Leek

A soil-borne fungus (Sclerotium rolfsii) that attacks plant stems right at the soil line during hot weather. It hits over 500 different plant species. Two telltale signs to look for: white fan-shaped fungal growth on the lower stem, mulch, and soil surface, and tan-brown spherical sclerotia (they look like mustard seeds) on infected tissue. Most active during sustained heat with humid conditions.

Triggers: Optimal at 86°F (30°C) soil and air temperature with humid conditions. Inactive below 70°F. Most damaging during sustained mid- to late-summer heat waves. It extends further north in warmer-than-normal seasons.

Risk fades when: Sustained cooler weather — highs below 80°F and overnight lows below 70°F for 5+ days — reduces fungal activity. The sclerotia (resting bodies) persist in soil for years, so resolution is seasonal, not curative.

A seedling killer caused by several different fungi working together. It hits vegetables, flowers, herbs, microgreens, and cover-crop seedlings the same way — seeds rot before they emerge, or young seedlings collapse right at the soil line. Wet seed-starting mix and poor airflow in seedling trays are the classic conditions.

Triggers: Wet soil or starting mix, poor drainage, seedlings packed too tightly, contaminated trays or media, and stagnant air all favor damping-off.

Risk fades when: Drying the soil surface and improving airflow slows new spread. Collapsed seedlings don't recover, but the rest of the tray can be saved.

Onion maggot is the most important early-season pest of onions, leeks, and garlic in northern temperate regions. Larvae feed on bulb basal plates and roots, killing plants and predisposing damaged bulbs to storage rot. First-generation damage can routinely reduce plant stands by over 50%. Three generations occur annually in northern regions; only the first is typically devastating to a young crop.

Where it lives: Across the US; a serious pest mainly in northern states

Triggers: Three generations per year in northern regions. Overwinter as pupae in soil. Adults emerge late April-May. Adult: small grayish-yellow fly resembling slender housefly. Females lay eggs at soil base of onion plants.

Risk fades when: Cool, wet weather favors onion maggot while hot, dry summer weather is detrimental to its survival, so pressure eases during midsummer heat between flights; the first (spring) generation is the largest and most damaging, and destroying culls and crop debris reduces overwintering pupae (Wisconsin Hort, UMaine Extension).

This alert is for allium white rot, not Botrytis neck rot, which is mostly a problem in storage. White rot is allium-specific and causes yellowing, wilt, decay of the basal plate (where roots attach), white fungal growth, and tiny black poppy-seed-like resting bodies (sclerotia). It thrives in cool, moist soil.

Triggers: Cool moist soil favors infection. Development is optimal around 60-65°F and slows sharply above the upper 70s.

What it looks like: On onion or garlic, leaves yellow, die back and wilt, oldest leaves collapsing first, while the bulb scales decay from the base. Roots rot so the plant pulls up easily. Fluffy white mold wraps the bulb base early on, later flattening into a mat dotted with black specks about the size of a poppy seed.

Disease or overwatering? Pull a yellowing onion or garlic plant. Fluffy white mold or black poppy-seed specks at the bulb base, with rotted roots, point to white rot. Leaves yellowing from soggy soil come with a firm bulb base, intact roots, and no mold or specks.

Will it recover? Infected onion and garlic plants do not recover, and the black specks survive in soil for over 20 years. Do not move soil, cull bulbs or debris from that bed. Next time, plant only clean sets, transplants and seed cloves from a source with no white rot, and never follow onion-family crops with onion-family crops; rotation alone will not clear it.

Risk fades when: White rot is markedly inhibited above 78°F and reduced by drying soil, though the sclerotia persist in soil for years.

Source for the signs above: UC IPM Pest Management Guidelines: Onion and Garlic, White Rot

An allium-specific rust on garlic, onion, leek, shallot, and chives. Produces orange to reddish pustules on older leaves first. Favored by cool, humid weather.

Triggers: Optimal infection is near 59°F with saturated humidity for several hours. The disease stays active in cool 57-75°F weather with dew or high humidity.

