What Is Onion Soft Rot – Learn About Soft Rot In Onions


By: Mary Ellen Ellis

An onion with bacterial soft rot is a squishy, brown mess and not something you want to eat. This infection can be managed and even completely avoided with good care and cultural practices, but once you see the signs of it, treatment is not effective.

What is Onion Soft Rot?

Soft rot in onions is a common disease caused by several types of bacteria. It most commonly affects onions while they are being stored, but contamination or the damage that leads to contamination often occurs during or around harvest. The disease can cause a lot of destruction and significantly diminish yields.

Bacterial soft rot infections strike already mature onions. The signs of onion soft rot start with softness at the neck of the bulb. As the infection creeps in, the onion will appear water soaked. Then, one or more scales in the bulb will become soft and brown. If you squeeze an infected bulb, it will emit a watery, smelly substance.

How Onion Bacterial Soft Rot Spreads

Onions become infected with soft rot bacteria through soil, water, and infected plant debris. The infection gets into bulbs through wounds and damage. The infection is most likely to take hold during warm and humid conditions.

Any damage to leaves or bulbs can cause the infection to get in, including hail and rain damage, sun damage, freezing, bruising, and cutting the tops of the bulbs during harvesting. Damage while the bulb is still in the ground, and after it has been harvested, can lead to infection.

A pest called onion maggot can also spread the disease between plants.

Managing Soft Rot in Onions

Once the disease has set in, there is no treatment that will save a bulb, although it tends to infect just one or two scales. You can prevent infection in several ways, though:

  • Avoid overwatering your onion plants, especially when it is hot out.
  • Make sure your onions are planted in ground that drains well and that you give them space for airflow and to dry out between waterings.
  • Avoid damage to the entire plant while the bulb is developing.
  • Handle harvested bulbs gently to avoid bruising and other types of damage that can lead to infection during storage.
  • Make sure the onion is fully mature before you harvest it; the drier the tops are, the more protected the bulb is from infection.
  • If your onions do get damaged, like after a big storm, you can spray the damaged areas with a copper-based spray to protect against infection.

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Texas Plant Disease Handbook

Allium cepa

Black Mold: (fungus – Aspergillus niger) Black mold is generally a post-harvest disease, although it may be seen on mature onions in the field. The disease can be recognized by the presence of black powdery spore masses of the fungus on the outer scales. High temperatures (85oF-95oF) and moisture favor disease development. Bulbs should be protected from moisture during harvesting and shipping.

Botrytis Leaf Blight/Blast (fungi – Botrytis allii, B.squamosa, and B. cinerea): Botrytis leaf blight or blast occurs sporadically in Texas, usually early in the season. Several species of Botrytis infect onion. Seedlings may be infected (See Photo). Neck rot is caused by B. allii, leaf fleck is caused by B. cinerea, and leaf blight is caused by B. squamosa. White flecks are found along the length of the leaf (See Photo) and usually have greenish halos. With numerous flecks, the tip of the leaf may die. Non-pathogenic causes of flecks can include: cold rain, sleet, and sandblasting. Fungicides used to control purple blotch will also control Botrytis leaf blight.

Downy Mildew (fungus – Peronospora destructor): Downy mildew is an occasional disease of onion in the Lower Rio Grande Valley of Texas. Symptoms consist of white to light green spots on leaves, which later darken. A fuzzy, gray growth is seen on the leaf surface, particularly during periods of high humidity (See Photo). Lesions enlarge and leaf tissue dies. Lesions may resemble those caused by the purple blotch fungus. Fields should be monitored closely, particularly during prolonged cold, wet weather, when the disease is more likely to occur. Fungicides that are highly effective against downy mildew, such as Ridomil and Aliette, should be applied following the first report of downy mildew in the growing area.

Fusarium Basal Plate Rot (fungus – Fusarium oxysporum f. sp. cepae): The disease develops at the base of the bulb, causing it to become soft. A semi-watery decay progresses from the base of the scales upward (See Photo). The disease may not be noticed until after harvest, when the entire bulb is destroyed. The fungus is soilborne and enters the bulb through wounds, insect injuries or through root scars at the base. High soil temperatures (77oF – 82oF) favor disease development. Losses can be reduced with a 4-year rotation out of onions. Cultivars can also vary in resistance.

Leaf Variegation (Chimera): The leaves have distinct yellow or white longitudinal segments (See Photo). Affected plants occur very infrequently. This is a genetic abnormality.

Mushy Rot (fungus – Rhizopus spp.): Bulbs have soft areas around the neck. In the neck area, there is a white fuzzy growth with black speckling. This is a post-harvest problem that occurs when onions that are not properly cured or stored are transported at high temperatures.

Neck Rot (fungus – Botrytis allii, Botrytis sp.): This disease is frequently not noticed in the field because damage usually occurs during transit and storage. Diseased tissue at the base of the crown becomes sunken and watersoaked in appearance. A gray fungal growth later forms on the surface (See Photo), which can be followed by other fungi and bacteria, causing decay. Small, black-resting bodies (sclerotia) can sometimes be found on scales. Careful handling of the crop at harvest and prompt drying of onions with heat and air ventilation are the best means of controlling this disease.

Pink Root (fungus – Phoma terrestris): Pink root is a soilborne disease that affects roots. Diseased roots turn pink, shrivel and die (See Photo). As the plant sends out new roots, they also become infected and die. Affected plants do not usually die, although they may develop tip blight. Severe infection will reduce bulb size. The fungus can be introduced to a field by using transplants grown in infested soil. Once a field becomes infested, the fungus remains in the soil for many years. Soil fumigation has been shown to be an effective, but expensive, control measure. Resistant onion cultivars are one management approach, as is a long rotation out of onions.

