Diseases such as mildew and rusts can be treated with any one of a multitude of fungicides available at all good garden centres. Poor air circulation is often the cause and simply keeping the bonsai in a well ventilated position and thinning the foliage helps to prevent many of these problems.
Some trees are more susceptible than others, even trees of the same variety. Infected leaves should be removed and disposed of. An annual winter wash is good practice for deciduous trees and some conifers, to rid the bonsai of any over wintering diseases. This also cleans the trunk and branches, removing algae and lichens.
Root rot can usually be prevented by simply using free-draining soil, composed of at least one-third grit. If leaves wilt and begin to wither when the tree is not dry, there is usually a problem with the roots. Carefully inspect root system and remove all brown, rotten roots. Pot in a mixture of at least one half grit and position in a shady area, misting regularly.
Cover the whole tree with a plastic bag if possible, creating a humid micro environment. Remove the bag every few days to prevent mildew developing.