Answer: It sounds as if your tomatoes had powdery mildew, a fungus which thrives in specific temperature (usually moist/humid) conditions without good air circulation amongst plants. It appears as a whitish/grayish powder on leaves and stems.
Powdery mildew overwinters on living plants, and can be difficult to eradicate. There are some things you can do to minimize its effects. Powdery mildew is unique among plant diseases in that it doesn't require a wet leaf surface to spread. It can thus thrive during hot, dry weather. The first line of defense is to grow resistant varieties.
Here are some general rules for helping control fungal diseases. Start by making sure that your plants are getting enough direct sunlight. (Eight to ten hours a day is generally the minimum for plants that flower or bear fruit.)
You'll also want to make sure that there's enough room between plants for air to circulate freely. Overcrowding not only makes plants more susceptible to diseases, if leaves touch other plants, those diseases can easily be spread.
The general advice to inhibit the spread of fungal diseases is to avoid wetting leaf surfaces. In the case of powdery mildew, you can actually inhibit infection with periodic strong sprays of water (not so strong as to damage the
plant.) After the new growth of affected plants reaches about six inches long and UNTIL THE TEMPERATURE REACHES 90 degrees F, you may apply dusting sulfur to foliage every 14 days. If necessary apply fungicide. Fungicide works much better as a preventative measure, before the powdery mildew becomes a problem. There is nothing that you can treat the soil with.
If possible at this point, remove any plant matter before tilling, as you are correct that the fungus can still be there. Rotate where you plant crops each year (in other words, plant tomatoes in a different section of the garden this year), which helps reduce the build-up of plant specific pests and diseases. Be sure to provide plenty of space between all plants for air circulation. Good cultural practices are your best defense!
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