Stop the Rot: Publications and Resources

Videos

Videos

Stop the Rot: Optimized Management Practices for Onion Disease

This video summarizes practical options for onion producers to manage bacterial diseases of onion based on results generated over 6 years of research and extension by onion specialists from 12 universities. This ‘Stop the Rot’ project (2019-51181-30013) was funded by the Specialty Crops Research Initiative of the USDA National Institute of Food and Agriculture from 2019-2025 to characterize the bacterial pathogens that affect onion production in the USA and optimize management practices for onion growers and packers. 22 minutes. Posted November 2025. 

Combating Bacterial Disease of Onion: How Do We Stop the Rot?

Bacterial diseases impact onion production across the USA and the world. A wide diversity of bacteria cause diseases of onion. The pathogens are ubiquitous and very difficult to manage. We lack rapid methods of detecting and identifying the pathogens, we have limited understanding of why they cause diseases of onion, there are no highly resistant commercial onion cultivars, and there are no systemic, curative bactericides that are very effective against these pathogens. This $4M ‘Stop the Rot’ project was funded by the Specialty Crops Research Initiative of the USDA National Institute of Food and Agriculture (project 2019-51181-30013), starting in 2019, to characterize bacterial pathogens that affect onions in the USA, and optimize effective management practices for onion growers and packers. The project involved research and extension specialists from 12 universities, with a stakeholder advisory panel of diverse onion stakeholders from across the USA to provide grassroots guidance for the project.

How to Diagnose Onion Bacterial Bulb Rot (English Language Video)

View the different forms of bulb rot caused by bacterial pathogens and how to distinguish bacterial bulb rot from other non-bacterial look-alikes.

Diagnosing onion bacterial rots, produced by the Cornell team – English version.

Cómo diagnosticar La putrefacción Bacteriana de la Cebolla (Español)

Vea las distintas formas de la putrefacción bacteriana y aprenda cómo distinguir de otras enfermedades de las cebollas.

Diagnosing onion bacterial rots, produced by the Cornell team – Spanish version.

How to Identify Foliar Symptoms of Bacterial Diseases in Onion

View the different forms of foliar symptoms of bacterial diseases of onion and how to distinguish bacterial diseases from other non-bacterial lookalikes.

Rolling Onions to Reduce Bacterial Bulb Rot

Learn how onion foliage may be rolled over (about 1-3 weeks prior to pulling/lifting) in order to reduce bacterial bulb rot in onion. 4 min. Christy Hoepting and Sarah Mertson, CCE Cornell Vegetable Program. Posted May 20, 2025

Onion Bacterial Inoculation Workshop

Join “Dr. Death” Mike Derie and Stop the Rot project director Dr. Lindsey du Toit, as they present an informal work session on inoculating onion field trials with pathogenic bacterial strains, to artificially create bacterial disease in the onions. Both presenters share their long combined experience in research trials in eastern Washington State, investigating the most effective management practices for combating bacterial disease in onion crops. The work session was presented to team members, graduate students, and post-doctorates working on the Stop the Rot project.

Red Scale Necrosis Assay Time-Lapse Video

1 min. Claudia Nischwitz. Posted Jan. 20, 2021.

Evaluation of Post-Harvest Treatments on Onion

29 min. Tim Waters and Lindsey du Toit. Posted Dec. 18, 2020

Combatting Onion Bacterial Diseases with Pathogenomics Tools and Enhanced Management Strategies

3 min. Antoinette Machado and Brandon Sandoval. Part of virtual field day. Posted Sep. 1, 2020.

Experimental Design Workshop

In this informal work session, Dr. Lindsey du Toit, Project Director for the Stop the Rot project, shares her 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, and will be of interest to early career researchers as they prepare to run their own field trials.

