One theory is that replant disease is due to a whole menagerie of tree pathogens - fungi, bacteria, nematodes, viruses and other organisms. These parasitise the living tissues of the mature tree, hastening senility and death, and survive in the soil and decaying roots after the tree has died. Putting a young traumatised tree with an immature root system into this 'broth' of pathogens can be too much for an infant tree to cope with. Any new root growth is rapidly and heavily colonised, so that shoot growth is virtually zero. This is especially true if it is on a dwarfing rootstock, which by its nature will be relatively inefficient. As a rule, replant disease persists for around fifteen years in the soil, although this varies with local conditions. Pathogens survive in dead wood and organic matter until exposed to predation by their home rotting away, and will also depend on whether the original orchard was planted with dwarf or standard trees. Standards have more vigorous - therefore larger - roots, and are thus likely to take longer to degrade.
It is good organic rotation practice not to follow ‘like with like’and this rule applies to long lived trees as much as annual vegetables. In the case of temperate fruit trees, the 'Pomes and Stones' rule for rotation should be observed- don’t follow a ‘pome’ fruit (with an apple-type core - apples, pears, medlar, quince) with a tree from the same group. A ‘stone’ fruit (ie, with a plum-type stone, such as plum, cherry, peach, apricot, almond) should be alright, and vice-versa. However, rotation is not always easy in a well planned old orchard when the site it occupies may well be the best available, and starting another orchard elsewhere may not be practical. In this case, and replanting is unavoidable, a large hole should be dug out, and the soil removed and replaced with ‘clean’ soil from a site where susceptible plants have not been grown. Using trees on vigorous rootstocks which will have a better chance of competing with the pathogens, or plants grown in large containers with a large root ball may also have a better chance of resisting replant disease. The extra time to cropping may be offset if new trees are planted a few years in advance of old trees finally falling over, furthermore, if the old orchard was grubbed - i.e. trees were healthy when removed, it is unlikely that replant disease would be a problem as pathogen levels may never have been high. The malady is worse where trees have died in situ- pathogens are likely to have contributed to the death and therefore be at a higher level in the soil.