Stop the Rot: Publications and Resources

Technical Reports

  1. Stop the Rot Collated Summaries of Year 1 Technical Reports. Compilation of the final Year 1 topic summaries, August 2021.



  1. 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
  2. July 2022. MacKay et al.  Combating Onion Bacterial Diseases with Pathogenomics Tools and Enhanced Management Strategies: Research Objectives and Progress Towards Reducing Crop Losses. Poster presented at the 14th International Conference on Plant Pathogenic Bacteria in Assisi, Italy.
  3. 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. 
  4. Belo, T., du Toit, L., Waters, T., Derie, M., Schacht, B., & LaHue, G. (2021, 7-10 November). Combating Onion Bacterial Diseases Through Nitrogen Fertility Management [Poster Presentation]. 2021 ASA, CSSA, SSSA International Annual Meeting, Salt Lake City, UT. Poster presentation by Stop the Rot researcher Tessa Belo summarizing Season 1 trials on the effectiveness of nitrogen fertility management strategies for combating onion bacterial disease.




Plant Disease Management Reports

Irrigation and nitrogen management




Cultural practices

Post-harvest treatments


Cultivar trials


Extension Bulletins and Educational Materials

  1. Dutta, B., and Gitaitis, R. 2020. Bacterial diseases of onion in Georgia. University of Georgia Cooperative Extension Bulletin B1534.
  2. Wohleb, C.H., Waters, T.W., du Toit, L.J., and LaHue, G. 2021. Washington State University Extension Onion Alert, 1 September 2021.



  1. 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.
  2. 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.
  3. Red Scale Necrosis Assay time-lapse video. 1 min. Claudia Nischwitz. Posted Jan. 20, 2021.
  4. Evaluation of post-harvest treatments on onion. 29 min. Tim Waters and Lindsey du Toit. Posted Dec. 18, 2020.
  5. Combating bacterial diseases of onion: How do we stop the rot? 14.41 min. Lindsey du Toit, Heather MacKay, Darrell Kilgore, and Matthew Ziegler. Posted Dec. 15, 2020. (1,613 views).
  6. Diagnosing onion bacterial rots, produced by the Cornell team. English Spanish
  7. Combating 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.


Peer-reviewed scientific articles

  1. Belo, T., du Toit, L. J., and LaHue, G. 2023. Reducing the risk of onion bacterial diseases: A review of cultural management strategies. Agronomy Journal 115:459-473
  2. 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.
  3. Zhao, M., Shin, G.-Y., Stice, S., Bown, J. L., Coutinho, T., Metcalf, W. W., Gitaitis, R., Kvitko, B., and Dutta, B. 2023. A novel biosynthetic gene cluster across the Pantoea species complex is important for pathogenicity in onion. MPMI 36(3):176-188.
  4. Khanal, M., Timilsina, S., Bhatta, B. P., Bophela, K., Coutinho, T., Cochran, K., and Malla, S.. 2022. Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot. Int. J. Syst. Evol. Microbiol. 72:005311. DOI 10.1099/ijsem.0.005311
  5. Zhao, M., Tyson, C., Chen, H., C., Paudel, S., Gitaitis, R., Kvitko, B., Dutta, B. 2022. Pseudomonas alliivorans sp. nov., a plant-pathogenic bacterium isolated from onion foliage in Georgia, USA. Systematic and Applied Microbiology, Vol. 45.
  6. Gaurav, A., Divya, C., Stice, S. P., Myers, B. K., Gitaitis, R. D., Venter, S. N., Kvitko, B. H., Dutta, B. 2021. Pan-genome-wide analysis of Pantoea ananatis identified genes linked to pathogenicity in onion. Frontiers in Microbiology vol 12:2381
  7. Koirala, S., Zhao, M., Agarwal, G., Stice, S., Gitaitis, R., Kvitko, B., & Dutta, B. 2021. Identification of two novel pathovars of Pantoea stewartii indologenes affecting Allium sp. and millets. Phytopathology. 10.1094/PHYTO-11-20-0508-R.
  8. Stumpf, S., Leach, L., Srinivasan, R., Coolong, T., Gitaitis, R., Dutta, B. Foliar chemical protection against Pantoea ananatisin onion is negated by thrips feeding. 2021 Phytopathology. 111(2):258-267. doi: 10.1094/PHYTO-05-20-0163-R. Epub 2021 Jan 13. PMID: 32748732.
  9. 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 Frontiers in Plant Science
  10. Zhao, M., Kvitko, B. H., Gitaitis, R. D., and Dutta, B. 2021. Bacterial streak and bulb rot of onion. Plant Health Instructor.  DOI: 1094/PHI-E​​-2021-0421-01​
  11. Stice, S. P., Thao, K. K., Khang, C. H., Baltrus, D. A., Dutta, B., Kvitko, B. H. 2020. Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion. Current Biology;S0960-9822(20)30779-X.


Popular articles

  1. No more crying over rotting onions? Researchers gain insight into bacteria threatening Vidalia onion production. EurekAlert! June 2023. (Brian Kvikto, Bhabesh Dutta, Gi Yoon (Gina) Shin)
  2. McKay, H., du Toit, L., and Hoepting, C. 2023. Stop the Rot project update: Get ready for a roll out of research results. Onion World July/August 2023:6-7.
  3. Bhabesh’s group submitted an article to Onion World that just came out (January 2022), summarizing their work in GA for the Stop the Rot project:
  4. 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. Dec. pp. 6 – 8. Available from:
  5. Stop the Rot Halftime Report:  Project update Onion World March/April 2022 (Heather, Lindsey, Christy)
  6. 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. Onion World Magazine July/August 2021
  7. 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.
  9. du Toit, L.J., Waters, T., Derie, M., and Darner, J. 2020. Battling onion bacterial diseases with bactericides. Onion World, December 2020: 6-11.
  10. Hoepting, C., and du Toit, L. 2020. Stop the Rot! National U.S. team to combat bacterial diseases of onion with fierce collaboration. Onion World, July/August 2020: 8-11.
  11. Dutta B. and Gitaitis R. 2020. Onion World July/August 2020 ‘Disease Quiz’ to highlight onion bacterial diseases.


Additional research news and information

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.


Other resources

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.