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Garden Help Desk: What to do about rotting layers in your onions

By USU Extension - | Nov 13, 2021

Courtesy Meredith Seaver

Decaying layers like this can show up in both home grown and store purchased onions. The normal, healthy part of the onion can be used for cooking once the affected layers are trimmed off.

Why do some of my onions get rotten layers on the inside? It’s always on the inside and there are always some layers that look normal. What can I do to protect the rest of my onions? Are the normal layers safe to eat?

This sounds like it could be Botrytis neck rot, a fungal disease, or Bacterial soft rot, another common disease of onions. Both can look similar on the inside of an onion bulb at first. The infections occur during or shortly before harvest, so prevention is the only solution.

With Bacterial soft rot, the infection begins in the garden before harvest. Affected layers show symptoms at the neck of the bulb first and the decay can move down to the base of the layers over time. There may be just one layer, or two or three adjacent layers affected. The decaying layers may also have a bad odor when you cut into the onion.

Even though a Bacterial soft rot infection happens before or while you’re harvesting your onions, you won’t start seeing decayed layers in your onions until the bulbs have been in storage for a while. You may not see any signs of disease until you cut open an infected onion.

The fungus that causes Botrytis neck rot can be in onion seeds, in the soil or carried in the wind. Onion bulbs are at greatest risk of infection during harvest when the bulbs are more likely to be wounded or if onion tops are still green, fleshy and more susceptible to infection. The infected layers may look “watery” at first at the neck of the bulb and then turn brown. The decay will move down through the infected layers until reaching the bottom of the onion bulb. Eventually the layers will dry and turn brown. Onion bulbs with Botrytis neck rot often feel soft at the neck and the entire bulb can feel spongy.

Courtesy Meredith Seaver

Over time, decay caused by Bacterial soft rot or Botrytis can extend to the base of the layers.

If the damage to the onion isn’t too extensive, the decayed portions can be trimmed away and the normal parts can still be used for cooking.

Bacterial soft rot and Botrytis neck rot are two different diseases, one bacterial and the other fungal, but there are some basic things home gardeners can do to reduce the chances of seeing either disease in their stored onions.

  • Rotate your onion plantings from year to year
  • Use disease-free seeds if you start your onions from seed
  • Water deeply, consistently, but not frequently
  • Avoid overhead irrigation and overspray from nearby sprinklers
  • Stop watering when onion tops fall over
  • Lift and loosen your onions from the soil after the top fall over with a spading fork instead of pulling them from the soil by their tops
  • Leave the onions in the garden to dry for a week or two
  • Once the tops are dry, trim them to about an inch or two long
  • Make sure your storage area is cold and has good ventilation
  • Set aside any bulbs that were damaged, blemished or still have some green in their tops and use them first

I noticed a couple of months ago that my Fragrant sumac has some kind of fungus. What can I spray so that the fungus doesn’t come back next year?

Your sumac leaves didn’t have a fungal infection. The bumps on the leaves are galls caused by eriophyid mites. Their feeding and saliva cause the leaves to develop the galls (excess growth). The mites are much smaller than spider mites and you wouldn’t be able to see them without a microscope or a very good hand lens.

There are many different eriophyid mites that can affect plants in our area. For example, the small black spots that you might see on pear leaves are caused by an eriophyid mite called the Pearleaf blister mite, and eriophyid mite activity can cause stunted or deformed petals on some flower species. Eriophyid mites are host-specific, meaning each species of mite feeds only on a certain species or family of plants or a certain part of a plant. Your Fragrant sumac leaf gall mites aren’t going to damage other plants in your landscape.

Courtesy Meredith Seaver

Eriophyid mite feeding caused stunted and missing petals on this echinacea. Promptly removing infested flowers and good fall cleanup can reduce this problem.

Your mites were living inside the galls on the leaves and the galls provided protection from predators and the elements.

Eriophyid mites leave their snug little homes in the fall before the leaves drop and move back onto their host plants for the winter. In the spring when the leaves come out the mites will move back onto the leaves.

Eriophyid mite damage doesn’t generally affect the health of their host plants, so chemical controls aren’t recommended, but an application of dormant oil in the early spring at bud break can reduce their numbers while also protecting beneficial insects.


Eriophyid mites caused the galls on these sumac leaves. Their feeding doesn't affect the health of the sumac.


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