What it looks like: Mostly on garlic, also onion and chives. Tiny flecks on the leaf blades grow into oval to diamond-shaped, reddish to dull orange pustules, older leaves first. Later in the season the pustules can look dark. Badly hit leaves are covered in pustules, turn yellow, dry and die, and bulbs come out smaller.

Disease or overwatering? Raised reddish to orange pustules that shed reddish spores mark rust on garlic and onion. Leaves yellowing from wet soil have no pustules. Pustules that turn dark late in the season are still rust, from black spores forming inside them.

Will it recover? Pustule-covered leaves yellow, dry and die, and do not recover. Next time, keep garlic and other onion-family crops out of that ground for 2 to 3 years, pull volunteer onion-family plants, keep onion-family plantings apart, and plant in well-drained soil.

Risk fades when: Rust thrives in cool saturated air. Dry foliage or heat above the favorable range lowers new infection pressure.

Source for the signs above: UC IPM Pest Management Guidelines: Onion and Garlic, Rust

Aphids are soft-bodied sap-sucking insects that cluster on tender new growth. Most established plants tolerate moderate populations and will outgrow damage on their own, but aphids are the most important plant virus vectors in the garden, transmitting more than 100 plant viruses including potato leafroll, cucumber mosaic, and turnip mosaic. Honeydew excreted while feeding supports sooty mold growth and attracts ants that protect aphids from natural enemies.

Where it lives: Throughout the United States

Triggers: Optimal development at ~75°F (green peach aphid) per UC IPM Floriculture; melon aphid develops fastest above 75°F. Many species heat-intolerant above 90°F and crash in mid-summer. Soft new growth and over-fertilization with high N favor population buildup. Females give live birth parthenogenetically most of growing season — one generation in ~1 week under optimal conditions.

Risk fades when: Per UC IPM and Clemson HGIC, populations crash in mid-summer heat (>90°F) for many species, return in cooler conditions

The main foliar disease of onions, garlic, leeks and shallots in warm humid weather. It starts on the older, lower leaves as small sunken water-soaked spots with pale centers. Those enlarge into oval lesions, several centimetres long, that turn purple to brown and develop concentric light and dark rings - a zonate bull's-eye that is the diagnostic sign. Ringed lesions that merge or encircle a leaf girdle it, and everything above wilts, collapses and dies back from the tip. Leeks show this as classic leaf-tip dieback. The fungus is a close relative of the one that causes early blight on tomatoes, and behaves much the same way: it overwinters on infected debris and cull piles, spreads by wind and splashing water, and needs persistent leaf wetness to infect. Infection often follows injury - abrasion from blowing sand, damage from another fungus, or the wounds and succulent necks left after topping at harvest. That last route is why curing matters: dry the necks before topping and cure bulbs thoroughly, or the same fungus follows the crop into storage.

Triggers: Alternaria porri overwinters on infected bulbs and crop debris and can be seedborne in onion. Spores are dispersed by rain, irrigation water, wind, and by people and equipment moving through a wet crop. Older leaves are the most susceptible, and tops become more prone as plants mature. Infection often follows injury - from other fungi such as Botrytis, or from sand and dust during windstorms. Colorado State: warm, moist weather after midseason favors Alternaria, and the pathogen enters mature leaves and bulbs through wounds and the succulent necks left after tops are removed. UC IPM uses consecutive nightly leaf wetness above 12 hours as the signal to shorten spray intervals. UMass notes that Stemphylium leaf blight looks nearly identical and needs microscopy to separate, but management is the same.

What it looks like: Oval tan to brown spots on onion or garlic leaf blades, with yellow streaks running out along the blade in both directions that later turn brown. Purple blotch spots deepen to purple and can show dark brown rings. A spot can girdle and kill the leaf, and seed stalks too.

Disease or overwatering? Deep purple spots with dark rings on onion leaves point to purple blotch. Leaves pale and limp from overwatering have no spots or rings. Stemphylium leaf blight looks very similar and is managed the same way, and both often move into onion downy mildew spots, so check for downy mildew too.

