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Fungus: Botrytis Blight (Brown leaves)
"Dead-end" corners, thick stands of trees, or low areas, where air lies stagnant, can promote a fungal problem called Botrytis Blight. This is characterized by brown spots on the leaves and/or flower buds. In advance cases, all the lower leaves will rapidly turn brown and die. The bulb itself is not damaged, but the sudden loss of leaves will reduce the number of flowers next year. This photo shows what may happen to your lilies if the weather stays cool for prolonged periods and you do not spray a fungicide. It is best to hit your lilies with your rose spray BEFORE symptoms appear. Old time growers used to refer to advanced stages as "Fire Blight" because it progresses rapidly if not checked by fungicide. (Sometimes when the weather is cooler than normal flowers will not open properly, with one or more "missing" petals, smaller than normal flowers or buds in odd shapes. If you see odd flowers, start checking for Botrytis, as usually it is the cause.)
This is a temporary difficulty, DO NOT dig and destroy your lilies! They are not permanently infected. Fungus lies on top of the soil waiting for the right combination of events to grow and multiply, just like mushrooms. It is a normal occurrence in nature and part of the earth's "Master Recycling Plan".
Fungal difficulties can arise in any garden when the weather is cold and damp during spring or fall or during hot and humid weather during summer. Providing good air circulation and cleanup of old lily stems in the winter are the best defenses against Botrytis. If you spray roses for Blackspot or Powdery Mildew, spray your lilies at the same time. If you have experienced Botrytis or Stump Rot in the past, keep your garden free of weeds over winter and spray the soil and sprouts when they first emerge in spring, don't wait until you see a problem.
During fungus attacks, your goal is to keep as many leaves as possible on the stem to rebuild the bulb for next year. If there is deep mulch around the lily stems, remove all but a thin layer to let the top layer of soil dry quickly. Now spray your entire lily bed with a good fungicide with copper hydroxide or copper sulfate as the base. It should be blue in color and leave a blue residue on the leaves, not pretty for cutting the blooms, but you want to keep the fungus spores from causing any more damage. If you grow roses, then you already know to clean up fallen leaves and not put them into the compost; ditto with the lily stems/leaves, keep weeds pulled and let the air circulate freely around the stems. (This is the same "fix" as for "Stump Rot", whereby the stem just gets soggy and gelatin-like and usually the top of the crown turns brown.)
Organic gardeners: In addition to reducing humid conditions, try a baking soda mixture (1/4 teaspoon, per quart of water with horticultural oil as a "spreader-sticker") sprayed weekly on the foliage during wet/cold Spring and Autumn days works reasonably well to prevent fungus from taking hold, but will not stop an infection that has progressed very far. Reapply after rain.
Wild Lily bulbs making up the genus Lilium belong to the family Liliaceae comprising of approximately 200 genera made up of approximately 2,000 lily species. There are in the neighborhood of 110 to 120 Lilium species depending on whose classification you reference. For the full article, click Knowledge Base