Pickling Shallot Problems: Rot, Rust, Thrips and Soil Diseases

Wet soil causes more losses than any pest

The single biggest cause of failure is water sitting around the bulbs. It shows in three ways: bulbs planted in autumn that never emerge because they rotted before rooting, clumps that yellow and collapse in mid-winter with a soft sour base, and bulbs that come out of the ground in early summer already breaking down at the neck. All three have the same answer, which is drainage rather than treatment.

If you lose plants this way, do not replant into the same spot the following autumn without changing the ground. Raise the bed four to six inches (10 to 15 cm), work in coarse grit, and stop any irrigation to the row once the tops start yellowing. A crop that evolved on sand dunes will accept almost any hardship except standing water.

A sour or oniony smell rising from the base of a clump you have just disturbed means rot has already started underground, whatever the tops look like. Lift that clump and check the rest of the row rather than waiting.

Leaf problems you can cut away

Rust appears as raised orange or rusty-brown pustules scattered along the tops, most often in mild damp weather where clumps are crowded. Rub one with a finger and orange powder comes off, which separates it from ordinary leaf scorch. It spreads through a bed readily but it lives on the leaves, not the bulbs, and the clump survives it.

Downy mildew shows as pale oval patches on the leaves that carry a grayish furry growth in damp weather, and the affected leaf collapses from that point. Both diseases respond to the same measures: cut the affected tops off, carry them out of the garden rather than composting them, widen the spacing next season, stop watering over the tops, and cut out any nitrogen feeding, which produces exactly the soft crowded growth these diseases prefer.

If either arrives late in the season, when the tops are already yellowing, simply lift the crop. The bulbs are made by then and nothing is gained by treating leaves that are dying anyway.

Insects: thrips, leaf miner and onion fly

Onion thrips arrive in hot dry weather and feed down in the crowded neck where leaves meet the bulb, leaving silvery mottled streaks that spread until the tops look bleached and twisted. Part the leaves and look at the base of a clump to find them; they are tiny yellow-brown slivers that run when disturbed. Because this crop is dying down by the time the hottest weather arrives, thrips often do less real harm here than on other alliums, but a heavy attack in a late season costs you bulb size.

Allium leaf miner punches a neat row of small white dots down a leaf, and the larvae then tunnel down into the neck and the bulb itself. Those dots are the moment to act, because once larvae are in the bulb nothing helps and the bulb is unusable. Onion fly larvae attack the base plate directly and the plant simply collapses.

For all three, a fine insect mesh laid over the row and sealed at the edges during the adult flight periods is the only genuinely reliable defense. Keeping the bed free of grassy weeds removes the hosts thrips breed on, and a hard spray of water into the necks knocks thrips numbers back. Lift and destroy any plant with tunneling or maggots at the base rather than leaving it in the row.

White rot is the one you cannot fix

White rot is the disease that ends a bed. Plants yellow and wilt without obvious cause, and a lifted plant shows white cottony fungus over the base plate studded with black grains the size of poppy seeds. Those grains survive in the soil for fifteen years or more, waiting for the next allium root. There is no cure, no spray and no soil treatment available to a gardener.

If you find it, lift the affected plants together with the soil around them, bag them and dispose of them away from the garden. Do not compost any of it, clean soil off tools and boots before moving to another bed, and never plant onions, garlic, leeks, chives or pickling shallot in that ground again. Start a fresh bed as far away as the plot allows, using bulbs you saved from a clean row rather than bought-in stock of unknown origin.

The prevention is rotation and clean stock. Leave at least three years, preferably four, before any allium returns to a given bed, and keep back your own replanting bulbs each year so you are not importing soil disease with a bag of bulbs.

1. Walk the row every week and look at the base Most trouble is visible where the leaves meet the bulb a week before it shows on the tops. Part the leaves of two or three clumps each time you pass.
2. Record what you saw, where, and on what date Rust and thrips tend to arrive at about the same point each year. One season of dated notes tells you when to have the mesh ready instead of reacting after the damage is done.
3. Remove rather than treat Cutting infected tops off and carrying them out of the garden solves leaf problems more reliably than any spray, and this crop can afford the loss of leaf late in its season.
4. Keep suspect clumps out of your seed stock If part of the bed had trouble, lift, dry and store those bulbs separately and eat them. Never mix them into the bulbs you are keeping back to plant in autumn.

Track which bed each row was in every year. Allium rotation only works if you can prove where the alliums were three years ago, and memory alone is not reliable enough on a small plot.