Will it recover? A leaf girdled by a spot dies and will not recover. Moderate temperatures and humid, dewy weather favor both diseases. Since they so often follow onion downy mildew, keeping downy mildew under control is the main way to prevent them next time.

Risk fades when: Infection stops without free moisture on the leaf. Dry weather and good airflow halt new lesions, but existing ones stay and the leaf tissue above a girdling lesion will not recover. The disease also follows the crop into storage through wounds and wet necks, so curing is part of resolution, not an afterthought.

Source for the signs above: UC IPM Pest Management Guidelines: Onion and Garlic, Purple Blotch and Stemphylium Leaf Blight

Microscopic soil-dwelling roundworms that burrow into plant roots and cause swollen knots (galls). Above ground, the plant looks stunted, yellowed, and wilted even with plenty of water. They attack over 2,000 plant species, so almost nothing is safe. They're most active in warm soil (70-85°F) and do more damage in sandy soils, where they move easily. Once a bed has them, populations stick around for years.

Triggers: Soil temperatures of 70-85°F are ideal for them; below 60°F they go dormant. Sandy soils make it easy for them to move and reproduce, while heavy clay slows them down considerably. In warm soil, a full generation completes in about 27 days.

Risk fades when: Activity drops sharply once soil cools below 60°F. Damage stops accumulating for the season, but the population stays in the soil and returns when warmth does.

Thrips are tiny (1/16 inch) slender insects with fringed wings that puncture and rasp leaf surfaces, leaving silver stippling with black frass dots. The biggest concern is virus vectoring: western flower thrips is the principal vector of tomato spotted wilt virus (TSWV) and impatiens necrotic spot virus (INSV), which affect more than 600 plant species. Greenhouse and high tunnel infestations can be devastating.

Where it lives: Throughout the United States

Triggers: Hot dry weather; greenhouse/high tunnel environments. Female lays eggs inside leaf tissue. 2 larval stages feed; 2 non-feeding pupal stages in soil/litter. Lifecycle 10-21 days. Many overlapping generations. Bridge crops (spring wheat, peach, strawberry per NC State) build populations before vegetable hosts available.

Risk fades when: Infestations are worst in hot, dry weather; cool conditions slow development and heavy rain or overhead irrigation knocks populations down sharply, so risk fades as the weather turns cool and wet and rebuilds the following spring (UK Entomology, Cornell IPM).

Onions lose fights with weeds, and they lose badly. The reason is anatomical: an onion has a shallow, sparse root system and upright, narrow leaves that never close a canopy or shade the ground. Nebraska Extension states it plainly - due to their shallow root systems, onions compete poorly with weeds. A weedy onion bed does not just look untidy. Every week of shaded, crowded growth costs leaves, and because bulb size is set by the number and size of leaves at bulb initiation, lost leaves mean a permanently smaller bulb. The window that matters is from emergence through bulb initiation; after the bulb starts sizing, weeds cost less. The catch is that the same shallow roots that lose to weeds are easily severed by a hoe. Cultivate shallowly, close to the surface, and do not hill soil up around the plants. Mulch lightly instead: it suppresses weeds and conserves moisture without root damage.

Triggers: Nebraska Extension: due to their shallow root systems, onions compete poorly with weeds; shallow cultivation is necessary and the soil should not be hilled up around the plants. Light mulch decreases weeds and conserves soil moisture. The critical period runs from emergence through bulb initiation, because per Iowa State Extension bulb size is largely determined by the number and size of the leaves at bulb initiation - leaf growth lost to weed competition cannot be recovered once bulbing starts.

Risk fades when: Leaf growth lost to weeds is not recoverable - once bulbing begins the onion makes no new leaves, so the bulb is capped at whatever top growth survived. Weed early and often rather than waiting for a big clean-up. Cultivate shallowly and close to the surface; onion roots sit just below it and a deep hoe cuts them. Never hill soil up around onions. A light organic mulch suppresses weeds and steadies soil moisture at the same time, which also helps prevent split and double bulbs.