and asymptomatic onion bulbs were completed, with a manuscript in preparation. Dickeya and Pectobacterium, soft rot bacteria, were found in asymptomatic but not in symptomatic bulbs from Georgia. Virome analyses of symptomatic bulbs revealed bacteriophages. We are isolating those that infect Pantoea ananatis and P. agglomerans. One purified and characterized to date is in the Autographiviridae. MLSA of Rahnella and Enterobacter strains was initiated. R. perminowiae, R. aceris (most prevalent), R. aquatalis, R. rivi, and R. sonasera were identified. All were non-pathogenic except a WA isolate, an Ewingella sp. (first report on onion). We compiled 81 Pantoea genomes (66 P. agglomerans) for the survey plus international isolates. There was no link between P. agglomerans geographic source and phylogeny. Consistent with P. ananatis, presence of the HiVir gene cluster in P. agglomerans correlated with pathogenicity on onion. Genomic comparison identified a region in the HiVir cluster conserved enough to design a PCR primer set for virulent Pantoea strains. Plasmid-borne copper resistance gene clusters (copABCDRS) were found in about half the sequenced P. agglomerans strains, in three clusters (A, B, and C). The A type was most common, with P. agglomerans strains resistant to 200 ppm copper sulfate. Strains with a B2 sub-type were resistant to at least 300 ppm. Cop genes were more prevalent in onion pathogenic strains (20/26) vs. non-pathogenic strains (14/40). Strains with cop genes were alt positive (tolerant of sulfur). Cop genes might clarify why copper treatments been ineffective in some trials. A3. Diagnostic tools Species-specific PCR assays were designed for P. agglomerans and P. ananatis, with primers and probes specific to the HiVir gene cluster. An assay designed to HiVirD looks promising. Assays for P. ananatis and P. agglomerans will be evaluated in Year 4. Samples of soil, seed, irrigation water, and onion plants from NY, WA and CA were sent to Woodhall for validating the diagnostic assays. A4. Phenotypic screening methods The 2021-22 WA onion cultivar trial used 3 cultivars from each of 4 maturity groups, inoculated with Pantoea agglomerans and Burkholderia gladioli. Differences in bulb yield of inoculated vs. non-inoculated plots were greater for earlier maturing cultivars. Blocking inoculations by cultivar maturity avoided confounding maturity at inoculation with susceptibility to bacterial pathogens. Severe heat stress in June 2021 impacted earlier maturing cultivars more (yield and bacterial diseases). The trial was repeated in 2022, with bulbs to be rated in Feb. 2023. In GA, 52 Vidalia onion cultivars and the USDA NPGS Allium germplasm collection were evaluated for resistance to P. ananatis in an inoculated field trial. A 2022 cultivar trial in CA was inoculated and harvested. Bulb rot incidence and yield will be measured. A 2022 cultivar trial was planted in NY. Bulbs from non-inoculated plots in the CA, WA and NY cultivar trials will be used to compare phenotypic screening using bulb injection vs. scale inoculation. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT Results of Year 2 trials were finalized in Year 3 once bulbs in storage were rated for bacterial rots. Trials in Year 3 focused on management options that showed promise in Years 1 and 2, including irrigation practices (WA, OR), fertility practices (WA, GA, PA), cultural practices (WA, GA, NY), pesticide programs (WA, PA, UT, GA, CA, OR, CO), and postharvest disinfection (WA, CO). Year 3 trial results are pending. Recent results with practical application include: In OR, drip irrigation reduced bulb rot but not bulb yield compared to overhead irrigation. In CA, bacterial leaf blight and bulb rot were less prevalent, and bulb yield was greater, in drip vs. overhead irrigated plots. Changing irrigation frequency did not affect bacterial bulb rots in WA in Year 2. In WA, early termination of overhead irrigation did not affect bulb yield but reduced bacterial bulb rot. In OR, early termination of drip irrigation reduced bulb yield but not bacterial bulb rots. In GA, N-fertility rates and timing of final N application did not affect bulb rot in Year 3, with low disease pressure. In GA trials, LifeGard + copper bactericides reduced bulb rots. In contrast, coppers and Lifegard had no effect on bacterial bulb rots in WA, PA, and UT. Year 2 WA trials on 3 cultural practices: Undercutting treatments did not affect bacterial leaf blight, bulb rot, or bulb yield. Rolling tops increased bacterial leaf blight but not bulb yield or bulb rot. Early topping increased bacterial bulb rot vs. normal and late topping as necks had not cured by early topping, resulting in injury to moist, green necks predisposed to infection. Cultural practice trials were repeated in Year 3 in WA, with harvest bulbs to be evaluated in storage in Feb. 2023. Year 2 and 3 trials in GA showed clipping onion necks 3 or 5 inches long led to less bacterial bulb rot vs. clipping 1 inch long. Following 3 years of trials, growers in GA are training workers to leave onion necks 3-5 inches long when clipping by hand, or growers are switching from straight-blade undercutters to chain diggers for harvest to reduce bacterial bulb rot. Year 2 trials in WA and CO again indicated no benefit to applying ozone or hydrogen peroxide + peroxyacetic acid products to onion bulbs in storage. The products do not penetrate wrapper scales. A WA grower-co-operator trial had similar results. RISK MODELING Given challenges in gathering proprietary data from commercial onion farms and storage facilities, we refocused on field data collected in Stop the Rot field trials. Using knowledge from the trials, we are developing a simple risk-scoring approach for growers based on work done for an Onion ipmPIPE project. We will test this approach with onion stakeholders in Year 4. ECONOMIC ASSESSMENTS Co-PI Colson completed preliminary economic analyses of: Year 1 GA trials assessing onion yield and losses to center rot under low vs. high input vs. grower standard practices; returns for bactericides used by growers in GA, NY, and WA; nitrogen application rates for 2 years in NY. Colson developed an annual survey of the Stakeholder Advisory Panel in Year 3. Results were communicated to grant leadership and factored into team activities. OUTREACH AND EXTENSION Year 3 outreach included publication of results of Year 1 and 2 trials, and articles in trade publications and newsletters summarizing new knowledge, that have a wide reach to onion growers and industry. Outreach has included: Articles in Onion World, Veg News, and in newsletters of the National Onion Association, regional grower associations, and extension services; Presentations at grower meetings, conferences, field days and tours; Re-launch and updating of Alliumnet.com. Visits increased significantly, driven by the combined annual meetings of NARC, W-4008, and Stop the Rot in 2022. PROJECT MANAGEMENT Coordination, communication, and integration have been supported by monthly videoconferences, bi-monthly conference calls, and annual meetings of the project team and SAP.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Manzeal Khanal, Sujan Timilsina, Bed Prakash Bhatta, Khumbuzile Bophela, Teresa Coutinho, Kimberly Cochran, and Subas Malla. (2022). Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int. J. Syst. Evol. Microbiol. 2022;72:005311. DOI 10.1099/ijsem.0.005311
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Mei Zhao, Chris Tyson, Hsiao-Chun Chen, Sujan Paudel, Ron Gitaitis, Brian Kvitko, Bhabesh Dutta, Pseudomonas alliivorans sp. nov., a plant-pathogenic bacterium isolated from onion foliage in Georgia, USA, Systematic and Applied Microbiology, Volume 45, Issue 1, 2022, 126278, ISSN 0723-2020, https://doi.org/10.1016/j.syapm.2021.126278. https://www.sciencedirect.com/science/article/pii/S0723202021001016)
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Shin, Gi Yoon, Amy Smith, Teresa Ann Coutinho, Bhabesh Dutta, and Brian Kvitko. Validation of species-specific PCR assays for the detection of Pantoea ananatis, P. agglomerans, P. allii and P. stewartii. (2022) Plant Disease. https://doi.org/10.1094/PDIS-08-21-1810-SC
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2022. Effects of bactericide and herbicide applications on bacterial leaf blight and bulb rot of onion, Pasco, WA, 2021-22. Plant Disease Management Reports 16:V150.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2022. Effects of late-season cultural practices on bacterial leaf blight and bulb rot in an onion crop, Pasco, WA, 2021-22. Plant Disease Management Reports 16:V149.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2022. Efficacy of disinfectants applied to onion bulbs in storage for control of bacterial bulb rots, Pasco, WA, 2021-22. Plant Disease Management Reports 16:V148.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2022. Susceptibility of 12 onion cultivars to bacterial leaf blight and bulb rot in Pasco, WA, 2021-22. Plant Disease Management Reports 16:V151.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dutta, B., and Tyson, C. 2022. Evaluation of digging methods on post-harvest incidence of external and internal bacterial bulb in onion, Georgia, 2021. Plant Disease Management Reports 16:V109.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dutta, B., and Tyson, C. 2022. Evaluation of harvesting methods on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2021. Plant Disease Management Reports 16:V108.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dutta, B., and Tyson, C. 2022. Evaluation of neck-clipping length on post-harvest incidence of external and internal bacterial bulb rot in onion, Georgia, 2021. Plant Disease Management Reports 16:V107.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Dutta, B., Foster, M.J., and Donahoo, W.M. 2022. Evaluation of bactericides and plant defense inducers to manage internal bacterial rot of onion in Georgia, 2021. Plant Disease Management Reports 16:V044.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Sidhu, J., Dubose, J. and Fernberg J. 2022. Evaluation of bactericides for management of bacterial leaf blight and bacterial bulb rot in onions, 2021 (California). Plant Disease Management Reports 16:V026.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Aegerter, B. (2022) Stop the Rot: Update on bacterial bulb rot research. Presentation at the Annual Muck Vegetable Growers Conference in Ontario, Canada, April 7, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Rob Wilson, Kevin Nicholson, and Brenna Aegerter (2022). The influence of irrigation method (solid-set sprinkler irrigation or drip irrigation) on the incidence and severity of bacterial diseases in onions grown in Northeast California. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Hoepting, C.A., S. K. Caldwell and E. R. van der Heide. 2022. Evaluation of selected pesticides for control of bacterial bulb rot in onion, NY, 2021. Plant Disease Management Reports 16:V168
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Hoepting, C.A., S.K. Caldwell, and E.R. van der Heide. 2022. Evaluation of cultural practices to reduce bacterial bulb rot in onions that are failing to lodge, NY, 2021. Plant Disease Management Reports 16:V167.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Machado Burke, A., M. Uchanski, and J. Davey. 2022. Evaluation of bactericides to manage slippery skin in onion in Colorado, 2021. Plant Disease Management Reports 16:V128.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mei Zhao, Shaun Stice, Gi Yoon Shin, Teresa Coutinho, Ron Gitaitis, Brian Kvitko, and Bhabesh Dutta (2022). A novel biosynthetic gene cluster across the Pantoea species complex is important for pathogenicity in onion. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Bhabesh Dutta, Brian Kvitko, Mei Zhao, Brendon Myers, Gaurav Agarwal, Gi Yoon-Shin, Sujan Paudel, Santosh Koirala, Bamidele Sangoyomi, and Ronald Gitaitis (2022). An overview of basic and applied research on diverse bacterial diseases on onion in Georgia. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gi Yoon Shin, Bhabesh Dutta and Brian Kvitko (2022). Genetic basis of HiVir, a phytotoxin gene cluster of onion pathogen Pantoea ananatis. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lindsey du Toit, Brian Kvitko, Heather MacKay and the Stop the Rot project team members (2022). Surveys of bacterial pathogens in onion production regions of the U.S.: Preliminary results from 2020 and 2021. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Brian Kvitko, Gi Yoon Shin, Amy Smith, Jo Ann Asselin, Paul Stodghill, Bhabesh Dutta (2022). A pathogenomics approach to identify virulence -associated genes of Pantoea spp. pathogenic on onion. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Verushka Ibanez, Christopher Liakos, Jacquie van der Waals, Teresa Coutinho, Pedro Lebre (2022). Bacterial biome of storage onion bulbs sampled in Georgia and Washington States. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
