Answer: The dome should be removed or at least propped open as soon as seeds germinate because they need air circulation. The dome also causes extreme heat build up if set in direct sun and this can cook your seeds or plants. The following may help you trouble shoot.
It sounds like the seedlings may have been too moist. Start out with soil that is just barely moist, like a well wrung out sponge. Plant your seeds and cover them with the dome or plastic wrap to maintain humidity, but open it as soon as they start to sprout and put them immediately into bright light. Make sure there is also some air circulation where you keep them as stagnant air can encourage fungal growth. Next, make sure the plants are thinned enough to allow for ample light and air to filter through them. Also, do not over fertilize them. They do not need fertilizer until they have several sets of true leaves. You might try watering by dribbling water gently and slowly out of a small pitcher onto the soil rather than spraying them -- wet foliage will also encourage fungal growth. Finally, make sure all of your tools and equipment are clean and that you are using a relatively sterile potting mix such as a soilless seed starter of peat, vermiculite and possibly perlite. Other causes can also be too high or low a temperature or too little light -- many gardeners find it necessary to use supplemental lights for seedlings. An ordinary shop light fisture with one warm and one cool colored bulb will do. Leave the plants within and inch of the bulbs and leave the lights on for 16 hours a day. Last of all, you might have luck watering them with chamomile tea when you see the problem appear.
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