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. https://alliumnet.com/wp-content/uploads/2021/09/StoptheRot_Year1_summaries.pdf

Presentations

1. 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 14^th International Conference on Plant Pathogenic Bacteria in Assisi, Italy.
2. 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. 
3. 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

• 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.
• Belo, T., L. du Toit, T. Waters, M. Derie, and G. LaHue. 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

 

Bactericides

• 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
• 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 (PDMR), the American Phytopathological Society (APS), V128.
• 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. 
• 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.
• 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. PDMR 16:V044.
• 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.
• Dutta B. 2021. Evaluation of bactericides and plant defense inducers to manage center rot of onion in Georgia, 2020. Plant Disease Management Reports 15:V027.
• 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.
• Hoepting, C.A., S. K. Caldwell and E. R. van der Heide. 2021. Evaluation of selected pesticides for control of bacterial bulb rot in onion, 2020. Plant Disease Management Reports 15.V108
• Hoepting, C.A., S. K. Caldwell and E. R. van der Heide. 2021. Variety evaluation and effect of copper bactericide on bacterial bulb rot in onion, 2020. Plant Disease Management Reports 15:V107.

 

Cultural practices

• 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.
• 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. 
• 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. PDMR 16:V107.
• 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. PDMR 16:V108.
• Dutta, B., and Tyson, C. 2022. Evaluation of digging methods on post-harvest incidence of external and internal bacterial bulb in onion, Georgia, 2021. PDMR 16:V109.
• Dutta B. 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.
• Dutta B. 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.
• du Toit, L.J.,  M. L. Derie, B. Gundersen. 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.

 

Post-harvest treatments

• 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.
• du Toit, L.J., M. L. Derie, B. Gundersen. 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.

 

Cultivar trials

• 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.
• Mazzone, J.D. and Gugino, B.K. 2022. Evaluation of the susceptibility of thirteen sweet, Spanish onion cultivars to center rot in Pennsylvania, 2015 and 2016. Plant Disease Management Reports 16:V027 

 

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. https://extension.uga.edu/publications/detail.html?number=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. https://mailchi.mp/wsu/wsu-onion-alert-sept1-2021-1305808?e=72ba613792

 

Videos

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. 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 https://pubmed.ncbi.nlm.nih.gov/35442877/
2. 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 (1).  https://doi.org/10.1016/j.syapm.2021.126278
3. 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
4. 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. https://www.researchgate.net/publication/349422413_Identification_of_two_novel_pathovars_of_Pantoea_stewartii_subsp_indologenes_affecting_Allium_sp_and_millets
5. Stumpf, S., Leach, L., Srinivasan, R., Coolong, T., Gitaitis, R., Dutta, B. Foliar chemical protection against Pantoea ananatisin 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/
6. 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 https://doi.org/10.3389/fmicb.2021.00184.
7. 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​
8. 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. https://doi.org/10.1016/j.cub.2020.05.092

 

Popular articles

1. 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: https://onionworld.net/2022/01/26/getting-to-the-root-cause-of-rot/
2. 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: https://issuu.com/columbiamediagroup/docs/onion_world_december_2021?fr=sNDA4ZDI1Mjg1MDI
3. Stop the Rot Halftime Report:  Project update Onion World March/April 2022 (Heather, Lindsey, Christy) https://issuu.com/columbiamediagroup/docs/onion_world_march-april_2022/16
4. 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
5. 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
6. https://issuu.com/columbiamediagroup/docs/onion_world_july-august_2020
7. 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
8. 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.
9. Dutta B. and Gitaitis R. 2020. Onion World July/August 2020 ‘Disease Quiz’ to highlight onion bacterial diseases. https://issuu.com/columbiamediagroup/docs/onion_world_july-august_2020/20

 

Other resources

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.