Grower FAQs about Bacterial Diseases of Onions

Articles

Popular articles

  1. Hoepting, C. A. 2024. How much rot you got? Pre-harvest assessment of bacterial bulb rot in onion and management options. Cornell Cooperative Extension – Cornell Vegetable Program Newsletter, Veg Edge 20(20):6-8.
  2. Neupane, R., Mazzone, J. D. and Gugino, B. K. 2024. Rotten to the Core: The Center Rot Disease of Onion. PennState Extension.
  3. LaHue, G., Belo, T., and du Toit, L. 2023. Cultural management strategies to reduce the risk of onion bacterial diseases. Crops & Soils Magazine September-October 2023:2-8.
  4. Kvitko, B., Hoepting, C., and du Toit, L. 2023. Using DNA evidence to address cases of mistaken identity of bacteria causing onion diseases. Onion World September/October 2023:20-22.
  5. Schwiezer, C. 2023. Onion Field Day. Growers get chance to learn, network with experts. Basin Business Journal 27 Sep. 2023:13-17.
  6. Hoepting, C.A. 2023. The onion rot race. August 30, 2023 Veg Edge, 19(21):7-8.
  7. Hoepting, C.A. 2023. Rolling onions that are “dying standing up” to stop the rot. August 23, 2023 Veg Edge, 19(20):6-7.
  8. Kvitko, B., Dutta, B., Shin, G. Y. 2023. No more crying over rotting onions? Researchers gain insight into bacteria threatening Vidalia onion production. EurekAlert!
  9. Mackay, H., du Toit, L.J. and Hoepting, C. 2023. Stop the Rot – Rollout of research results. Onion World. July/August 2023.
  10. Hoepting, C.A. 2023. Mid-July/early bulbing signals onset of disease in onion. July 13, 2023 Veg Edge, 19(14):4-5.
  11. 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.
  12. Schattenberg, P. 2022. Novel species of pathogenic bacteria of onion identified in Texas. AgriLife Today, May 9, 2022.
  13. 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.
  14. 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.
  15. Waters, T. 2021. Where Were All the Thrips in 2021? Washington State University Extension Onion Alert, 1 September 2021.
  16. LaHue, G. 2021. Two Critical Pieces of the Puzzle: Irrigation & Nitrogen Management Impacts on Bacterial Bulb Rots. Washington State University Extension Onion Alert, 1 September 2021.
  17. 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.
  18. 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.
  19. Belo T., LaHue G.T., du Toit L., and Waters,T. 2021. When to water? How do irrigation frequency and final irrigation timing influence onion bacterial diseases? Onion World Magazine. December 2021. pp. 6 – 8.
  20. 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.
  21. 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.
  22. Nischwitz, C. 2021. Bacterial Bulb Rot Diseases in Utah. Utah Pests Quarterly Newsletter, Vol. 15, Spring 2021.
  23. Dutta, B., and Gitaitis, R.D. 2021. Disease quiz II. Onion World, February 2021:13, 20.
  24. du Toit, L.J., Waters, T., Derie, M., and Darner, J. 2020. Battling onion bacterial diseases with bactericides. Onion World, December 2020:6-11.
  25. 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.
  26. du Toit, L.J. and Hoepting, C. 2020. Stop the Rot: National U.S. Team to Combat Bacterial Diseases of Onion with Fierce Collaboration.  July/August 2020 issue of Onion World magazine.
  27. Dutta B. and Gitaitis R. 2020. ‘Disease Quiz’ to highlight onion bacterial diseases. Onion World, July/August 2020.
  28. Wohleb, C.H., Waters, T.W.,  and du Toit, L.J. 2021. Washington State University Extension Onion Alert, 9 June 2021.
  29. Brian German. 2020. Samples Needed to Help ‘Stop the Rot’ Project. AgNetWest, March 2020.
  30. Brian German. 2020. Stop the Rot Project to Combat Onion Bacterial Diseases. AgNetWest. February 2020.
  31. National Onion Association. 2019. $4M given for onion bacterial disease research. Vegetable Growers News, 11 Sep. 2019.
  32. Keller, D. 2019. Stop the rot. Combating onion bacterial diseases. Onion World, November 2019, pp. 24-26.

