Agriculture: Onion and Garlic Pest Management Guidelines

Bacterial Bulb Diseases

  • Center rot: Pantoea agglomerans (Erwinia herbicola or Enterobacter agglomerans)
  • Enterobacter Bulb Decay: Enterobacter cloacae
  • Slippery skin: Burkholderia gladioli pv. allicola
  • Soft Rots: Dickeya (=Erwinia) chrysanthemi, Bacillus cereus, Klebsiella sp., Lactobacillus sp., Pectobacterium (=Erwinia) carotovorum ssp. carotovorum
  • Sour skin: Burkholderia (Pseudomonas) cepacia
  • Symptoms and Signs

    In onion and garlic, bacterial diseases cause bulb rot, which develops any time between preharvest and 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
    • the neck becomes soft when pressed.

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

    Foliar symptoms Bulb symptoms
    Center rot


    • One or more of the younger leaves have yellow flagging.
    • Tan-to-dark green, water-soaked lesions on infected leaves.
    • Leaves wilt and die back.
    • Scapes become weak and collapse.


    • Narrow, water-soaked lesions form on older leaves while young leaves appear healthy.
    • Leaf tips later die and turn white.
    • Plants may be stunted.
    Individual infected scales within the bulb are discolored or rotten, while the adjacent scales remain healthy.
    Enterobacter bulb decay Water-soaked lesions on leaves. Individual infected scales within the bulb are discolored or rotten while adjacent scales remain healthy.
    Slippery skin
    • One or two leaves near the center of the plant wilt, turn yellow, die back at the tips.
    • Other leaves appear healthy.
    • Scales in or near the center of the bulb rot.
    • In severe infections, squeezing the neck causes the inner scales to slip out.
    Soft rots
    • Water-soaked areas on leaves.
    • Eventually leaves turn mushy
    • Rot begins in the inner scales, and eventually the entire bulb turns into a soft, watery rot.
    • Infected bulbs have a pungent smell.
    Sour skin
    • Individual infected scales within the bulb are discolored or rotten while adjacent scales remain healthy.
    • Cutting a cross-section of the bulb reveals a tan-colored, slimy ring.
    • Infected bulbs smell foul.

    Comments on the Disease

    These diseases are primarily a problem on onions. Water is essential for entry and spread of the bacteria. Bacteria enter the bulb through wounds and dying lower leaves. The 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.

    Soft rots generally appear just before or at harvest, or during storage.

    Center rot initially affects aboveground tissues but causes bulb rot if the crop is infected late in the season.

    Sour skin occurs on both onion and garlic but usually is only a concern on onion. The bacteria enter the crop through wounds and water-soaked tissue. Once in a leaf, bacteria continue to grow down the blade into the bulb. 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 controls are critical for preventing these diseases. Preventive applications of copper can reduce their development under conditions that favor the diseases, but no pesticides are effective after they have developed.

    Cultural Control

    Use the following cultural methods to manage bacterial diseases:

    • To reduce the amount of these bacteria in the soil, rotate to a nonhost (such as small grains, corn, cotton, or safflower) for 2 or more years, and eliminate volunteer onions and weeds.
    • Use drip or furrow irrigation instead of sprinkler irrigation, if feasible. If sprinklers must be used, switch from sprinkler irrigation to furrow or drip irrigation once onions start to bulb (when the bulb is about twice the diameter of the neck).
    • Choose varieties with tight necks. These are often less susceptible to several bacterial bulb diseases, especially soft rots and sour skin.
    • Apply nitrogen fertilizer only as necessary; avoid excess nitrogen application.
    • Plant seed and transplants that are pathogen-free.
      • Purchase seed from reputable suppliers.
      • Inform seed suppliers if seeds test positive for seedborne pathogens.
    • 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. If these diseases are detected, consider harvesting early.
    • Store bulbs at 32 to 36ºF (32–34ºF for sour skin) with good ventilation to prevent condensation from forming on the bulbs.
    • Handle bulbs carefully to avoid wounding and prevent entry sites for the pathogens, especially prior to harvest.
    • Use good sanitation during both the growing season and harvest.

    Chemical Control

    For most bacterial bulb diseases, pesticide applications are not necessary if the proper cultural methods are used.

    Apply a copper bactericide soon after a large-scale wounding event such as hail or high winds, or if there is a risk that the necks will get very wet when the crop reaches full maturity and the necks are at their maximum size (2–4 weeks before harvest). Copper bactericides are only effective as a preventive application; applications are ineffective after symptoms develop.

    Common name Amount per acre REI‡ PHI‡
    (Example trade name) (hours) (days)
    Not all registered pesticides are listed. The following are ranked with the pesticides having the greatest IPM value listed first—the most effective and least likely to cause resistance are at the top of the table. When choosing a pesticide, consider information relating the pesticide's properties and application timing, honey bees, and environmental impact. Always read the label of the product being used.
      (Basic Copper 53)# Label rates See label 0
      MODE-OF-ACTION GROUP NAME (NUMBER1): Multisite contact (M1)
      COMMENTS: Repeat applications at 7- to 14-day intervals, if necessary, to maintain control. Not all copper compounds are approved for use in organic production, so be sure to check individual products. Basic Copper 53 is allowed with restrictions in organically certified crop. OMRI certification expires December 31, 2019; after this date, check organic status before applying in organic onion or garlic production.
      (Kocide 2000) 0.75–1.5 lb 48 0
      MODE-OF-ACTION GROUP NAME (NUMBER1): Multisite contact (M1)
      COMMENTS: Labeled for onion, garlic and leek. Can cause phytotoxicity to leaves (see Special Precautions on label).
    Restricted entry interval (REI) is the number of hours (unless otherwise noted) from treatment until the treated area can be safely entered without protective clothing. Preharvest interval (PHI) is the number of days from treatment until the harvest may take place. In some cases, the REI exceeds the PHI. The longer of these two intervals is the minimum time that must elapse before harvest.
    1 Group numbers are assigned by the Fungicide Resistance Action Committee (FRAC) according to different modes of action. Fungicides with a different group number are suitable to alternate in a resistance management program. In California, make no more than one application of fungicides with mode-of-action group numbers 1, 4, 7, 9, 11, or 17 before rotating to a fungicide with a different mode-of-action group number; for fungicides with other group numbers, make no more than two consecutive applications before rotating to fungicide with a different group number.
    # Acceptable for use on organically grown produce.
    Text Updated: 02/19
    Treatment Table Updated: 02/19