James Woodhall, Miranda Harrington, Ben Wood, Gi Yoon Shin, and Brian Kvitko (2022). Developing nucleic acid amplification tests for onion pathogenic bacteria. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Mei Zhao, Michael Derie, Timothy Waters, Bhabesh Dutta, and Lindsey du Toit (2022). Evaluation of resistance screening methods for bacterial diseases of onion. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gabriel LaHue, Tessa Belo, Michael Derie, Bhabesh Dutta, Erik Feibert, Beth Gugino, Christy Hoepting, Jennie Mazzone, Stuart Reitz, Timothy Waters, Rob Wilson, and Lindsey du Toit (2022). Reducing the risk of onion bacterial diseases through irrigation and nitrogen management. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Brenna Aegerter, W. M. Donahoo, Jane Davey, Michael Derie, Lindsey du Toit, Bhabesh Dutta, Eric Feibert, M. J. Foster, Christy Hoepting, Antoinette Machado, Claudia Nischwitz, Stuart Reitz, Jaspreet Sidhu, Mark Uchanski, Timothy Waters, and James Woodhall (2022). Evaluation of bactericides and plant defense inducers to manage bacterial rots of onion in seven states in the U.S. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lindsey du Toit, Michael Derie, Christy Hoepting, and Bhabesh Dutta (2022). Evaluation of late-season cultural practices for managing onion bacterial bulb rots. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Timothy Waters, Mark Uchanski, Lindsey du Toit, Michael Derie, and Jane Davey (2022). Evaluation of post-harvest treatments for control of bacterial rots in onions. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Kirti Rajagopalan, Ananth Kalyanaraman, and Hossein Noorazar (2022). Predictive modeling of bacterial disease risk in onion bulb crops. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Greg Colson, Lindsey J. du Toit, Bhabesh Dutta, and Christy Hoepting (2022). Economic assessments of management strategies for onion bacterial rots. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lindsey du Toit and Heather MacKay (2022). Stop the Rot: Overview of research to combat onion bacterial diseases with pathogenomic tools and enhanced management strategies. Presentation at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Belo, T., du Toit, L., Waters, T., Derie, M., Schacht, B., & LaHue, G. (2021). Combating Onion Bacterial Diseases Through Nitrogen Fertility Management. Poster presented at 2021 ASA, CSSA, SSSA International Annual Meeting, Salt Lake City, 7-10 November 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
MacKay, H., du Toit, L., Aegerter, B., Colson, G., Coutinho, T., Dutta, B., Gugino, B., Hoepting, C., Kvitko, B., LaHue, G., Malla, S., Nischwitz, C., Reitz, S., Sidhu, J., Uchanski, M., Waters, T., Wilson, R., Woodhall, J., Asma, M.(presenting author). 2022. Combating onion bacterial diseases with pathogenomics tools and enhanced management strategies: Research objectives and progress towards reducing crop losses. Poster presentation at 14th International Conference on Plant Pathogenic Bacteria, July 2022, Assisi, Italy.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gi Yoon Shin, Bhabesh Dutta and Brian Kvitko. Genetic Basis Of Hivir-Mediated Red Onion Scale Necrosis, A Phytotoxin Gene Cluster Of Pathogenic Pantoea Ananatis. Poster presentation at American Phytopathological Society Plant Health 2022 Conference, Pittsburgh, August 6-10, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Ram Neupane, Jennie Mazzone, Christine Hoepting, Beth Gugino. Identification And Pathogenicity Of Bacteria Isolated From Symptomatic Onion Leaves And Bulbs In Pennsylvania And New York In 2020 And 2021. Poster presentation at American Phytopathological Society Plant Health 2022 Conference, Pittsburgh, August 6-10, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Benjamin B. Wood, Mackade Murdock, and James Woodhall. A Survey Of Bacterial Species Associated With Onion Rots In The Treasure Valley Of Southwest Idaho And Eastern Oregon. Poster presentation at American Phytopathological Society Plant Health 2022 Conference, Pittsburgh, August 6-10, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lindsey du Toit, Heather MacKay, Gi Yoon (Gina) Shin, Brian Kvitko, Brenna Aegerter, Christopher Cramer, Beth Gugino, Christine Hoepting, Subas Malla, Claudia Nischwitz, Stuart Reitz, Mark Uchanski, James Woodhall, Bhabesh Dutta. Distribution And Pathogenicity Of Bacteria Collected In Surveys Of Onion Crops Across Production Regions In The U.S. In 2020 And 2021. Poster presentation at American Phytopathological Society Plant Health 2022 Conference, Pittsburgh, August 6-10, 2022
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Christy Hoepting and Emma van der Heide (2022). Influence of applied nitrogen on bacterial bulb rot in muck-grown onion in New York. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Brenna Aegerter, W. M. Donahoo, Jane Davey, Michael Derie, Lindsey du Toit, Bhabesh Dutta, Eric Feibert, M. J. Foster, Christy Hoepting, Antoinette Machado, Claudia Nischwitz, Stuart Reitz, Jaspreet Sidhu, Mark Uchanski, Timothy Waters, and James Woodhall (2022). Evaluation of bactericides and plant defense inducers to manage bacterial rots of onion in seven states in the U.S. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Joe LaForest, Sarah Jean Swain, and Heather MacKay (2022). ALLIUMNET.COM website redesign to support collaborative onion research and extension. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Belo T. and LaHue G.T. (co-presenters), du Toit L., Waters T., Derie M., and B. Schact. 2021. Combatting onion bacterial diseases through irrigation management. Pacific Northwest Vegetable Association Annual Conference and Trade Show, Kennewick, WA, November 16th, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Pedro Lebre, Verushka Ibanez, Christopher Liakos, Jacqui van der Waals, and Teresa Coutinho (2022). The metavirome of onion bulbs in the U.S.A. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lindsey du Toit, Brian Kvitko, Heather MacKay and the Stop the Rot project team members (2022). Surveys of bacterial pathogens in onion production regions of the U.S.: Preliminary results from 2020 and 2021. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Verushka Ibanez, Christopher Liakos, Jacqui van der Waals, Teresa Coutinho, and Pedro Lebre (2022). A study on the bacterial inhabitants of storage onions: Identity and function. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Pedro Lebre, Verushka Ibanez, Christopher Liakos, Jacqui van der Waals, and Teresa A. Coutinho (2022). The metavirome of onion bulbs symptomatic and asymptomatic for bacterial bulb rots sampled from Georgia and Washington States in the U.S.A. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Christy Hoepting and Emma van der Heide (2022). Influence of variety on bacterial bulb rot of onion in New York State. Poster presented at the National Allium Research Conference, Denver, CO, February 28-March 1, 2022.
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Websites
Status:
Published
Year Published:
2022
Citation:
The Alliumnet website www.alliumnet.com has been updated regularly with new content generated during the reporting period. The site contains information resources for researchers, extension staff, and producers on the management of onion pests and diseases, links to current and recently completed research projects funded by federal and other grants, information on upcoming research meetings and conferences, and archives of previous research meetings. The Alliumnet website is developed, maintained, and hosted by the Southern IPM Center and the Center for Invasive Species and Ecosystem Health at the University of Georgia.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
du Toit, L. 2021. Stop the Rot: How can the results benefit you? Presentation at the Pacific Northwest Vegetable Association Annual Conference and Trade Show, Kennewick, WA, November 16th, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Belo T., LaHue G.T. du Toit L., Waters T., Derie M., and B. Schact. 2021. Combatting onion bacterial diseases through nitrogen fertility management . Presentation at the Pacific Northwest Vegetable Association Annual Conference and Trade Show, Kennewick, WA, November 16th, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Woodhall, J. 2021. Stop the Rot: Diagnostic and bacterial survey results for Washington, Idaho and Oregon. Presentation at the Pacific Northwest Vegetable Association Annual Conference and Trade Show, Kennewick, WA, November 16th, 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Aegerter, B., Wilson, R., Sidhu, J., Putman, A. 2022. Stop the Rot: Combating onion bacterial diseases with pathogenomic tools and enhanced management strategies. Presentation at the California Garlic and Onion Symposium, February 7th, 2022.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Wohleb, C.H., Waters, T.W., du Toit, L.J., and LaHue, G. 2021. Washington State University Extension Onion Alert, 1 September 2021. https://mailchi.mp/wsu/wsu-onion-alert-sept1-2021-1305808?e=72ba613792
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gugino, B. 2022. Identification and management of common foliar and bulb diseases of onion. Presentation at the 2022 Mid-Atlantic Fruit and Vegetable Convention Proceedings, Pennsylvania Vegetable Growers Association, Richfield, PA, February 1st, 2022.
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Other
Status:
Published
Year Published:
2021
Citation:
du Toit, L. and Waters T. 2021. To disinfect or not? Can postharvest applications of disinfectants reduce bacterial bulb rots in storage? Article in Onion World Magazine, July/August 2021, pp. 6 - 9. https://issuu.com/columbiamediagroup/docs/onion_world_july-august_2021/6
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Belo T., LaHue G.T., du Toit L., and T. Waters. 2021. When to water? How do irrigation frequency and final irrigation timing influence onion bacterial diseases? Onion World Magazine. December 2021. pp. 6 8. https://issuu.com/columbiamediagroup/docs/onion_world_december_2021?fr=sNDA4ZDI1Mjg1MDI
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Dutta, B. & Zhao M. 2022. Getting to the Root Cause of Rot: Progress in the Stop the Rot Project in Georgia. Onion World Magazine, February 2022, pp. 16 17. https://onionworld.net/2022/01/26/getting-to-the-root-cause-of-rot/
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
MacKay, H., du Toit, L. & Hoepting, C. 2022. Stop the Rot Halftime Report: News from the Stop the Rot Project on Onion Bacterial Diseases. Onion World Magazine, March/April 2022, pp. 16 - 17. https://issuu.com/columbiamediagroup/docs/onion_world_march-april_2022/16
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
MacKay, H. & du Toit, L. 2022. Stop the Rot Year 3 Highlights: Global study of bacterial rot yields interesting results with production practices. National Onion Association Newsletter, Volume XL, Issue 3, April 2022, pp. 6 7.
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
MacKay, H., du Toit, L. & Havey, M. 2022. A Collaborative Effort: Joint Allium Research Meeting Showcases Latest Research on Onion Production, Pests and Diseases. Onion World Magazine, May/June 2022, pp. 14 16. https://onionworld.net/2022/05/13/a-collaborative-effort-joint-allium-research-meeting-showcases-latest-research-on-onion-production-pests-diseases/
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Schattenberg, P. 2022. Novel species of pathogenic bacteria of onion identified in Texas. AgriLife Today, May 9, 2022. https://agrilifetoday.tamu.edu/2022/05/09/novel-species-of-pathogenic-bacteria-of-onion-identified-in-texas/
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
LaHue, G. 2021. Two critical pieces of the puzzle: Irrigation and nitrogen management impacts on bacterial bulb rot. WSU Onion Alert, September 1, 2021.
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
du Toit, L. & Waters, T. 2021. To disinfect or not? Can postharvest applications of disinfectants reduce bacterial bulb rots in storage? WSU Onion Alert, September 1, 2021.
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Wilson, R., Nicholson, R. and Aegerter, B. 2022. The influence of irrigation method on bacterial diseases of onion in northeast California, 2021. Plant Disease Management Reports 16:V154.
- Type:
Theses/Dissertations
Status:
Accepted
Year Published:
2022
Citation:
Lliakos, Christopher. 2022. Bacterial microbiome of healthy and diseased storage onion bulbs from Washington State, USA. M.Sc. Thesis, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2022
Citation:
Belo, T.R.D. 2022. Reducing the risk of onion bacterial diseases through irrigation and nitrogen fertility management. M.S. Thesis. Department of Crop and Soil Sciences. Washington State University.
- Type:
Theses/Dissertations
Status:
Published
Year Published:
2022
Citation:
Machado Burke, Antoinette. 2022. Evaluation of Bactericides and Plant Defense Inducers in the Presence and Absence of Onion Pathogens Pantoea SPP. and Burkholderia gladioli in Colorado. M.S. Thesis. Department of Horticulture and Landscape Architecture, Colorado State University. https://mountainscholar.org/handle/10217/235581
- Type:
Theses/Dissertations
Status:
Other
Year Published:
2022
Citation:
Ibanez, Verushka. (In prep. 2022). Bacterial microbiome of healthy and diseased storage onion bulbs from Georgia, USA. M.Sc. Thesis, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa.
- Type:
Other
Status:
Published
Year Published:
2022
Citation:
Pennsylvania Vegetable Disease Update and Pennsylvania Vegetable and Berry Current Issues are written weekly and biweekly and distributed via a listserv, posted on the Penn State Extension website and are further distributed by the Pennsylvania Vegetable Marketing and Research Program newsletter that is mailed, faxed or emailed to all PA vegetable growers who participate in the check-off program. Diseases of onion were included in articles between May 2022 and September 2022.
