Its never a good idea to use what is known to have had disease. Leaves that have fallen from a tree earlier than its supposed to should not be used in the compost.
Crabapple trees sometimes loses their leaves much earlier than usual--cedar apple rust--is sometimes the cause and the homeowner is advised to try to keep the undersides of the tree as clean free of debris as possible.
The fungus that infiltrates the leaves can then invade the soil if not cleaned up and cause re-appearance at a later date.
If the compost bin doesn't reach such temperature heights that could possibly kill bacteria, its much better to garbage the leaves rather than take a chance such disease can spread.

I have a roof garden. I'm not composting the leaves. I threw them away. The infected tree was in a very large cedar planter. Since I got rid of the infected tree there is a lot dirt left in the planter.

I would like to use that planter and the dirt left in it for another healthy tree, but fear the dirt houses the bacteria. I was asking if there was someway to kill the bacteria in the soil.

Since posting the question I did some research and came upon information that suggested using Agrimycin. Do you have any experience with that?

Any potting soil is totally replaced because of the potential of a plant disease and if the plant that was growing in that potting soil was infected with a plant disease it is not a good idea to reuse the potting soil that diseased plant grew in. Replace the potting soil, because it is most often less expensive, in the long run, then replacing the plants you are trying to grow.

Depending on how much soil you are talking about, maybe you could use a bleach solution to sterilize the soil and the planter?

Bleach. That would definitely kill the bacteria. Have you ever done that?
I'd have to rinse it out a few times to get all the bleach out.
I already ordered some Agrimycin. I read that although it is normally used for livestock, it can be used on plants systemically or sprayed on them for bacterial leaf spot.
I have a couple of other trees that are showing the beginning stages of it so I want to treat them with something systemic to stop it before it really takes hold.

If it wasn't a roof garden I would throw the soil away. It's the not the money, it's the fact that we had to carry
it up the stairs ... a couple hundred pounds of soil if not more. That's why I'm trying to save it.

The bacteria aren't in the soil. Refill the empty space as needed and plant with confidence.

Wow. You are so right. I just read about how it spreads...twigs, leaves and fruit. You just have to get rid of the affected leaves that fall on the soil. What was I thinking? You don't throw away the soil from a plant that
gets mold or mildew....just the leaves. Thanks for the heads up.

"The bacterium Xanthomonas pruni overwinters in twigs that are infected late in the season about the time leaves are shed. The following spring, when environmental conditions are favorable, bacteria ooze out onto the surface of these twigs. The bacteria are then spread by windblown or splashing rain and can result in new infections throughout the growing season. The bacteria come in contact with healthy leaves, fruit and current-year twigs and enter the tissues through stomata or lenticels when surface moisture is present. Once inside healthy tissues, the bacteria multiply and disease develops.

Warm temperatures (70-85 degrees F, 2l-29 degrees C) with light rains, heavy dews or fogs and windy weather are most conducive for disease development and spread. The disease makes little progress when weather is hot and dry."