Managing Bacterial Bulb Rot is All About the Neck of the Onion

Single onion plant with 2.5-inch bulb that has been cut longitudinally through the neck and into the bulb. The onion scales are discolored a brownish color in the neck and in inner 3 scales in the upper portion of the bulb.
|
Christy Hoepting, Extension Vegetable Specialist
  • Agriculture
  • Vegetables
The ‘Stop the Rot’ project wrapped up in August 2026 after 6 “rotten” years - lol! It was an ambitious project involving 24 scientists from across the country who set out to research the complete system of bacterial diseases of onion to develop practical, economically sound strategies for pathogen detection and management that will improve profitability and sustainability of onion production. Over these years, we sure did talk a lot about rot! One thing that kept coming up was the neck of the onion. Focusing on the neck part of the onion plant proved to be central to managing bacterial onion bulb rot. This article provides the 6 major take-aways related to neck management and rot prevention.

Bacterial Pathogens Commonly Infect the Neck Region of the Onion Plant

Soilborne bacterial pathogens are splash-dispersed onto onion plants where they usually infect plants in the neck region. If there is moisture in the neck, the pathogen can multiply in the neck tissue and move down the neck into the bulb. Because most bacterial pathogens of onions are “neck-dwellers”, their location makes it difficult for foliar applications of bactericides with contact activity to be effective - the bacteria are protected in the neck. Products with contact activity, including copper bactericides, sanitizers, and biological control products, failed to control bulb rot in 9 “Stop the Rot” field trials in California, Colorado, New York and Washington. The Stop the Rot team does not recommend foliar sprays of copper bactericides, sanitizers, or biological control products to manage bacterial diseases of onion in any region aside from Georgia.

Georgia was the only place where foliar applications of copper bactericides proved effective, providing 77-88% control. Stop the Rot scientists theorized that bactericides were effective in Georgia because the dominant bacterial pathogens in that winter area of production are “leaf-dwellers” located where contact foliar sprays can contact the bacteria. “Leaf-dwelling” Pseudomonas spp. and Pantoea spp. dominated in Georgia onion fields surveyed during the cooler winter months, while in all other major onion growing regions “neck-dwelling” Pantoea spp. and Burkholderia spp. were dominant during the hotter summer months when onions are grown.

Subsequent investigation indicated the most likely reason copper-based bactericides have been ineffective in most onion producing regions is that many of the bacteria in these regions are resistant to copper. Stop the Rot researchers found that 50% of the strains of Pantoea agglomerans from Washington and California and 90% of the tested strains of Burkholderia spp. from New York and have genes that confer resistance to copper. This was confirmed by testing bacterial strains on agar media amended with different concentrations of copper.

Close-up of the inner leaf axil of an onion plant that is no longer putting on new leaves. Black wet soil splashes can be seen in the leaf axils.
Contamination Source

Rain/irrigation water splash disperses soil contaminated with bacteria into the necks of onion plants.

Single onion plant with 2.5-inch bulb that has been cut longitudinally through the neck and into the bulb. The onion scales are discolored a brownish color in the neck and in inner 3 scales in the upper portion of the bulb.
Spreads Down the Neck

Bacteria infect neck tissue and spread down the neck into the bulb.

Close up of a 5-foot section of onion row where 75% of the onion plants are beginning to lodge (tops fall down).
Period of Greatest Vulnerability

Onion crops are highly susceptible to bacterial infection from maximum neck size until the neck is dry.

Protect Late-Stage Standing Onions from Rain Splash

If “rot rain” is in the forecast when at least 80% of the onions in a field have soft necks and the foliage still has some green color (moisture), the field may be rolled gently to lay down any upright plants so that rain cannot splash infested soil into the neck. Stop the Rot studies in New York showed that rolled onions had 35-57% less bulb rot than non-rolled onions. Rolling onions is especially effective when onion plants are “dying standing up”, which happens when thrips or disease has ravaged the foliage to the extent that it does not have enough weight to lodge properly. 