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Progress 09/01/20 to 08/31/21
Outputs
Target Audience:Stakeholders involved in the U.S. onion industry are the primary audience for this project. This includes onion producers (farmers), packers, shippers, and associated stakeholders engaged in various capacities in onion production, distribution, and marketing, e.g., agronomists, crop consultants, farm managers, field workers; personnel associated with agricultural supply companies (fertilizer and pesticide dealers, irrigation supply companies, etc.), seed companies, and dealers; onion breeders (public and private); and onion storage and shipping/transport personnel and companies. Public and private research and extension specialists, undergraduate students, graduate students, and postdoctorates working with diverse aspects of onion production are also a target audience for this project. The target audiences reached during this reporting period included: Onion growers, packers, processors and associated stakeholders in all 7 onion-growing regions of the US; Extension professionals in the 12 onion-growing states that are represented in this project; The project's Stakeholder Advisory Panel members represent onion farms, regional onion associations, and major vegetable seed companies (including onion breeders and plant pathologists) from across the U.S., with one international member. Panel members conducted further outreach to their own networks on behalf of the project. Panel members who are industry representatives include Greg Bird (President of the Michigan Onion Committee), Bob Ehn (California Garlic and Onion Research Advisory Board), Charles Hall (Executive Director of the Georgia Fruit and Vegetable Growers Association), Robert Sakata (President of the Colorado Fruit and Vegetable Growers Association). Four Masters students, two PhD students and four postdoctorates have worked on research directly related to the Stop the Rot project objectives in this reporting period. They are conducting their research in Washington State, Georgia, Texas, Pennsylvania, Colorado, and South Africa. We used several channels to reach our target audience during this reporting period, including grower meetings and field days, conferences and workshops, the Alliumnet.com website, industry newsletters, trade publications and extension videos. Project team members also reached out directly to growers in each of the onion-growing regions to recruit them for participation in the bacterial field surveys. Approximately 1,008 growers, agronomists and industry professionals were reached directly through presentations at conferences, workshops, field days and grower meetings in this reporting period. Many of the events were necessarily shifted away from in-person to virtual format due to COVID-19 constraints across the USA and in South Africa, which made it difficult to accurately count the number of people who were reached through presentations. Approximately 2,796 people have viewed our series of project videos. Communication and outreach materials and specific activities are reported in detail in the list of products. Changes/Problems:Bacterial surveys: managing workloads in the regional labs Two meetings were held in December 2020 (virtual) where the regional labs reviewed Season 1 work on bacterial surveys and planned for Season 2 surveys. The workload in Season 1 associated with processing onion survey samples proved to be very challenging for the labs, but the Season 2 survey program was greatly streamlined by reducing the number of visits to each survey location as well as the number of strains to be isolated from each sample collected in the field or in storage. Postdoctorate Shin (UGA) prepared a review session for the team on 30 June 2021 on using the SILVA database (in comparison with RDP and GenBank) for identifying bacterial isolates to genus-level based on 16S rDNA sequences. Following the session, the co-PIs agreed to switch from using RDP to SILVA as the preferred database for identifying bacterial isolates to genus-level that are collected in each regional lab for the state surveys each season. Risk-based modeling: access to commercial production data Access to production data from growers and packers has been very limited as stakeholders are reluctant to share proprietary crop information in a highly competitive market. In addition, growers do not always have detailed environmental data records, particularly for soil moisture status which we hypothesize is one of the most important risk factors in bacterial disease development. This has affected the ability of the team to develop and evaluate bacterial disease risk models. To resolve this, we plan to focus on collecting more data from our project field trials in Year 3, including deploying additional sensors to monitor environmental conditions in the trial plots. Weather-related problems Winter storms in Texas in January 2021 led to severe commercial onion crop losses and curtailed the bacterial survey in commercial fields for Year 2. Excessive heat and drought in Utah in summer of 2021 also caused significant commercial crop losses there, but bacterial surveys were still conducted. In UT research trials, onion plants stopped growing just as the crops were at bulb initiation due to extreme heat, and by harvest the plants were still very stunted. Final results are not available yet. Cancellation of LabGuru licenses During Year 2, we decided to centralize and simplify the compilation of regional bacterial survey data, using an Excel spreadsheet instead of proprietary software from LabGuru. We did not renew the LabGuru licenses for Year 2 so the funds ($3,800) were instead allocated to support additional staff time for redesign of the Alliumnet website. COVID19 impacts The lack of in-person SAP meetings has led to a shortfall in reported cost-share funding, since almost all SAP members had committed their travel and time to attend team meetings as part of their match. We plan to replace this with the value of strains donated to the project from pre-existing collections held by several team members and collaborators - these strains allowed us to move ahead with preliminary pathogenomics work while the Season 1 bacterial surveys were completed. In WA, restrictions regarding travel and hotel stays increased in-state travel expenses considerably (no sharing of hotel rooms, more cars needed to travel between Mount Vernon and Pasco each time. In addition, a positive COVID-19 incident in the WA program in Nov. 2020 resulted in that individual being on medical leave for 3 weeks, which added to the workload of others in the program working on this project, with delayed ability to make as much progress on the survey work (bacterial strain identifications) as planned. In PA, the University mandated COVID-19 restrictions delayed processing of the Year 1 bacterial survey samples from PA and NY. In addition, the inability to extract DNA for sequencing and conduct pathogenicity testing prior to putting the isolates into long-term storage significantly increased the labor and material costs required for this portion of the survey. However, as restrictions are beginning to lift and more people can access the lab, PA team members are finalizing the genera identifications of select isolates as well as running the onion pathogenicity tests. PA and other states anticipate there will be more opportunities for Extension and outreach in Season 3. At the University of Pretoria, the research undertaken in Year 2 was largely computer-based so both MSc students and their advisors either worked from home or from the lab (there was a rotational scheme in place because of COVID restrictions so the University of Pretoria lab is limited in the number of staff/students that can be present in the lab each day). Due to COVID-based restrictions, Postdoctorate Shin was not able to secure a visa to allow her to start her position with the Kvitko group at UGA in September 2021. A temporary position was created for her in the lab of collaborator Coutinho at the University of Pretoria until early 2021, when she was granted a visa to travel to Georgia. Dr. Shin contributed to project objectives from South Africa by genotyping and phenotyping South African Pantoea strains, which will ultimately add diversity and robustness to our analysis, and she conducted bioinformatics analysis. Shin also conducted a meta-analysis of published and unpublished Pantoea species-specific PCR primer sets, which will simplify Pantoea species identifications. Many of the states involved in this project could not hold regular in-person meetings and other events such as field days for sharing results or demonstrating field trials from this project. If COVID constraints continue to ease up over the next year, we anticipate more in-person events will take place for all team members. Other changes New SAP members joining in this period included: Larry Duell (CO), Margreet Asma (Netherlands), Kalie Christensen (WI), David Burrell (GA). Russell Hamlin and Kerrick Bauman stepped down from the SAP due to time constraints. New team members joining in Year 2 included: Paul Stodghill and Jo Ann Asselin of the USDA-ARS in Ithaca, NY. Their work is not funded through Stop the Rot but their current research is highly complementary to this project, so they are collaborating with the Stop the Rot team on the pathogenomics objective. What opportunities for training and professional development has the project provided?STUDENTS The grant has provided the opportunity for several graduate students and post-doctorates to work on different aspects of the project, as described below. Verushka Ibanez, MSc student at the University of Pretoria, South Africa. Dissertation title: Metagenome analysis of healthy and diseased onion bulbs from Georgia. Anticipated completion date: October 2021. Advisors: Teresa Coutinho, Pedro Lebre. Christopher Liakos, MSc student at the University of Pretoria, South Africa. Dissertation title: Metagenome analysis of healthy and diseased onion bulbs from Washington State. Anticipated completion date: October 2021. Advisors: Teresa Coutinho, Jacquie van der Waals, Pedro Lebre. Tessa Belo, MS student in the Soils & Water program at the Northwestern Washington Research and Extension Center of Washington State University. Advised by collaborator LaHue and co-advised by PD du Toit. Thesis topic: Impacts of irrigation and fertilization practices on bacterial diseases in onion bulb crops in the Columbia Basin. Expected completion date: Spring 2022. Antoinette Machado, MS student at Colorado State University in January 2020, supervised by co-PI Uchanski. Thesis topic: Evaluation of bactericides and plant defense inducers to manage center rot of onion in Colorado. Expected completion date: Spring 2022. Bed Prakash Bhatta, a PhD student at Texas A&M AgriLife Research - Uvalde is being trained on isolation, culture, and inoculation of bacteria under this project. Thesis topic: Breeding for anthracnose and Fusarium wilt resistance in watermelon. Ram Neupane, Plant Pathology PhD student at Pennsylvania State University (started Spring 2021). Thesis topic will be related to bacterial diseases of onion. Dr. Mei Zhao, postdoctorate in co-PD Dutta's program at the University of Georgia, is focusing on the bacterial survey, identification and characterization of bacterial isolates in GA, and assisting with greenhouse and field evaluations. Dr. Hossein Noorazar, postdoctorate at Washington State University, is focusing on data analysis and disease risk modeling efforts, supervised by co-collaborators Rajagopalan and Kalyanamaran. His part-time appointment on the project started in fall 2020. He initially focused on hypothesis extraction tools and exploring satellite imagery, and is now working with data provided by members of the team to identify factors that influence development of bacterial diseases. Dr. Navdeep Singh, postdoctoral research associate at Washington State University (started 16 Sep. 2020), primarily is working on other projects but is contributing to this work, particularly Objective B1, and will be engaged in this research until Fall 2022. Dr. Gi-Yoon (Gina) Shin, postdoctorate in co-PI Kvitko's lab at the University of Georgia, is assisting with the bacterial survey, investigating the pathogenomics of Pantoea spp. that are pathogenic and non-pathogenic on onion, and identifying target regions of the genomes for developing molecular diagnostic tools for onion bacterial pathogens. In Utah, five undergraduate students have been working on this project with collaborator Nischwitz (making media, culturing bacteria, storage evaluations, molecular identification of bacteria, conducting red scale necrosis tests, and helping with foliar and bulb assays). One student is writing an undergraduate research grant proposal for a side project identifying the gut bacteria of thrips in Utah and their potential as bacterial bulb rot pathogens. In New Mexico, two graduate students assisted with bacterial surveys in four autumn-sown onion fields. Shaun Stice, supervised by co-PI Kvitko, was a PhD student at the University of Georgia at the start of the project. He completed research on the genetic basis of P. ananatis virulence of onion as well as distribution of identified virulence loci among Pantoea isolates. He graduated in 2021. Dr. Gaurav Agarwal was a post-doctoral research associate under PI Dutta who assisted with the pathogenomics investigation of Pantoea spp. PROFESSIONAL DEVELOPMENT WSU team members (du Toit, Derie, and Waters) were hosts for training on 21-22 July 2021 for two team members from Texas A&M University (technician Khamal and PhD student Bhatta) to review methods for lab, greenhouse, and field trials on onion bacterial diseases. Postdoctorate Shin (UGA) prepared a review session for the team on 30 June 2021 on using the SILVA