Peer-reviewed scientific articles

  1. Shin, Gi Yoon, et al. 2025. Plasmids encode and can mobilize onion pathogenicity in Pantoea agglomerans. The ISME Journal 9.1: wraf019. https://doi.org/10.1093/ismejo/wraf019
  2. Mnguni,F.C., Shin, G.Y., du Toit, L.J., Derie, M.L., Coutinho, T.A. 2025. Ewingella allii sp. nov. isolated from a diseased onion plant in the Columbia Basin of Washington State, USA. Antonie van Leeuwenhoek, 118(8):115. https://doi.org/10.1007/s10482-022-01775-z
  3. Kvitko, B. H., Charkowski, A. O, and Joshi, J. R. 2025. Mechanisms of Enterobacterales Plant Necrotrophy and Host Specificity: Two Types of Bacterial Necrotroph. Annual Review of Phytopathology 63. https://doi.org/10.1146/annurev-phyto-121823-080201
  4. Khanal, M., C.S. Cramer, and S. Malla. 2025. First Report of Serratia sarumanii Causing Plant Disease: A Case from Onion. Plant Disease.  https://doi.org/10.1094/PDIS-08-25-1713-PDN
  5. Khanal, M., B.P. Bhatta, L. Kaur, and S. Malla. 2025. Curtobacterium uvaldense nov., Falsirhodobacter allii sp. nov., Pseudomonas texasensis sp. nov., three novel species, including a pathogen, isolated from onions in Texas, USA. ISJEM. Submitted.
  6. Jordan, S., Pothier, J.F., De Maayer, P., Broders, K., Kvitko, B.H., Coutinho, T.A. and Smits, T.H., 2025. Design of genus-specific semi-nested primers for simple and straightforward identification of Enterobacter strains. BMC Microbiology, 25(1), p.456. https://doi.org/10.1186/s12866-025-04175-1.
  7. Neupane, R., Mazzone, J., Hoepting, C., and Gugino, B. 2025. A three-year bacterial survey of onion fields across Pennsylvania and New York.  Plant Disease Progress, online: 29 July 2025. https://doi.org/10.1094/PHP-03-25-0094-S.
  8. Neupane, R., Gugino, B., and Roman-Reyna, V. 2025. Identification of a Burkholderia Species Causing Onion Bulb Rot Disease. Plant Disease: https://doi.org/10.1094/PDIS-12-24-2675-SC.
  9. Wilson R., Aegerter B., and LaHue, G. T. 2024. The influence of sprinkler and drip irrigation on the incidence and severity of bacterial disease in onions grown in northeast California. Plant Health Progress 25:293-298. https://doi.org/10.1094/PHP-01-24-0002-RS.
  10. Paudel, S., Zhao, M., Dutta, B., and Kvitko, B. 2024. Thiosulfinate tolerance gene clusters are common features of Burkholderia onion pathogens. Mol. Plant Microbe Interact. 37:507-519. https://doi.org/10.1094/MPMI-01-24-0005-R.
  11. Liakos, C., Ibanez, V., Lebre, P. H., Derie, M. L, van der Waals, J., du Toit,L., Dutta, B., Kvitko, B., Cowan D.A., and Coutinho, T. A. 2024. The bacterial and viral communities associated with onion bacterial bulb rot. Phytobiomes Journal: in press, PBIOMES-11. https://doi.org/10.1094/PBIOMES-11-23-0121-R.
  12. 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.
  13. 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. https://doi.org/10.1094/MPMI-11-22-0246-R.
  14. 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 Allium fistulosum × Allium cepa Front. Microbiol. 13:1094155. https://doi.org/10.3389/fmicb.2022.1094155.
  15. LaHue, G., Belo, T., and du Toit, L. 2023. Cultural management strategies to reduce the risk of onion bacterial diseases. Crops & Soils Magazine September-October 2023:2-8. https://doi.org/10.1002/crso.20305.
  16. Koirala, S., Myers, B., Shin, G. Y., Gitaitis, R., Kvitko, B. H., and Dutta, B. 2023. Evaluating options to increase the efficacy of biocontrol agents for the management of Pantoea under field conditions. Plant Disease 107:2701-2708. https://doi.org/10.1094/PDIS-11-22-2710-RE.
  17. Khanal M., Bhatta, B. P., 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 Disease 107:1721-1729. https://doi.org/10.1094/PDIS-09-22-2206-SR.
  18. 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.
  19. 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.
  20. 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. https://doi.org/10.3389/fmicb.2022.1054813.
  21. Zhao, M., Tyson, C., Chen, H.C., Paudel, S., Gitaitis, R., Kvitko, B., and Dutta,B. 2022. Pseudomonas alliivorans 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.
  22. Shin, G.Y., Smith, A., Coutinho, T.A., Dutta, B., and Kvitko, B. 2022. Validation of species-specific PCR assays for the detection of Pantoea ananatis, agglomerans, P. allii and P. stewartii. (2022) Plant Disease. https://doi.org/10.1094/PDIS-08-21-1810-SC.
  23. 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. Int. J. Syst. Evol. Microbiol. 72:005311. https://doi.org/10.1099/ijsem.0.005311.
  24. Khanal, M., B.P. Bhatta, S. Timilsina, S. Ghimire, K. Cochran, and Malla, S. 2022. Curtobacterium allii nov., the actinobacteria species causing onion bulb disease. Antonie van Leeuwenhoek, 116:83-96. https://doi.org/10.1007/s10482-022-01775-z.
  25. Zhao, M., Kvitko, B.H., Gitaitis, R.D., and Dutta, B. 2021. Bacterial streak and bulb rot of onion. Plant Health Instructor. https://doi.org/10.1094/PHI-E-2021-0421-01.
  26. Stumpf, S., Leach, L., Srinivasan, R., Coolong, T., Gitaitis, R., and Dutta, B. 2021. 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/.
  27. 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.
  28. Koirala, S., Zhao, M., Agarwal, G., Stice, S., Gitaitis, R., Kvitko, B., and 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.
  29. Agarwal, G., Choudhary, D., Stice, S. P., Myers, B.K., Gitaitis, R.D., Venter, S.N., Kvitko,B.H., and Dutta, B. 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.
  30. Stice SP, Thao KK, Khang CH, Baltrus DA, Dutta B, and Kvitko BH. 2020. Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion. Current Biology 2020;S0960-9822(20)30779-X. https://doi.org/10.1016/j.cub.2020.05.092.