Rolling onions prior to pulling/undercutting is a way of preventing new bacterial infections from occurring. For plants that are infected but the bacterial infection has not yet moved down the neck into the bulb, protecting open necks from collecting water by rolling the tops could avoid the favorable conditions that accelerate progression of bacterial infection into the bulb. For more information on rolling onions, see our video Rolling Onions to Reduce Bacterial Bulb Rot.

Two 4-row beds of onions side-by-side. In the bed on the left, about 60% of the onion tops have fallen over. In the bed on the right, all of the onion tops are laying down.

Onions can be gently rolled (right) to lay down upright onions (left) so that the necks are protected from rain splashing bacteria-contaminated soil into the necks

Dry Neck Tissue is Impassable for Bacterial Infections

Green neck tissue contains moisture, which is critical for the bacteria to multiply and move down the neck into the bulb. Bacteria cannot reproduce or move in dry neck tissue. Topping/harvesting when neck tissue is green (moist) creates a wound that is an “open door” for bacterial infection. The greener the neck tissue at topping/harvesting, the greater the risk of bulb rot. A Stop the Rot study in Washington showed that topping/harvesting onions when the foliage had only 5% green tissue and the necks contained 60% moisture significantly reduced bub rot by 65-89% compared to topping/harvesting onions with 90% green foliage and 90% moisture in the neck.

Ways to Win the “Rot Race”

Dry green necks before the bacteria can multiply in the necks and move into the bulbs.

  1. Pulling/undercutting onions to speed up drying of onion foliage. Ideally, Mother Nature will be kind and deliver warm sunny weather with a light breeze to dry onion foliage rapidly vs. days of rainy weather. Pulling/undercutting onions too early can reduce bulb size and yield.
  2. Avoid late applications of nitrogen (after initiation of bulbing). This promotes vegetative growth and delays maturity, resulting in thick-necked onions that take longer to dry and delays drying into unfavorable late season field conditions.
  3. If neck tissue is green, top onions to leave at least 2-3 inches of neck length. This increases the distance that a bacterial infection at the tip of the topped neck must travel to get to the bulb, which ‘buys time’ for the neck to dry down and become impassable for the bacterial infection to spread into the bulb. Georgia studies showed that leaving necks 2-3 inches long when onions were topped with green necks reduced bulb rot by 36-66% compared to onions that were topped with a neck length of 0-1 inch.
  4. Rolling mature onions to prevent water from pooling in the necks can make conditions less favorable for bacterial infection to spread into the bulb. 
  5. Use heated forced air curing for healthy onions. When onions are harvested with >5% green foliage and >60% neck moisture, they can be cured with heated forced air in a building. Since new bacterial infections can occur at the tips of green necks after topping onions, leaving a 2- to 3-inch-long neck and using postharvest curing can quickly dry down the neck tissue to prevent bacterial infections from entering the bulbs. Only healthy onions should be cured postharvest with heated air, not those already infected in the necks with bacteria because the warm/hot temperatures used for postharvest curing are favorable for bacteria and accelerate movement of bacterial infection from the neck into the bulb.
  6. Skip the disinfectant. Multiple years of trials in Washington and Colorado showed that applying disinfectants like ozone or hydrogen peroxide to onion bulbs in storage does not prevent any latent infections in the bulbs from developing in storage because these products cannot penetrate the outer, dry wrapper scales to the site of infection in the necks or bulbs.

Once bacterial infection has spread into the bulb, there is nothing that can be done. 

Contact Christy Hoepting, Onion Specialist, CCE Cornell Vegetable Program:
(585) 721-6953 cell, cah59 [at] cornell.edu (cah59[at]cornell[dot]edu)

This work is supported by the Stop the Rot: Combating Onion Bacterial Diseases with Pathogenomics Tools and Enhanced Management Strategies, project award no. 2019-51181-30013, from the U.S. Department of Agriculture’s National Institute of Food and Agriculture. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and should not be construed to represent any official USDA or U.S. Government determination or policy.