database (in comparison with RDP and GenBank) for identifying bacterial isolates to genus-level based on 16S rDNA sequences. Following the session, the co-PIs agreed to switch from using RDP to SILVA as the primary database for identifying bacterial isolates to genus-level that are collected in each regional lab for the state surveys each season. How have the results been disseminated to communities of interest?In this reporting period, we have been actively reaching out to growers and stakeholders to: share new information and learning from the project as well as current scientific understanding of onion bacterial diseases and their management; understand growers' current state of knowledge about causes and management of bacterial diseases of onion, and identify priority concerns for growers and the onion industry as regards management of bacterial diseases. Information has been shared with growers and stakeholders through a range of communication channels, including the newly revamped Alliumnet website, research summaries, extension bulletins, articles in trade publications and presentations at growers' meetings and field days. Results were also shared at professional scientific meetings (American Phytopathological Society's Plant Health 2021 Online. REACHING GROWERS AND ONION INDUSTRY STAKEHOLDERS: Outreach to growers and onion industry stakeholders, field representatives and extension staff has occurred through informal visits with growers during field surveys, grower meetings, field days and technical workshops. Our Stop the Rot video playlist https://www.youtube.com/playlist?list=PLajA3BBVyv1zf2obB16bNEdQPQeLW_XB_ now contains several videos aimed at growers and the onion industry (introduction to rot identification, in both English and Spanish; a longer video providing an overview of bacterial diseases in onion and current management options; a short video of the experimental equipment for our field trials of post-harvest disinfection treatments.) A short time-lapse video of the Red Scale Necrosis (RSN) assay has been added. We plan to include more short videos from field surveys and laboratory work during the next year. Refer to details above for statistics on number of views for each video and two awards given for the 14-minute video on the whole project produced by WSU. Outreach and dissemination of preliminary results to onion stakeholders and the industry has been conducted a number of informational articles in trade publications and extension newsletters (see list of publications) and websites/online alerts. Outreach to growers and industry stakeholders through the Stop the Rot Stakeholder Advisory Panel: Our 14-member Stakeholder Advisory Panel (SAP) brings a diverse range of expertise and experience to the project. The Panel includes growers, pathologists and onion breeders from onion growing regions across the US. Four new members joined the Panel in Year 2: Larry Duell of Gowan Seeds in Colorado; Margreet Asma, seed pathologists with Bejo Zaden in the Netherlands; David Burrell of National Onion Labs in Georgia; and Kalie Christensen of Gumz Farms in Wisconsin. Panel members are active in sharing information about the project to growers and onion industry stakeholders through their own regional and national networks in 12 states, and in bringing insights and information into the project from their networks. Our second annual meeting with the SAP was held on February 5th, 2021 by videoconference. Several panel members have participated in team work sessions on phenotypic screening methods as subject matter experts. Panel members have actively participated in our monthly project team meetings by videoconference and they continue to receive project updates, notes from the monthly meetings and our internal project team newsletters. REACHING ACADEMIC RESEARCHERS, EXTENSION PROFESSIONALS AND GRADUATE STUDENTS The project team now includes 24 research collaborators from 12 states, representing all seven major U.S. onion growing regions, as well as onion bacteriologist Prof. Teresa Coutinho from South Africa. During this year, Prof Steven Beer of Cornell and Drs. Paul Stodghill and Jo Ann Asselin of the USDA-ARS also joined the team as collaborators. We hold monthly team videoconferences to share preliminary results and experiences and discuss recent findings. These monthly meetings of 1.5 to 2 hours have facilitated research and Extension collaborations within the project. Almost all the project collaborators are also involved in extension services and education in their regions, which makes for efficient transfer of new information and research results from the team to extension professionals and thence to growers. Technicians and graduate students from each of the regional teams also join our monthly meetings and contribute actively to the discussions, providing feedback on methods and protocols and sharing their latest results with the full team in a collegial setting. Once final results of 2020 field trials became available in spring 2021 after evaluation of bulbs in storage, we compiled results from the first season's bacterial surveys and field trials into a summary of Year 1 research findings. The summary is available on Alliumnet.com https://alliumnet.com/wp-content/uploads/2021/09/StoptheRot_Year1_summaries.pdf. Preliminary results of the national bacterial survey were shared at the American Phytopathological Society annual meeting, 2021 Plant Health Online, and will be shared with relevant agencies in each participating state. The results of Year 1 field trials in participating states have been published in 12 peer-reviewed Plant Disease Management Reports (see list of publications). Five articles have been published in scientific journals (see list of publications). Four Research on Demand presentations were shared at Plant Health 2021 Online, the annual conference of the American Phytopathological Society. What do you plan to do during the next reporting period to accomplish the goals?OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial surveys: In the next reporting period, we plan to repeat the bacterial surveys in all the onion regions. In addition, directed surveys will be carried out using a real-time PCR assay being developed for Pantoea agglomerans strains virulent on onion, based on whole genome sequencing of bacterial strains collected in this survey and strains received from other collections. Regional labs will again send both pathogenic and non-pathogenic isolates of Pantoea to UGA, endeavoring to represent the diversity found in their regions. As strains of the other genera are characterized, each lab will send pathogenic and non-pathogenic strains that represent the diversity detected in the samples. Strains sent to UGA will be identified to species using MLSA schemes and tested for pathogenicity on onion. Metadata and results will be added to the NOBSC database and made available publicly on Alliumnet. During the next two years of the project, regional labs will also plan for long-term storage and back-up of their regional collections. The NOBSC will only include strains that are in the national collection. A2. Pathogenomic analyses, virulence factors & bacterial community analyses Additional strains of P. agglomerans will continue to be added to the NOBSC as Year 2 survey collections are finalized at each regional lab. A subset of those strains will be subjected to whole genome sequencing and examined to identify putative virulence factors associated with the ability to cause diseases on onion, as detailed above for strains evaluated in Year 2 to validate the virulence factors identified in the first 2 years of this project and for testing the molecular diagnostic tools being developed for onion-pathogenic strains of Pantoea spp. .. Results of the bacterial community analyses from asymptomatic and symptomatic bulbs collected from a field in each of GA and WA will be published in Year 3, when the two MS students working on this aspect of the project will graduate. The results will help assess potential interactions among the complex microflora associated with asymptomatic and symptomatic onion bulbs. Results from both students' work will be used to design additional microbial community analyses to increase our understanding of how non-pathogenic, pathogenic, and opportunistic bacteria and other microflora interact in onion bulbs. A3. Molecular diagnostic tools We will use the results of initial pilot studies in Year 2 to evaluate how to undertake directed surveys for onion bacterial pathogens using molecular diagnostic tools. This will entail collecting onion seed lots as well soil, debris, and water trap samples from fields at critical stages of onion production. Real-time PCR assays of DNA extracted from these materials, using the molecular diagnostic tools in development, should inform us of the relative importance of potential inoculum sources of onion bacterial pathogens in different regions of the US. Results of the pathogenomics work in Years 1 and 2 revealed that it will be challenging to design a sensitive real-time PCR assay for Pantoea spp. pathogenic on onion that works across all onion production regions. We have detected substantial regional variation in the pathogenicity of P. agglomerans strains collected across 12 states during the Season 1 and 2 surveys. For example, all the Idaho and Oregon strains of P. agglomerans tested to date were RSN-, and very few P. agglomerans strains collected in Washington have been RSN+, even when isolated from symptomatic plants or bulbs. This is in contrast to GA, where a majority of P. agglomerans strains collected were RSN+. Therefore, our approach in Year 3 will be to design an assay which detects the presence of the HiVir cluster and, potentially, other genes associated with virulence to onion, and then use a decision support system to identify the associated risk of that bacterial species being pathogenic on onion. The regional survey results will be important for developing a decision support system relevant to different onion production regions of the US. A4. Phenotypic resistance screening methods Based on results of the lab and greenhouse onion phenotyping protocols evaluated in Years 1 and 2, the focus of this project will shift to field evaluations. Dutta at UGA will screen commercial short-, medium-, and long-day cultivars as well as diverse Allium germplasm from the USDA NPGS for resistance to P. ananatis by treating the seed of these cultivars and inoculating plants in the field at various growth stages. Field phenotypic screening trials also will be completed in TX and WA in Season 3 with pathogens predominant in each state. Cultivars planted will reflect those suitable to each region as well as germplasm with diverse phenotypic reactions from Season 1 trials. Based on results of the WA Season 2 cultivar trial, modifications will be incorporated into the Year 3 cultivar field trial in WA. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT Lab, greenhouse, and field trials will be continued in Year 3 to evaluate irrigation practices, fertility practices, pesticide programs, cultural practices, and postharvest bulb treatments for control of bacterial diseases of onion. Specific aspects investigated in each region will be prioritized based on regional practices and constraints, and on stakeholder priorities as well as results from Years 1 and 2 of the project. Results from Season 1 and 2 trials will besharedat the team and SAP meetings to refine research plansfor Season 3, in an iterative approach guided by stakeholders to ensure translation of results into practical tools. Data from Stop the Rot field trials in Years 1 and 2 will be used to inform and validate disease risk models. Data on onion production practices, crop microclimate, and bacterial diseases will be sought to assess whether the risks of diseases can be modeled statistically, to predict if a grower should sell bulbs at harvest or can store bulbs with minimal risk of bacterial rots. ECONOMIC ASSESSMENTS The potential for adoption of management recommendations based on results of these trials will be assessed annually by the SAP and stakeholders with economist Colson. Economic analyses will be integrated into various trials based on inputs (expenses) and outputs (marketable yield). Work on this objective will include: Drafting an academic article reporting survey findings. Assisting the Extension team and grant leadership to incorporate findings from field trials into website and outreach materials. Working with team members as field trial data becomes available to translate findings into cost-benefit analyses. OUTREACH AND EXTENSION Results from Year 2 work will be shared in research summaries; on Alliumnet.com; in project newsletters, trade publications, regional websites, and presentations at growers' meetings and field days. Plans are underway to develop more videos, "quick guides", highlights of annual project results, training and extension materials, and an interactive map of the USA with results of the bacterial disease surveys. The newly redesigned Alliumnet.com website will be maintained to provide a home for national onion research collaborations, including USDA projects, National Allium Research Conference information and proceedings, links to National Onion Association meetings and events, and the W-1008, W-2008, and W-3008 (and the future W-4008) onion multi-state project reports, activities, and meeting details. PROJECT MANAGEMENT AND COORDINATION The third annual project team meeting is scheduled for March 1, 2022 in Denver CO, and the Stakeholder Advisory Panel videoconference is scheduled for March 25, 2022.Regular monthly videoconferences for the full team, regular meetings for the co-PIs every two months, and weekly meetings of the PD and Project Manager will continue in Year 3.
Impacts
What was accomplished under these goals?
OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial disease surveys, NOBSC Onion foliage and bulbs were surveyed in southern states in 12/2020 to 06/2021, and in northern states from spring to fall 2021. To date, 84 bacterial genera have been identified from 2,594 isolates. Distribution and pathogenicity vary among regions. Few genera produce symptoms on onion. Prevalent genera include: Pantoea, Pseudomonas, Burkholderia, Enterobacter and Erwinia. The GA survey showed temporal progression in genera on foliage. A subset of 612 strains were sent to UGA for the NOBSC. A2. Onion bacterial pathogenomics To design molecular diagnostic tools for onion-pathogenic Pantoea strains, we targeted P. agglomerans. We showed that P. agglomerans strains use similar onion-virulence genes as P. ananatis, but strains with these genes are uncommon. Whole genome sequencing for 32Pantoeastrains showed a perfect correlation between red scale necrosis phenotype and presence of the HiVir operon. PCR primers were designed to detect the HiVir cluster in 3 Pantoea species, which appears necessary for infection. Strains without the alt gene, which imparts tolerance to sulfur compounds, do not colonize onion well. Bacterial DNA extracted from symptomatic and asymptomatic onion bulbs from GA and WA revealed differences in bacterial communities between the types of bulbs, and between GA and WA bulbs. Genes involved in pathogenicity, detoxification and secretions systems were identified in the metagenome-assembled genomes of the known pathogens of center rot. A3. Diagnostic tools In Year 2 we: Verified the specificity and sensitivity of a real-time PCR assay for P. agglomerans; Developed a low-cost water trap to sample irrigation and rain water for onion pathogens; Demonstrated that a bulk soil DNA extraction method will need optimization for muck soils. Public Pantoea species-specific PCR primers were evaluated and new PCR primers designed for P. agglomerans using the strains described above. HiVir operon sequences generated for 58 Pantoea strains are being used to design primers for HiVir+ onion-pathogenicstrains of Pantoea. Genomic DNA was purified from 20 genomes sequenced for P. agglomerans, P. ananatis, and P. allii strains (15 HiVir+/RSN+ and 5 HiVir+/RSN-) to design diagnostic tools for onion-pathogenic strains. A4. Phenotypic screening methods Four cultivars (short-day [SD] dehydration, SD sweet, long-day [LD] dehydration, and LD sweet) were selected to represent what might be susceptible (sweet) vs. partially resistant (dehydration) to bacterial pathogens. Plants were inoculated with P. ananatis in a greenhouse with spray inoculation and cut leaf-tip methods at two inoculum concentrations. No consistent pattern emerged in disease severity among cultivars with either method or inoculum concentration. A cultivar field trial in WA was repeated in Season 2 using 3 cultivars from each of 4 maturity groups. The trial was irrigated with sprinklers instead of center-pivot to cease irrigation at the recommended time for each maturity group. Bulbs are in storage to be rated for bacterial rot in Feb. 2022. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT Results of Year 1 trials were finalized once onion bulbs in storage were rated for bacterial storage rots. Field trials in Year 2 investigated the impacts of irrigation practices (WA, OR, GA trials), fertility practices (WA, NY, GA, OR, PA), cultural practices (WA, GA, NY), pesticide programs (CO, UT, WA, NY, GA, TX), and postharvest disinfection practices (WA) on development of onion bacterial diseases. In both years, field trials focused on practices and products currently used by onion growers to reflect stakeholder priorities and concerns. When feasible, trials involved inoculated and non-inoculated plots, using local bacterial strains to ensure adequate disease pressure for differentiating treatment effects. Some valuable results with potential application have been shared with stakeholders: Using drip vs. overhead irrigation reduced internal bacterial rot incidence without significant effects on marketable yield or size class distribution. Earlier termination of final irrigation reduced bacterial rot without affecting marketable bulb yield. Earlier termination of the final N application resulted in less bacterial rot in GA trials, but not in WA trials due to high residual N at the WA site. Copper-based bactericides significantly reduced internal bulb rot incidence in the 2020 GA trial. In the WA and NY 2020 trials, copper and other bactericide treatments had no effect on incidence or severity of bacterial bulb rot at harvest or after 5 months of storage. WA trials on undercutting, rolling tops, and the timing of topping showed no significant effects on marketable yield or bacterial bulb rots. GA trials evaluating harvesting methods showed significantly less bacterial bulb rot when using: a chain digger vs. a straight-blade undercutter; mechanical harvest vs. manual harvest; topping onion necks to a length of 3 or 5 inches vs. 1 inch. NY trials showed rolling tops had no effect on bacterial bulb rots, while quick artificial curing with forced heated air reduced bacterial bulb rots by 50%. WA trials indicated no benefit to applying ozone or hydrogen peroxide + peroxyacetic acid products to onion bulbs in storage for managing bacterial rots, probably because the products do not penetrate the dry wrapper scales. RISK MODELING The risk modeling team received crop and weather data for the 2017 production season from 5 onion fields planted to the same cultivar in the Columbia Basin of the Pacific Northwest. Excess late-season irrigation was hypothesized as a contributor to bacterial rots in these fields. Large amounts of field data are needed on plant water uptake and transpiration needs based on soil moisture status, weather, and plant growth stage, in order to extract signals from data and help identify hypotheses as the basis for risk-based decision-making. To this end, data was collected in NY trials by team members in Year 2. ECONOMIC ASSESSMENTS Surveys were delivered to onion growers, the project team and the SAP. Growers estimate that, on average over the past 5 years, >10% of the onion crop in their area was lost to bacterial diseases. Approx. 20% of growers reported losses of >50% of the onion crop in their area in the past five years due to bacterial diseases. Respondents consider the most effective management strategies are irrigation and water management, and post-harvest curing (forced air and heating). The average grower is very concerned about bacterial diseases, limited in their ability to identify the diseases or bulb rot pathogens, and feels only moderately equipped to manage them. Growers rely on information from University-based extension services to manage onion bacterial diseases. OUTREACH AND EXTENSION Year 1 outreach focused on increasing awareness of bacterial pathogens of onion, and sharing results of Season 1 field trials. Outreach has included (for a total of 3,897 direct contacts): Articles and quizzes in Onion World and Veg News, with wide circulation in the onion industry; Articles in newsletters of the National Onion Association, regional grower associations and extension services; Presentations at grower meetings and conferences; Release of 2 videos on diagnosing, understanding and managing bacterial bulb rots; Field days and tours in 7 states; A session on onion bulb rot at the NY Empire Producers Expo in Jan. 2021; Overhaul of the Alliumnet.com website serving members of the Allium research and extension community. PROJECT MANAGEMENT Coordination, communication and integration across the team and with SAP members have been supported by monthly videoconferences, bi-monthly conference calls, annual team and SAP meetings, and the adoption of the Project Charter. Work sessions included: streamlining work in regional laboratories; developing phenotypic screening methods; developing diagnostic tools.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Agarwal Gaurav, Choudhary Divya, Stice Shaun P., Myers Brendon K., Gitaitis Ronald D., Venter Stephanus N., Kvitko Brian H., Dutta Bhabesh (2021). Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion. Frontiers in Microbiology vol 12:2381 https://www.frontiersin.org/article/10.3389/fmicb.2021.684756
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Koirala, S., Zhao, M., Agarwal, G., Stice, S., Gitaitis, R., Kvitko, B., & Dutta, B. 2021. Identification of two novel pathovars of Pantoea stewartii subsp. indologenes affecting Allium sp. and millets. Phytopathology. 10.1094/PHYTO-11-20-0508-R. https://www.researchgate.net/publication/349422413_Identification_of_two_novel_pathovars_of_Pantoea_stewartii_subsp_indologenes_affecting_Allium_sp_and_millets
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Stumpf, S., Leach, L., Srinivasan, R., Coolong, T., Gitaitis, R., Dutta, B. Foliar chemical protection against Pantoea ananatis in onion is negated by thrips feeding. Phytopathology. 2021 Feb. 111(2):258-267. doi: 10.1094/PHYTO-05-20-0163-R. Epub 2021 Jan 13. PMID: 32748732. https://pubmed.ncbi.nlm.nih.gov/32748732/
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Stice, S., Shin, G.Y., Armas, S.D., Koirala, S., Galvan, G.A., Siri, M.I., Severns, P.M., Coutinho, T.A., Dutta, B., and Kvitko, B. 2021. The distribution of onion virulence gene clusters among Pantoea spp. Frontiers in Plant Science https://doi.org/10.3389/fmicb.2021.00184
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Zhao, M., Kvitko, B.H., Gitaitis, R.D., and Dutta, B. 2021. Bacterial streak and bulb rot of onion. Plant Health Instructor. DOI: 10.1094/PHI-E-2021-0421-01
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
da Silva, A., H.I. de Jesus, B. Dutta. 2021. Effects of irrigation method, nitrogen rate, and fertilizer application timing on bacterial diseases in Vidalia onion, Georgia 2020. Plant Disease Management Reports 15:V012.
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Dutta, B., Tyson, C., Edenfield, J., Williams, Z., Tanner, S., Shirley, A., Reeves, B., and Powell, S. 2020. Evaluation of onion growth stage directed chemical applications and thrips management program on center rot incidence in onion bulbs in Georgia, 2019. Plant Disease Management Reports 14:V091
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Dutta, B., Tyson, C., Edenfield, J., Williams, Z., Tanner, S., Shirley, A., Reeves, B., and Powell, S. 2021. Evaluation of onion growth stage directed chemical applications and thrips management program on center rot incidence in onion bulbs in Georgia, 2020. Plant Disease Management Reports 15:V023. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Dutta, B. and Tyson, C. 2021. Evaluation of harvesting methods on post-harvest incidence of center rot and sour skin in onion, Georgia 2020. Plant Disease Management Reports 15:V025. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Dutta, B. and Tyson, C. 2021. Evaluation of digging methods on post-harvest incidence of center rot and sour skin in onion, Georgia 2020. Plant Disease Management Reports 15:V026. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Dutta B. and Foster M.J. 2021. Evaluation of bactericides and plant defense inducers to manage center rot of onion in Georgia, 2020. Plant Disease Management Reports 15:V027. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
du Toit, L.J., Derie, M.L., Gundersen, B., Waters, T.D., and Darner, J. 2021. Efficacy of bactericides for management of bacterial leaf blight and bulb rots in an onion crop in Pasco, WA, 2020. Plant Disease Management Reports 15:V107. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
du Toit, L.J., Derie, M. L., and Gundersen, B. 2021. Efficacy of disinfectants applied to onion bulbs in storage for control of bacterial bulb rots, Pasco, WA, 2020-2021. Plant Disease Management Reports 15:V102. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
du Toit, L.J., Derie, M. L., and Gundersen, B. 2021. Efficacy of late-season cultural practices on bacterial leaf blight and bulb rots in an onion bulb crop in Pasco, WA, 2020. Plant Disease Management Reports 15:V100. https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Belo, T., du Toit, L., Waters, T., Derie, M., and LaHue, G. 2021. Effects of irrigation frequency and final irrigation timing on onion bacterial diseases in the Columbia Basin of Washington, 2020. Plant Disease Management Reports 15:V109 https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Hoepting, C.A., Caldwell, S. K., and van der Heide, E. R. 2021. Evaluation of selected pesticides for control of bacterial bulb rot in onion, 2020. Plant Disease Management Reports 15:V108 https://doi.org/10.1094/PDMR15
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Hoepting, C.A., Caldwell, S. K., and van der Heide, E. R. 2021. Variety evaluation and effect of copper bactericide on bacterial bulb rot in onion, 2020. Plant Disease Management Reports 15:V107. https://doi.org/10.1094/PDMR15
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Dutta, B., and Gitaitis, R. 2020. Bacterial diseases of onion in Georgia. University of Georgia Cooperative Extension Bulletin B1534.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Dutta, B., and Gitaitis, R.D. 2021. Disease quiz II. Onion World, February 2021:13, 20.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
MacKay, H.M. 2021. Stop the Rot! Researchers finish first year of field, lab work in 4-year project. Update in January 2021 newsletter of the National Onion Association.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Dutta, B. 2021. Onion disease management in Georgia. Vegetable and Specialty Crop News, February 2021.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Nischwitz, C. 2021. Bacterial Bulb Rot Diseases in Utah, Utah Pests Quarterly Newsletter, Vol. 15, Spring 2021. https://extension.usu.edu/pests/files/up-newsletter/2021/UtahPestsNews-spring21.pdf
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
MacKay, H., and du Toit, L. 2021. Progress report. Stop the Rot: A national collaboration to research, combat bacterial diseases of onion. Onion World, May/June 2021:12-14. https://issuu.com/columbiamediagroup/docs/onion_world_may_june_2021/12
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Hoepting, C.A. 2020. Stop the Rot: New York part of ambitious multi-state, multi-disciplinary, multi-year, multi-million-dollar project to combat bacterial diseases of onion. Cornell Cooperative Extension Cornell Vegetable Program extension newsletter, Veg Edge August 5, 2020: 16(18), pp 6-7. https://rvpadmin.cce.cornell.edu/pdf/veg_edge/pdf198_pdf.pdf
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Hoepting, C.A. 2021. Pesticides for onion bulb rot Do they Work? Featuring 2020 field trial results. Cornell Cooperative Extension Cornell Vegetable Program extension newsletter, Veg Edge July 21, 2021: 17(15), pp 6-7.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Hoepting, C.A. 2021. The rot race: Harvest practices to avoid bacterial bulb rot in onion. Cornell Cooperative Extension Cornell Vegetable Program extension newsletter, Veg Edge July 28, 2021: 17(16), pp 8-9.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Stop the Rot newsletter #1 in September 2020, which was also posted to the project page on Alliumnet.com https://bugwoodcloud.org/mura/alliumnet/assets/File/Newsletters/StopRotteamNewsletterSept2020(final).pdf
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
LaHue, G.T., Waters, T., and du Toit, L., 2020. Revisiting nitrogen management recommendations in the context of onion bacterial diseases. Progress report for Columbia Basin Onion Research Committee. Submitted 31 October 2020.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
du Toit, L.J., Waters, T., Derie, M., and Darner, J. 2020. Battling onion bacterial diseases with bactericides. Onion World, December 2020:6-11. https://issuu.com/columbiamediagroup/docs/onion_world_december_2020
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Thompson, C. 2020. Organic Vidalia Onion Industry: Challenges in sour skin management. Vegetable and Specialty Crop News, 16 December 2020 (edits provided by B. Dutta)
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
du Toit, L., and Waters, T. 2021. To disinfect or not? Can postharvest applications of disinfectants reduce bacterial bulb rots in storage? Onion World, July/August 2021:6-9.