Plant Disease Management Reports

Irrigation and nitrogen management

Bactericides

Cultural practices

Presentations

Project Overview Oral Presentation Slides

  1. du Toit, L.J. 2025. Bacterial bulb rot management in onion. Invited presentation at 2025 California Garlic and Onion Symposium, 10 Feb. 2025, Tulare, CA.
  2. du Toit, L.J., Aegerter, B., Colson, C., Coutinho, T., Cramer, C., Dutta, B., Gugino, B., Hoepting, C., Kvitko, B., LaHue, G., Malla, S., Nischwitz, C., Reitz, S., Sidhu, J., Uchanski, M., Waters, T., Wilson, R., and Woodhall, J. 2025. From diagnostics to field and storage practices: Developing tools to manage onion bacterial diseases. National Allium Research Conference and National Onion Association Meeting, 1-5 Dec. 2025, Kaua’i, HI.
  3. du Toit, L.J. 2024. Stop the Rot: 2023-24 Trial results for Columbia Basin onion growers. Invited presentation, Onion Session, Pacific Northwest Vegetable Association Annual Convention & Trade Show, 13-14 Nov. 2024, Kennewick, WA.
  4. du Toit, L.J. 2024. Stop the Rot: Overview of the national onion bacterial project. Invited presentation, Onion Session, Pacific Northwest Vegetable Association Annual Convention & Trade Show, 13-14 Nov. 2024, Kennewick, WA. 
  5. du Toit, L. & Waters, T. (2023). Stop the Rot: Relevant Grower Results. Pacific Northwest Vegetable Association Meeting, Kennewick, WA, 15-16 November 2023. Oral presentation slides about Stop the Rot objectives and results summaries.
  6. du Toit, L. (2023). ‘Stop the Rot’ and Other Select Onion Research Projects at WSU. AUSVEG, HortInnovation, & SARDI Onion Growers’ Meeting, Murray Bridge, South Australia, 27 November 2023. Oral presentation slides discussing research projects and results.
  7. du Toit, L., et al. (2023). Stop the Rot: Combating Onion Bacterial Diseases with Pathogenomic Tools and Enhanced Management Strategies. International Congress of Plant Pathology, Lyon, France, 21-25 August 2023. Oral flash presentation slides summarizing the Stop the Rot project and enhanced management strategies.
  8. du Toit, L. (2023). Stop the Rot: A National Perspective on Bacterial Diseases of Onion. Southeast Regional Fruit and Vegetable Conference, Savannah, GA, 5-7 January 2023. Stop the Rot: A National Perspective on Bacterial Diseases of Onion.
  9. November 2021. du Toit, L.J. 2021. Stop the Rot: How can the results benefit you? Pacific Northwest Vegetable Association Annual Convention & Trade Show, 17-18 Nov. 2021, Kennewick, WA. Presentation to growers and onion stakeholders, providing an overview of what we are learning in the project at the halfway mark in our research.

Oral Presentation Slides

  1. Hoepting, C. 2023. Rolling Onions that are “Dying Standing Up” to Stop the Rot. National Allium Research Conference, Dec. 29-Nov. 2, 2023, San Antonio, TX.
  2. Derie, M., Aegerter, B., Colson, G., Coutinho, T., Cramer, C., Dutta, B., Gugino, B., Hoepting, C., Kvitko, B., LaHue, G., MacKay, H., Malla, S., Nischwitz, C., Shin, G., Uchanksi, M., Waters, T,, Woodhall, J., and du Toit, L. Progress at Combating Onion Bacterial Diseases with Pathogenomics Tools and Enhanced Management Strategies National Allium Research Conference, Dec. 29-Nov. 2, 2023, San Antonio, TX.

Posters

Related Resources

Extension Bulletins

  1. 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
  2. Dutta, B., and Gitaitis, R. 2020. Bacterial diseases of onion in Georgia. University of Georgia Cooperative Extension Bulletin B1534. https://extension.uga.edu/publications/detail.html?number=B1534

Related resources

Read about other new findings on managing onion bacterial diseases

  • Shock, C. C., Feibert, E. B. G., Rivera, A., and Wieland, K. D. 2022. Onion yield and internal quality increased by straw mulch and reduced by artificial heat, but not affected by kaolin particle film. HortSci. 57(11):1480-1486. https://doi.org/10.21273/HORTSCI16829-22

Other resources

Final report to NIFA

Year 5 annual project report to NIFA

Year 4 annual project report to NIFA

Year 3 annual project report to NIFA

Year 2 annual project report to NIFA

Stop the Rot Project Charter: Collaborative Agreement. Topics covered include principles for collaboration, project team organization and management, internal review and accountability, data management and confidentiality, authorship and acknowledgment, and conflicts of interest.

Stakeholder Meetings

2024 Stakeholder Advisory Panel Updates – March 27, 2024