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Any cutting of tree roots can hurt or kill a tree, which is why it's recommended you don’t do it unless the roots are damaging or invasive on a nearby structure like your home. You should never cut more than 15 percent of above-ground tree roots at one time. If you have any questions about cutting tree roots, contact your local arborist.

Generally, you should prune around 20% of an apple tree’s growth—and never more than 30%. This means that if you have a severely overgrown tree, it can take a few seasons to prune it back enough to produce the healthiest fruit. 

If you’re dealing with a newly planted or juvenile tree, hold off on pruning beyond the initial shaping. Wait at least a couple of seasons into fruit production since pruning can increase the number of water sprouts and unproductive foliage.

Pruning trees during the summer can be a bad idea because the new growth will take place during the hottest months of the year, which can stress your tree out. Similarly, pruning during the early fall can be a bad idea, too, because you’d be stimulating new growth when most trees are aiming to go dormant. 

Pruning recommendations will vary by the type of tree, but generally, waiting until winter to prune your trees is a good idea.

If you’re wondering whether you can plant a tree where the stump was removed, know that the soil conditions won’t be ideal, so you should avoid it. The soil beneath the previous tree will likely be depleted of nutrients, plus there may be roots left behind that will seriously hinder the growth of a new tree. Also, if you use salt or other chemical solutions to kill the stump, these can linger in the soil for months or even years and prevent healthy growth. It’s best to choose a different spot that’s at least three feet away for a new tree, or wait at least a year and thoroughly amend the soil before you plant.