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Stop the Rot Collated Summaries of Year 1 Technical Reports. Compilation of the final Year 1 topic summaries, August 2021. https://alliumnet.com/wp-content/uploads/2021/09/StoptheRot_Year1_summaries.pdf
- Type:
Other
Status:
Published
Year Published:
2021
Citation:
Wohleb, C.H., Waters, T.W., du Toit, L.J., and LaHue, G. 2021. Washington State University Extension Onion Alert, 1 September 2021. https://mailchi.mp/wsu/wsu-onion-alert-sept1-2021-1305808?e=72ba613792
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Dutta, Bhabesh (2020). Stop the Rot Research Project on Bacterial Diseases of Onion. Invited presentation at the Annual Meeting of the National Onion Association, August 11, 2020 (virtual meeting). (28 participants)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
November 19, 2020. WA, OR, ID Pacific Northwest Vegetable Growers (virtual) Annual Convention. Stop the Rot SCRI project update (Lindsey du Toit). 185 participants
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
December 4, 2020. OR, WA Hermiston Farm Fair. Understanding and managing Iris yellow spot virus and onion bacterial rots in Columbia Basin onion production (Lindsey du Toit). 213 participants
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Gaurav Agarwal, Santosh Koirala, Brian H. Kvitko and Bhabesh Dutta. 2021. Pan-genome of novel Pantoea stewartii subsp. indologenes identifies genes involved in onion pathogenicity and lateral gene transfer. Research on Demand presentation for American Phytopathological Societys annual meeting, Plant Health 2021 Online, 2-6 August 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
December 9, 2020. CO. Eastern Colorado Crop Production (virtual) Conference. Stop the rot project update (Antoinette Machado). 59 participants
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
January 6, 2021. GA Southeast Fruit and Vegetable (virtual) Conference. Onion disease update (Bhabesh Dutta). 45 participants
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2020
Citation:
Collaborator (Subas Malla) participated in South Texas Onion Committee meetings on June 12, 2020 and October 13, 2020. He highlighted and updated TX findings of the project to the Committee members. There were around 20 attendees at each meeting.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
MacKay et al. 2021. "Combating onion bacterial diseases with pathogenomics tools and enhanced management strategies: Research objectives and preliminary results." Research on Demand presentation for American Phytopathological Societys annual meeting, Plant Health 2021 Online, 2-6 August 2021. (All topic leads are co-authors).
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
January 14, 2021. NY. Empire State Producers Expo Onion Bulb Rot Session. (Lindsey du Toit, Bhabesh Dutta, Brian Kvitko, Christy Hoepting). 86 participants.
-Rotten Onions 101 Part I What kind of rot you got
-Rotten Onions 101 Part II The many ways onions rot
-Stop the Rot: Rot-free onions in the making Overcoming challenges to identify varietal tolerance to bulb rot.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Brendon Myers, Gaurav Agarwal, Ronald D. Gitaitis, Brian H. Kvitko and Bhabesh Dutta. 2021. Pan-genomic approaches to predicting virulence factors in Pantoea ananatis affecting Allium porrum and Allium fistulosum. Research on Demand presentation for American Phytopathological Societys annual meeting, Plant Health 2021 Online, 2-6 August 2021.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2021
Citation:
Santosh Koirala, Mei Zhao, Gaurav Agarwal, Ron Gitaitis, Shaun Stice, Brian Kvitko, and Bhabesh Dutta. 2021. Identification of two novel pathovars of Pantoea stewartii subsp. indologenes affecting Allium sp. and millets. Research on Demand presentation for American Phytopathological Societys annual meeting, Plant Health 2021 Online, 2-6 August 2021.
|
Progress 09/01/19 to 08/31/20
Outputs
Target Audience:Stakeholders involved in the U.S. onion industry are the primary audience for this project. This includes onion producers, packers, shippers, and associated stakeholders engaged in various capacities in onion production, distribution, and marketing, e.g., agronomists, crop consultants, farm managers, field workers; personnel associated with agricultural supply companies (fertilizer and pesticide dealers, irrigation supply companies, etc.), seed companies, and dealers; onion breeders (public and private); and onion storage and shipping/transport personnel and companies. Public and private research and extension specialists, undergraduate students, graduate students, and postdoctorates working with diverse aspects of onion production are another key target audience for this project. The target audiences reached during this reporting period included: Onion growers, packers, processors and associated stakeholders in all 7 onion-growing regions of the US; Extension professionals in the 12 onion-growing states that are represented in this project; The project's Stakeholder Advisory Panel members represent onion farms, regional onion associations, and major vegetable seed companies (including onion breeders and plant pathologists) from across the U.S. Panel members conducted further outreach to their own networks on behalf of the project. Panel members who are industry representatives include Greg Bird (President of the Michigan Onion Committee), Bob Ehn (California Garlic and Onion Research Advisory Board), Charles Hall (Executive Director of the Georgia Fruit and Vegetable Growers Association), Robert Sakata (President of the Colorado Fruit and Vegetable Growers Association). Four Masters students, one PhD student and three postdoctorates began working on research directly related to the Stop the Rot project objectives in this reporting period. They are conducting their research in Washington State, Georgia, Colorado and South Africa. We have used several channels to reach our target audience during this reporting period, including grower meetings, conferences and workshops, the Alliumnet.com website, industry newsletters and trade publications. Project team members also reached out directly to growers in each of the onion-growing regions to recruit them for participation in the bacterial surveys during the first season. Approximately 900 growers, agronomists and industry professionals were reached through in-person presentations at conferences, workshops and grower meetings in this reporting period. From early spring, methods of communication and presentation were necessarily shifted away from in-person to virtual format due to COVID-19 constraints across the USA and in South Africa, which made it difficult to accurately count the number of people who were reached. Changes/Problems:1. LATE RELEASE OF FUNDS FOR THE PROJECT The final release of funds in April 2020 by NIFA was later than expected as a result of the USDA NIFA headquarters being relocated from Washington DC to Kansas City, MO in 2019-20. This led to delays in issuing the subcontracts for the collaborating institutions, compounded further by delays associated with COVID-19 constraints implemented at the various institutions involved in this project. Consequently, invoicing and expenditure on the project for Year 1 has been delayed, and a significant portion of the Year 1 funds will be rolled over into Year 2 to cover work that was done in the last four months of Year 1 (May - August 2020). 2. PROBLEMS DUE TO COVID-19 IMPACTS, AND RESULTING CHANGES COVID-19 impacts on project work in this reporting period were principally due to temporary closures of labs and restrictions on travel for some team members. Most field work and field trials have proceeded as planned, with additional safety precautions and social distancing requirements in place for researchers, technical staff and students that added limitations and/or additional expenses to some of the work completed in Year 1. Overall, COVID-19 impacts have led to some of the work originally planned for Year 1 being rescheduled to Year 2 or later as some labs had to shut down completely during the first ~3 months of the pandemic. Several programs were unable to hire technical support for the project in a timely manner, which affected the capacity to get as much work done as had been planned. While this will require shifting of funds from Year 1 to Year 2 budgets, it is not expected to result in substantial changes in the scope of work, nor in any changes in the total budget for the work. We expect to be able to meet all the project's planned deliverables within the original approved budget. However, we will likely need to make use of the permitted one-year no-cost extension of the project because of delays in some aspects of the project. Specific changes in this reporting period as a result of COVID-19 impacts include the following: As a result of the labs closing at the University of Georgia, early work on pathogenomic tools was unavoidably delayed and technician salary will be shifted from Year 1 to Year 2 to complete this work. In addition, while field work proceeded as planned, the team was unable to access the labs to work on identification of the bacterial genera and species collected in the field. However, this will not lead to overall delays or changes in the work program. Collaborator Colson at the University of Georgia was unable to recruit a graduate student to work on economic assessments in Year 1 and Year 2 as planned. The recruitment has been rescheduled to Years 3 and 4 with no change in the planned scope of work on this objective. Field trials at The Pennsylvania State University have been rescheduled from Year 1 to Year 2 due to the university's COVID-19 restrictions on research and hiring of new employees. The salary allocated for the field technician will be used to cover the salary of a lab technician to process onion samples from PA and NY. Summer wages for the graduate student will be reallocated to project Year 4 and summer wage payroll wages will be reallocated to Year 2. Materials and supplies allocated for field trials in Year 1 will be reallocated to Year 2. Collaborator Malla completed one round of field surveys of 4 onion crops in the Rio Grande Valley before his lab at Texas A&M Agrilife Research was shut down and his team's travel was restricted. However, their field trials were not affected and proceeded as planned. As a result of the TX lab closure, bacterial isolates collected by the CA team in their field surveys were rerouted from the TX lab to PD du Toit's regional lab in WA for processing. Due to this change, WA requested $5,000 moved from TX to WA in the second year's budget. In New Mexico, co-PI Cramer was able to identify and visit only 4 of the 5 planned fields in the bacterial survey, and the fields were not visited at the exact times proposed due to a shortage of labor. Due to the shutting down of co-PI Kvitko's lab in Georgia and collaborator Coutinho's lab in Pretoria, the WA regional lab extracted DNA from four sets of nine onion bulbs, and sent the DNA to Genohub in TX for sequencing, so that collaborator Coutinho's students could continue their research into onion bulb microbiome characteristics. Funds will be shifted from the University of Pretoria budget allocation to UGA to cover this. Co-PI Hoepting requested a shift of funds saved on her nitrogen rate trial to travel expenses, since the mileage costs for her to travel to her nitrogen timing trial increased significantly as a result of COVID-19 restrictions. Co-PI Aegerter requested to shift funds from travel to lab supplies as she did isolations for all CA fields surveyed in 2020. 3. OTHER CHANGES IN THIS REPORTING PERIOD Bacterial strain database Instead of purchasing Filemaker Cloud to serve as the data platform for the proposed National Onion Bacterial Strain Collection (NOBSC), the team decided to purchase a license for LabGuru for each regional lab. The LabGuru software is already in use in some of the project's regional labs, provides an online system that can streamline management of onion bacterial strain data within the project. The total cost for LabGuru licenses for each regional lab is slightly less than the amount budgeted for Filemaker Cloud. Irrigation trials in NY Co-PI Hoepting proposed that since NY does not have many onion growers who irrigate their crops, she would not undertake irrigation trials in NY as a priority in Year 1. The team agreed. The resources will be directed to other aspects of the field research in NY. Directed surveys in Year 2 Soil, water, weeds and contaminated onion seed can all act as sources of inoculum for bacteria that may be pathogenic on onion. At our first annual meeting and in subsequent team videoconferences, the team discussed modifying the planned directed bacterial surveys in Year 2 to also include concurrent sampling of soil, water, weeds and seeds. Collaborator Woodhall's lab has the capacity for high-throughput analyses of bacterial DNA found in soil and water and Dr Woodhall is developing sampling protocols to share with the team, who will send their soil and water samples to him for analysis in Year 2. This work will complement the surveys of bacterial pathogens in onion foliage and bulbs. The proposed change to incorporate sampling of other sources of inoculum will not require any changes to the project budget. New project team member Prof. Steven Beer of Cornell University joined the project team this year as a collaborator. His lab is producing inoculum for field trials in NY, in support of co-PI Hoepting's field work. Prof. Beer will also be sending selected pathogenic onion bacterial strains from his own extensive collection to co-PI Kvitko's lab for the National Onion Bacterial Strain Collection (NOBSC). During the past 10 years, his program received hundreds of symptomatic onion samples from NY, PA, MI, GA, ME and OR. To cover the costs of producing inoculum and sending strains to the NOBSC, $5,000 will be shifted from the WA regional budget allocation to NY. The value of Beer's bacterial strains added to the NOBSC will be added as part of the cost-share budget once the final number of strains sent to UGA has been determined. Prof. Beer's program has NY onion stakeholder funding for continuing his assessment of onion genotypes for relative susceptibility and resistance to bacterial pathogens. This work is strongly complementary to the Stop the Rot project, and he will be collaborating with the project team in the development and testing of methods for phenotypic resistance screening in onions. There will be no cost to the Stop the Rot project budget for this. What opportunities for training and professional development has the project provided?STUDENTS The grant has provided the opportunity for several graduate students and post-doctorates to work on different aspects of the project, as described below. Verushka Ibanez, 1st year MSc student at the University of Pretoria, South Africa. Dissertation title: 16S rRNA profiling and functional genomics of onion bulbs displaying symptoms of center rot from Georgia. Advisors: Teresa Coutinho, Pedro Lebre. Expected completion date: December 2021 Christopher Liakos, 1st year MSc student at the University of Pretoria, South Africa. Dissertation title: 16S rRNA profiling and functional genomics of onion bulbs displaying symptoms of center rot from Washington State. Advisors: Teresa Coutinho, Jacquie van der Waals, Pedro Lebre. Expected completion date: December 2021 Tessa Belo joined the Soils & Water program at the Northwestern Washington Research and Extension Center of Washington State University as a MS student in the summer of 2020. She is advised by collaborator LaHue and co-advised by PD du Toit. Her project focus is on combatting bacterial rot in onions through fertilizer and irrigation management. Antoinette Machado started as a MS student at Colorado State University in January 2020, supervised by co-PI Uchanski. Shaun Stice, supervised by co-PI Kvitko, was a PhD student at the University of Georgia at the start of the project period. He has been conducting research on the genetic basis of P. ananatis virulence of onion as well as distribution of identified virulence loci among Pantoea isolates. Dr. Mei Zhao was recruited to co-PD Butta's program at the University of Georgia as a post-doctorate in January 2020, following completion of her PhD at that institution. She is focusing on the bacterial survey, identification and characterization of isolates in GA, and will also assist in greenhouse and field evaluations. Dr. Gaurav Agarwal is a current post-doctoral research associate under PI Dutta who will assist in pathogenomics of Pantoea spp. Dr. Hossein Noorazar is a postdoctorate at Washington State University who is focusing on data analysis and disease risk modeling efforts, supervised by co-collaborators Rajagopalan and Kalyanamaran. His appointment on the project (part time) is expected to start in fall 2020. Hossein will initially focus on getting trained on the hypothesis extraction tools and exploring relevant satellite imagery. PROFESSIONAL DEVELOPMENT In February 2020 a workshop was held at UGA to provide hands-on training for 10 project team members. The training covered basic methods for bacterial isolations from onion tissue, pathogenicity testing and sample processing. How have the results been disseminated to communities of interest?In this reporting period, our focus has been on sharing information and engaging with as many onion growers and industry stakeholders as possible. We have been actively reaching out to growers and stakeholders through different channels (described below) in order to share current scientific understanding of onion bacterial diseases and their management, to understand growers' current state of knowledge about causes and management of bacterial diseases of onion, and to identify priority concerns for the onion industry as regards management of bacterial diseases. By December 2020, we expect to have compiled the results and findings from the first season's bacterial surveys (except potentially for some bulbs in storage in several northern states) and the first season's field trials. We plan to share that information with growers and stakeholders through many of the same channels we have used for communication in this first year, i.e., Alliumnet website content, research summaries, extension bulletins, articles in trade publications and presentations at growers' meetings and field days. REACHING GROWERS AND ONION INDUSTRY STAKEHOLDERS: Outreach to growers and onion industry stakeholders and extension staff at informal meetings, grower meetings, field days and technical workshops has included the following activities: du Toit, Lindsey (2020). Shared information on the Stop the Rot SCRI project with two onion farms in Uvalde, TX on 19 Feb. 2020. Discussed opportunities to engage in the project. 