Agriculture: Onion and Garlic Pest Management Guidelines

Bacterial Bulb Rots

  • Bacterial bulb rots: Burkholderia (=Pseudomonas) cepacia, Burkholderia gladioli pv. allicola, Dickeya (=Erwinia) chrysanthemi, Enterobacter cloacae, Pantoea agglomerans (formerly Erwinia herbicola or Enterobacter agglomerans), Pectobacterium (=Erwinia) carotovorum ssp. carotovorum
  • Symptoms and Signs

    Multiple bacterial pathogens can cause bulb rot in onion and garlic. It is impossible to determine which pathogen is causing the disease based only on visible symptoms. Bulb rot symptoms can develop any time between bulbing and harvest or even during storage. Common bulb rot symptoms include:

    • softening and water-soaking of the bulb tissue
    • yellow to brown discoloration
    • progression of symptoms from the neck to the base of the bulb
    • a neck that becomes soft when pressed.

    Most of the bacterial bulb diseases also cause foliar symptoms. These symptoms distinctly differ from the natural senescence of the oldest leaves on healthy onions that occurs once plants reach mid-bulbing .

    Most commonly, the earliest symptoms of bacterial infection appear as water-soaked lesions on one or more of the younger leaves. The subtle water-soaking develops to a more visible necrotic bleaching of the foliage, and affected leaves may wilt and die back. As lesions progress, they can extend down into the base of the leaves, and then potentially into the neck and the bulb. In the bulb, the bacteria can cause a yellow to brown discoloration of the onion scales or garlic bulb. The bacteria can rot only the center, only the outer scales, or only certain scales. Infected scales can be firm or completely rotten and broken down or mushy.

    In garlic, narrow, water-soaked lesions form on older leaves while young leaves appear healthy. Leaf tips later die and turn white, and plants may be stunted.

    Symptoms of various bacterial bulb rots can be confused with Fusarium basal rot; the difference is that with bacterial bulb rot diseases, the rot progresses from the neck down, while with Fusarium, the rot progresses from the basal plate up. Botrytis neck and bulb rot also rots from the top down, but produces mycelia and sclerotia when conditions are right.

    Comments on the Disease

    Bacterial bulb rots are primarily a problem on onions. Water is essential for entry and spread of the bacteria. When bacteria enter through the neck, they cause internal rot; when bacteria enter the bulb through wounds and dying lower leaves, they cause external rot. The bacterial pathogens are soilborne and may spread through irrigation water or splashing water from rain or irrigation. Most of these pathogens are favored by warm temperatures (over 85°F) and wet conditions.

    Overhead irrigation (especially late in the season), excessive nitrogen fertilization, and the poor or slow curing of the necks also favor the development of this disease.


    Cultural control is critical for preventing bacterial bulb rots. In field trials, chemical control has not been found to be effective in California.

    Cultural Control

    Use the following cultural methods to manage bacterial bulb rots:

    • To reduce the amount of these bacteria in the soil, rotate out of onions or garlic for 2 or more years, and minimize volunteer onions and garlic, and weeds.
    • Use drip or furrow irrigation instead of sprinkler irrigation, if feasible. If sprinklers are used, consider switching from sprinkler irrigation to furrow or drip irrigation once onions start to bulb (when the bulb is about twice the diameter of the neck). Sprinklers increase the movement of bacteria from the soil to the leaves, sometimes by splashing the crop with the soil and its pathogens, and increase the moisture in the neck area, which seems to be critical to development of bulb rot.
    • When feasible, use water from cleaner sources (e.g., well water instead of surface water or reused water).
    • Choose varieties with tight necks because they tend to be less susceptible to several bacterial bulb rots.
    • Apply nitrogen fertilizer only as necessary; avoid excess nitrogen application, especially after bulb initiation.
    • Harvest only after onion tops are well matured (meaning that more than 90% of the tops have lodged) and minimize injury to maturing or harvested bulbs. 
    • Store bulbs at 32 to 36ºF (or 32–34ºF if Burkholderia is detected) with good ventilation to prevent condensation from forming on the bulbs.
    • Avoid wounding bulbs during cultivation or hand hoeing of weeds, and try to minimize bulb damage during harvest and handling as wounds can provide entry sites for bacterial rot pathogens.
    Text Updated: 02/24