Powdery mildew (fungus – Leveillula taurica): Powdery mildew occurs rarely in the Lower Rio Grande Valley of Texas. The earliest symptom is a pale discoloration of the leaf. Circular spots with white, powdery growth eventually occur. There are no control recommendations, since the disease is not a serious problem.

Purple Blotch (fungus – Alternaria porri): The fungus usually infects dead or dying leaf tissue. The first symptoms are small, white, sunken lesions. These lesions develop purple centers and enlarge (See Photo). The infection can encompass much of the leaf, leading to the death of tissue above the lesion (See Photo). The disease can be controlled with fungicides. In the Rio Grande Valley of Texas, the need to apply fungicides can be determined by monitoring leaf wetness during the growing season. Leaf wetness occurs as the result of dew, fog or rain. The action threshold is 12 hours of continuous leaf wetness.

Pythium Root Rot (fungus – Pythium sp.): This disease is most serious with young plants growing under conditions of high soil moisture and cool temperatures. Infected roots become water-soaked and flimsy (See Photo). Not all of the roots of the plant become infected (See Photo). The plants will not usually die, but severe infection can result in small bulbs. The loss of a substantial amount of roots will lead to tip dieback. Planting on raised beds will minimize the impact of this disease.

Soft Rot (bacteria – Erwinia carotovora subsp. carotovora and other species): Soft rot is one of the more prevalent causes of loss in storage onions. The soft rot bacterium can enter the neck tissues as plants approach maturity. In the field, plants wilt and die (See Photo). As the rot progresses, invaded scales become soft and foul-smelling. Onions with mechanical injuries, sunscald, or bruises are particularly susceptible to bacterial soft rot, especially if they have been held under warm, humid conditions.

Stemphyllium Blight (fungus – Stemphyllium vesicarium): Lesions are initially light yellow to brown and water-soaked. They elongate, often reaching the leaf tips, and become dark brown to black. The disease can become serious following periods of more than 24 hours of rainy weather. Fungicides used to control purple blotch will also control this disease.

Tip Blight (several causes): Infection by several species of fungi infecting leaves or roots can result in tip dieback. There can also be many non-pathogenic causes. These include: overcrowding, insect injury (particularly thrips and leaf miners), drought or salt stress, wind dessication, and occasionally, damage by ozone gas produced by lightning during severe thunderstorms.

Bacterial Blight (bacterium – Xanthomonas axonopodis pv. allii): This disease is not common in Texas. The symptoms are elongated chlorotic areas on one side of the leaf. These areas become sunken, water soaked and necrotic. Eventually, the leaf dies. The pathogen is seed borne, but could spread within a field following rain or overhead irrigation. Disease development is favored by temperatures greater than 68°F. There are no control recommendations.


What I Did

The first year I encountered the problem,

  • I checked my onions at least every other day. (Being on top of what’s happening is one of the most important things you can do.)
  • When I found an onion that didn’t look just right — I pulled it up.
  • All infected onions where taken off of my property in a plastic bag and discarded.

I may have lost 50 onions to this disease.

The second year I was on the look out and sure enough I again found this to be a problem.

I ordered a fungicide approved for use in organic gardens and sprayed my onions. Directions said to begin spraying two weeks after planting. My onions had already been in the ground two months. According to directions you are then to spray every 7 to 14 days through the growing season. I sprayed only twice.

A reader commented below — why would anyone use a fungicide for a bacterial problem!? – Great question!

At the time I knew even less about disease problems than I know now. My garden is healthy so I never have gotten into diseases. And even though it would seem common sense that one could not “fix” a bacterial problem with a fungal spray – the spray I used was the organic spray recommended for what sounded like the same problem I was having.

The reader’s question certainly brings to mind that common sense can escape us even with the most obvious things. It certainly did me.

I don’t really remember, but I probably lost a few less than the prior year.

The third year (last year) I found some onions infected. Not many. I did not spray at all.


Soft rot

A frustrating issue often dealt with during the storage season is soft rot. This disease is caused by bacteria commonly found in the soil and plant debris. It takes advantage of wounds caused by insects, weather (hale, freezes, sunscald), and rough handling (bruises, cutting tops during harvest) to enter the plant and break down tissue. Watch the video below for more information about diagnosing soft rot.

Work in the Eastern US has suggested that tighter plant spacing and alternatives to black plastic mulches can reduce the incidence of bacterial soft rots. It is suspected that the alternatively colored plastics reduce the soil temperature, making it less hospitable for bacterial diseases. The tighter row spacing changed plant structure (smaller leaves allowing for quicker plant maturity and die down, less places for puddling water in leaf crevices) in ways that seemingly reduced bacterial disease. In these trials, silver mulch, biodegradable plastic, and even bare ground had lower incidences of bacterial rots and higher yield compared to black plastic mulch. In trials using silver plastic, reducing plant spacing from 48 inches² down to 32 or 24 inches² increased overall yield (though it did change the sizes of onions harvested). See Cornell’s research report for more information.

Another aspect of bacterial soft rot management is to manage the insects and diseases that wound plants. An insect to pay special attention to is onion maggot. This insect is able to host bacterial pathogens in it’s gut and spreads them as it feeds.

In weather events that damage onion plants, a quick application of copper can reduce the chance that bacteria move into the wounds.

Proper maturation, curing, and storage is also critical. Allow the tops of plants to dry out as much as possible before harvest. Curing that allows the outer layers of the onion and the neck will prevent soft rot from entering and taking hold. Existing soft rot infections will be hastened by warm, humid storage areas. Another key aspect is making sure any onions with hints of soft rot do not make it into storage, so onions that show early signs of disease, knicks, or bruises should not be stored.


Watch the video: How to Diagnose Onion Bacterial Bulb Rot


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