1) Brian King, Dixondale Farms, which produces ~1 billion onion transplants/year for distribution to all 50 states in the USA; 2) Jay Carnes, Wintergarden Produce, which produces short- and medium-daylength, non-storage type onion cultivars. Reitz, Stuart (2020). Provided information on the project at the Idaho-Eastern Oregon Onion Growers' Meeting, Ontario OR, February 5, 2020. Nischwitz, Claudia (2020). Presented information about the project at the Utah Onion Association meeting, February 11, 2020 (Nischwitz, n=40 attendees) Lahue, Gabe (2019). Shared irrigation expertise with onion growers at the WSU Onion Cultivar Field Day, August 29, 2019 (LaHue). Uchanski, Mark (2020). The project was summarized at the Colorado Fruit and Vegetable Growers Association (CFVGA) Produce Day in Greeley, Colorado on Jan. 28, 2020. Grower introductions and recruitment also occurred at CFVGA annual conference Feb. 24-25, 2020 in Denver, CO. Dutta, Bhabesh (2020). Provided updates on onion bacterial disease management options in 5 different county meetings in Georgia, January-March 2020 (n=314 attendees in total) Dutta, Bhabesh (2020). Provided information at county meeting, Orange County NY, on management of bacterial bulb rot with growth-stage targeted copper management in onion (n=40 attendees). Meeting arranged by Cornell University Cooperative Extension. Uchanski, Mark (2020). 06/08/2020, Field visit, Eaton Colorado, with Fagerberg Produce. du Toit, Lindsey (2020). Visited in person or by phone with 12 individual onion growers, agronomists, and field reps in central WA regarding onion bacterial diseases between March and July 2020. Outreach to onion stakeholders and the industry though trade publications and newsletters has included the following informational articles: National Onion Association. 2019. $4M given for onion bacterial disease research. Vegetable Growers News, 11 Sep. 2019. https://vegetablegrowersnews.com/news/onion-researchers-earn-4-million-grant-to-combat-bacterial-disease/ USDA Announces Specialty Crop Award to Combat Onion Diseases. California Garlic & Onion Research Advisory Board News, Fall 2019, p. 4. https://www.cagarlicandonion.com/resources/newsletters/detail/id/17 Keller, Denise. 2019. Stop the rot. Combating onion bacterial diseases. Onion World, November 2019, pp. 24-26. https://issuu.com/columbiamediagroup/docs/onion_world_november_2019 Aegerter, Brenna (2019). Bacterial Bulb Rots of Onion. In: Field Notes newsletter, UCCE San Joaquin County, CA, November 2019 issue (mailed or emailed to 1,029 stakeholders, primarily growers and allied industry members). http://cesanjoaquin.ucanr.edu/newsletters/Field_Notes_Newsletter82270.pdf Thompson, C. 2019. Center rot disease in organic onion growing studied. Vegetable Growers News, November 2019. Arboleda, K. 2019. UGA Researchers working on disease control in Vidalia onions. Vegetable and Specialty Crop News, December 2019. AgNetWest February 2020 issue: Stop the Rot Project to Combat Onion Bacterial Diseases AgNetWest March 2020 issue: Samples Needed to Help 'Stop the Rot' Project In California, a newsletter article was written and one presentation given at a regional onion extension meeting in spring 2020, and a 1-page flyer produced to announce the project and ask that our CA team be alerted to possible bacterial problems in commercial onion fields. Onion World magazine May/June 2020 issue has a short overview of the Stop the Rot project in the report on the Utah growers meeting https://onionworld.net/magazine/ du Toit, Lindsey & Hoepting, Christy (2020). "Stop the Rot: National U.S. Team to Combat Bacterial Diseases of Onion with Fierce Collaboration". Comprehensive article about the project, published in the July/August 2020 issue of Onion World magazine. https://onionworld.net/magazine/ Onion World July/August 2020 issue has a short 'Disease Quiz' submitted by Bhabesh Dutta and Ron Gitaitis to highlight onion bacterial diseases. https://onionworld.net/magazine/ du Toit, L.J., Waters, T., Derie, M., and Darner, J. 2020. Battling onion bacterial diseases with bactericides. Onion World, in press (to be published in the September/October 2020 issue). Outreach to growers and industry stakeholders through the Stop the Rot Stakeholder Advisory Panel: Our 14-member Stakeholder Advisory Panel (SAP) brings a diverse range of expertise and experience to the project. The Panel includes growers, pathologists and onion breeders from onion growing regions across the US. Panel members are active in sharing information about the project to growers and onion industry stakeholders through their own regional and national networks, and in bringing insights and information into the project from their networks. Our first annual meeting/videoconference with the SAP was held on February 3, 2020 in Athens GA. Since then, SAP members have actively participated in our monthly project team meetings by videoconference and they continue to receive project updates, notes from the monthly meetings and our internal project team newsletter. REACHING ACADEMIC RESEARCHERS, EXTENSION PROFESSIONALS AND GRADUATE STUDENTS The project team now includes 25 research collaborators from 12 states, representing all seven major U.S. onion growing regions, as well as onion bacteriologist Prof. Teresa Coutinho from South Africa. Since our first annual in-person meeting in February 2020, we have held monthly team videoconferences to share preliminary results and experiences and discuss recent findings in our Year 1 work. These monthly meetings of 1 to 2 hours have facilitated research and Extension collaboration within the project. Almost all the project collaborators are also involved in extension services and extension education in their regions, which makes for efficient transfer of new information and research results from the team to extension professionals and thence to growers. Technicians and graduate students from each of the regional teams also join our monthly meetings and contribute actively to the discussions, providing feedback on methods and protocols and sharing their latest results with the full team in a collegial setting. What do you plan to do during the next reporting period to accomplish the goals?OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial surveys: The bacterial survey will be repeated in all 12 states. In addition, a directed survey will be completed two crops in each of ID, southern CA, and GA to monitor development of bacteria from asymptomatic plants to development of symptoms, using molecular diagnostic tools developed for Objective A3 during the first year. Selected strains generated from the survey in each state will be shipped to the UGA Athens campus on nutrient agar (NA) stab cultures, re-streaked, characteristics checked, and stored in 15% glycerol at -80oC. Nutrient broth cultures will be used to isolate genomic DNA and for differential virulence phenotyping. Strains will be tested at each of the six regional labs in the team using a red onion scale assay as a high throughput screening for bulb colonization phenotype, with results photographed. Isolates will be compared with a standardized panel of onion bacterial pathogens. Strains will be identified to species using MLSA schemes, and tested for ability to cause symptoms on onion leaves using a 5-day leaf blade inoculation protocol. Metadata and results will be added to the NOBSC database and made available publicly on Alliumnet. A2. Pathogenomic analyses, virulence factors & bacterial community analyses The strains of Pantoea agglomerans added to the expanding NOBSC will be sequenced and examined to identify putative virulence factors associated with the ability to cause diseases on onion (confirmed by pathogenicity tests described for Objective A1. The presence and identification of putative virulence factors will be completed using similar methods to those published by members of this team for identifying virulence factors of the related pathogen, P. ananatis. As described in the work accomplished/initiated in the first year of this project, the asymptomatic and symptomatic bulbs collected from the same field in each of GA and WA are being used to assess the microbial communities associated with symptomatic and healthy bulbs. This will help assess potential interactions among the complex of microflora in onion bulbs that can lead to development of bulb rots. Results of the first year's microbial community analyses will be used to design additional microbial community analysis work to increase our understanding of how non-pathogenic, pathogenic, and opportunistic bacteria and other microflora interact in onion bulbs. A3. Molecular diagnostic tools Recently identified loci of P. ananatis associated with onion virulence were named the HiVir loci and Onion Virulence Regions (OVR) A-D. These will be targets for developing rapid diagnostic markers. The same approach will be used by Dutta, Kvitko, Coutinho, and Woodhall to identify DNA targets in P. ananatis and P. agglomerans strains for developing robust and sensitive Taqman PCR and LAMP assays, i.e., virulence-associated DNA regions of each speciesfor designing primers and probes.The primer/probe sets will be evaluated with additional strains from the NOBSC. The most sensitive and specific (optimized) assays will be subjected to validation according to internationally recognized parameters (EPPO 2014; Roenhorst et al. 2018) using additional strains at UGA and UI-Parma to ensure assays are robust enough for use at all six Regional Labs for this team. Diagnostic tools developed in Year 1 will be tested in directed surveys in Seasons 2 and 3 to monitor P. agglomerans and P. ananatis in crops and bulbs. The tools will enable detailed epidemiological assessment of inoculum sources and development of bacteria on onion plants and other species, including weeds. This will be the foundation to extend the approach to other genera and species of onion bacterial pathogens, which is beyond the timeframe and resources of this project. A4. Phenotypic resistance screening methods Onion breeders from the project team and the Stakeholder Advisory Panel met by videoconference in July 2020 to review preliminary results and plan Year 2 work on developing resistance screening methods. Lab and greenhouse onion phenotyping protocols will be evaluated by Dutta at UGA to screen commercial short-, medium-, and long-day cultivars as well as diverse Allium germplasm from the USDA NPGS. Field phenotypic screening trials will be completed in GA, TX, and WA in Season 2 with pathogens predominant in each state, based on the surveys. Cultivars planted will reflect those suitable to each region as well as germplasm with diverse phenotypic reactions from Season 1 trials. Dr. Beer at Cornell University will do additional phenotypic screening studies in growth chambers to complement the work by Dutta et al. in Georgia as well as field trials under growers' production environments to validate correlation of lab, growth chamber, and greenhouse trials with field trials. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT Lab, greenhouse, and field trials will be continued in Year 2 on irrigation, fertility, pesticide programs, cultural practices, and postharvest practices. Studies have demonstrated these practices to have some influence on bacterial diseases, but they remain to be translated into integrated, practical management tools for regions across the U.S. Specific aspects investigated in each region will be prioritized based on regional practices and constraints, and on stakeholder priorities as well as results from Year 1 of the project. Asymptomatic colonization and symptomatic development of pathogens on plants and stored bulbs will be monitored with isolations onto agar media, use of molecular diagnostic tools, and visual ratings. Standardized protocols will be used to facilitate comparison of results among states, regions, and seasons. Results from Season 1 trials will besharedat the team and SAP meetings to refine research plansfor Season 2. This will be repeated after Season 2 to plan for Season 3 in an iterative approach guided by stakeholders to ensure translation of results into practical tools. Data from NY field trials in Year 1 will be used to inform and validate disease risk models in Year 2. Detailed records on onion production practices, crop microclimate, and bacterial diseases will be sought from growers to assess whether the risks of diseases can be modeled statistically, to predict if a grower should sell bulbs at harvest, or can store bulbs with minimal risk of bacterial rots. ECONOMIC ASSESSMENTS The potential for adoption of management recommendations based on results of trials will be assessed annually by the SAP and stakeholders with economist Colson. Economic analyses will be integrated into various trials based on inputs (expenses) and outputs (marketable yield). OUTREACH AND EXTENSION The redesigned Alliumnet website will be ready by December 2020. Results from Year 1 work will be shared in research summaries; on Alliumnet.com; in project newsletters, trade publications and presentations at growers' meetings and field days. The results of pesticide field trials in this project will be added to information in the current literature survey. The final product is expected to be a quick guide where a grower, Extension Educator or researcher could look up an active ingredient or product and quickly see how it performed in replicated field trials. A 5-minute extension video will be released in November 2020, covering: symptoms caused by different bacterial pathogens in inoculated bulbs and in naturally infected and inoculated onion crops; causes and disease pathways as well as current management options; Stop the Rot project objectives. The video will be shot in the Columbia Basin but will have broad applicability in other onion growing regions. PROJECT MANAGEMENT AND COORDINATION The second annual project team meeting and the Stakeholder Advisory Panel videoconference are scheduled for January 2021.Regular monthly videoconferences for the full team and monthly meetings for the co-PIs will continue in Year 2.
Impacts
What was accomplished under these goals?
OBJECTIVE A: PATHOGENOMICS TOOLS A1. Bacterial disease surveys Onion crop surveys were initiated in all 12 states during this reporting period. In southern states, crops were sampled from December 2019 to July 2020; in northern states, field sampling will be completed by October 2020 and post-harvest surveys by January 2021. In each state, we collect 10 samples from symptomatic onion plants in up to 5 fields, at least twice during the growing season and then again at harvest or in storage. Preliminary survey results in GA indicate seasonal changes in the predominant bacterial genera isolated from onion foliage (January to May 2020). In January and February, the predominant bacterial pathogens isolated were Pseudomonas spp. (P. viridiflava and P. coronafaciens). By March and April, Pantoea was the predominant genus isolated from 64% and 68% of the symptomatic foliage, respectively. When symptomatic onion bulbs in storage were sampled in May and June, Burkholderia spp. (65%), Rahnella spp. (18%), Pantoea spp. (14%) and Enterobacter spp. (3%) were isolated. A2. Onion bacterial pathogenomics We assembled a panel of previously collected Pantoea agglomerans strains associated with onion crops from PA (3 strains); WA (17 strains); GA (11 strains) and additional strains from CO, MI and NY. This strain panel, along with strains collected in Year 1 of the project, will be used for preliminary phenotyping and genotyping for identification of onion-virulence associated traits for P. agglomerans, to compare with onion-virulence genetic traits of P. ananatis identified recently by Kvitko and Dutta. Experiments to investigate the role played by bacterial communities in center rot involve meta-profiling (16S rRNA profiling) of onion bulbs.In GA and WA, nine healthy and nine diseased bulbs were collected from the same field in each state 16s rDNA sequencing was conducted on DNA extracted from these bulbs. Sequencing data are being analyzed by two graduate students in Coutinho's lab. A3. Diagnostic tools First iteration PCR primers were designed to identify the presence of two known P. ananatis virulence factor loci, HiVir and alt. PCR assays using these primers, combined with the red scale necrosis assay, were used to test a collection of Georgia isolates (n=90) and an international collection of Pantoea isolates (n=140) from Co-PI Coutinho. We observed a strong statistical correlation for the presence of alt, which confers tolerance to thiosulfinates, among Pantoea isolates collected from onion vs. non-onion isolation sources. Among P. ananatis isolates there was nearly perfect statistical correlation between positive HiVir PCR assay results and a positive red scale necrosis pathogenicity phenotype. Collaborator Woodhall assembled 20 DNA samples from onion bacterial isolates collected in the Treasure Valley area, to be used for assay validation purposes in Year 2. Methods for sampling and DNA extraction from soil, plant material, seed and water are being evaluated for use in Year 2 and a filter funnel trap was developed for sampling rain and irrigation water. A4. Phenotypic screening methods In GA greenhouse studies, team members evaluated methods of leaf inoculation (cut-tip and foliar spray) on cultivars Vidalia and Sapelo using a highly pathogenic GA strain of P. ananatis, for potential use in phenotypic screening trials. Twelve onion cultivars were selected for a phenotypic resistance screening field trial planted in April 2020 near Pasco, WA. Cultivars are grouped by daylength sensitivity for bulb initiation, so that inoculation can be timed for each of 4 maturity groups. This minimizes the risk of confounding cultivar maturity with susceptibility to bacterial infection at the time of inoculation, which will be important in developing phenotypic resistance screening methods that are valid under field conditions. Plants in the trial plots were inoculated on July 30 and August 13 with a CO2-backpack spray application of Burkholderia gladioli pv. alliicola and P. agglomerans. OBJECTIVE B: ONION BACTERIAL DISEASE MANAGEMENT B1-B5: Influence of onion production practices on bacterial diseases Field trials were established to investigate the influence on onion bacterial diseases of: irrigation practices (WA, CO, OR in progress; GA completed); fertility (WA, NY in progress; GA completed); cultural practices (WA, CO in progress); pesticide programs (CO, UT, WA, NY in progress; GA, TX completed); and postharvest practices (trials in CO, NY, OR, WA will begin in late summer-fall 2020). Field trials have prioritized practices and products currently used by growers, that reflect stakeholder priorities and concerns. When appropriate, inoculated and non-inoculated plots have been included in trials using local bacterial strains to ensure adequate disease pressure for differentiating treatment effects. The WA team is developing bins in which onion bulbs can be enclosed and treated with post-harvest products, to mimic treatments applied in commercial storage units. Preliminary results from GA bactericide trials indicated that the incidence of bulbs with center rot after one month of storage at 4oC was significantly less from plots treated with a copper product (Mankocide, Kocide 3000, Champ, Nordox, Mastercop, or NuCop), compared with plots treated with Oxidate 5.0, Leap, or Actigard (which had similar incidences of bacterial bulb rot as the non-treated check plots). Phytotoxicity to onion foliage was observed in plots treated with Oxidate 5.0 but not in plots with other treatments. B6. Bacterial disease prediction modeling The data modeling team received detailed crop production and disease records from a Columbia Basin farm for the 2017 season. The data will be used to develop and test preliminary bacterial disease risk models. ECONOMIC ASSESSMENTS A baseline grower survey was developed with the project team and the Stakeholder Advisory Panel, to assess onion growers': (a) experience with losses due to bacterial diseases and rots, (b) strategies used to reduce losses, and (c) perceptions of the efficacy of management practices that potentially could reduce losses.The survey is being distributed by project team and SAP members and online through the National Onion Association and other industry communication channels, and will establish a baseline against which to measure the impact of this project on growers' knowledge about bacterial diseases. OUTREACH AND EXTENSION Outreach focused on increasing general awareness of regional bacterial pathogens of onion, through: Newsletters, articles and presentations at grower meetings and conferences; Recruitment of growers in all onion-growing regions of the US to report symptoms of bacterial disease in their crops; A short video "How to Diagnose Onion Bacterial Bulb Rots", at the request of stakeholders (SAP members); A review of published pesticide efficacy trials for control of bacterial diseases of onion across the U.S. (in progress). PROJECT MANAGEMENT AND COORDINATION A fulltime Project Manager (PM) was hired in November 2019 for 4 years, to assist with communication, coordination and budget management. The following meetings were held: The annual team meeting, a training workshop and the annual SAP videoconference in Athens, GA in February 2020; Monthly videoconferences for the project team to share results, discuss progress and plan research. SAP members regularly join our monthly team videoconferences and receive the meeting notes to stay abreast of the team's work. Monthly videoconferences of the PD and co-PIs to discuss research direction and collaboration; Six work sessions on specific research topics, with SAP members participating as subject matter experts.
Publications
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
Arboleda, K. 2019. UGA Researchers working on disease control in Vidalia onions. Vegetable and Specialty Crop News, December 2019.
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
AgNetWest February 2020 issue: Stop the Rot Project to Combat Onion Bacterial Diseases
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
AgNetWest March 2020 issue: Samples Needed to Help Stop the Rot Project
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
USDA Announces Specialty Crop Award to Combat Onion Diseases. California Garlic & Onion Research Advisory Board News, Fall 2019, p. 4. https://www.cagarlicandonion.com/resources/newsletters/detail/id/17
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
Keller, Denise. 2019. Stop the rot. Combating onion bacterial diseases. Onion World, November 2019, pp. 24-26. https://issuu.com/columbiamediagroup/docs/onion_world_november_2019
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
du Toit, Lindsey & Hoepting, Christy. 2020. Stop the Rot: National U.S. Team to Combat Bacterial Diseases of Onion with Fierce Collaboration . Comprehensive article about the project, published in the July/August 2020 issue of Onion World magazine. https://onionworld.net/magazine/
- Type:
Other
Status:
Published
Year Published:
2020
Citation:
Dutta B. and Gitaitis R. 2020. Onion World July/August 2020 Disease Quiz to highlight onion bacterial diseases. https://onionworld.net/magazine/
- Type:
Other
Status:
Awaiting Publication
Year Published:
2020
Citation:
du Toit, L.J., Waters, T., Derie, M., and Darner, J. 2020. Battling onion bacterial diseases with bactericides. Onion World, in press (to be published in the September/October 2020 issue).
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
du Toit, Lindsey (2020). Onion Bacterial Diseases: Knowledge Gaps and a Federal Grant to Stop the Rot. Presentation on February 5, 2020 at University of Wisconsin & WI Potato and Vegetable Growers Association Grower Conference, Stevens Point WI.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Aegerter, Brenna (2020). New Research Project on Bacterial Diseases of Onion. Presentation on February 10, 2020 at California Garlic & Onion Symposium, Tulare CA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Uchanski, Mark (2020). Whats New in CSU Specialty Crops Research? Presentation on January 28, 2020 at Colorado Fruit & Vegetable Growers Association Produce Day, Greeley CO.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
du Toit, Lindsey (2019). Stop the rot: Combating onion bacterial diseases with pathogenomic tools and enhanced management strategies. WSU Onion Cultivar Field Day, 29 Aug. 2019, Connell, WA
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
du Toit, Lindsey (2019). Bacterial rots of onion: USDA SCRI project update and knowledge gaps. Pacific Northwest Vegetable Assoc. Annual Convention & Trade Show, 20-21 Nov. 2019, Kennewick, WA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2019
Citation:
Waters, Tim, and du Toit, Lindsey (2019). Onion bulb crop production and IPM practices. 3-hour workshop on 13 Dec. 2019 to review onion IPM program at CSS Farms, Kahlotus, WA.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
du Toit, Lindsey (2020). Onion fungal and bacterial bulb rots, and efficacious use of fungicides for disease control in onion production. Invited presentation, 5 Feb. 2020, Kennewick, WA
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2020
Citation:
Dutta, Bhabesh (2020). Stop the Rot Research Project on Bacterial Diseases of Onion. Invited presentation at the Annual Meeting of the National Onion Association, August 11, 2020 (virtual meeting).
- Type:
Journal Articles
Status:
Published
Year Published:
2020
Citation:
Stice SP, Thao KK, Khang CH, Baltrus DA, Dutta B, Kvitko BH. Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion. Current Biology 2020;S0960-9822(20)30779-X. doi:10.1016/j.cub.2020.05.092
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
National Onion Association. 2019. $4M given for onion bacterial disease research. Vegetable Growers News, 11 Sep. 2019. https://vegetablegrowersnews.com/news/onion-researchers-earn-4-million-grant-to-combat-bacterial-disease/
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
Aegerter, Brenna (2019). Bacterial Bulb Rots of Onion. In: Field Notes newsletter, UCCE San Joaquin County, CA, November 2019 issue (mailed or emailed to 1,029 stakeholders, primarily growers and allied industry members). http://cesanjoaquin.ucanr.edu/newsletters/Field_Notes_Newsletter82270.pdf
- Type:
Other
Status:
Published
Year Published:
2019
Citation:
Thompson, C. 2019. Center rot disease in organic onion growing studied. Vegetable Growers News, November 2019.
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