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In most cases, leaving tree roots underground is not a problem if the stump has been removed or ground below the soil. However, some larger roots may decompose, leaving dents in your soil. Additionally, some aggressive trees, including willows, oaks, elms, maples, and poplars may grow back from roots. Large aggressive trees with established root systems are more likely to grow back.

There are a few general rules to follow that will help you prune your trees correctly. One of the most important rules is to prune during the correct season for the type of tree you have. Typically, pruning should be during late winter. For younger trees, you should not remove more than a ⅓ of the tree's crown when pruning. Also, remember to remove dead and diseased branches first, then proceed with pruning the rest of the tree.

In most cases, you should not use a pruning seal on trees after trimming. Applying a sealant can interfere with the tree's natural healing process, and it does not guarantee protection from pathogens. Instead of sealing the cut, the best practice is to support the tree's natural recovery by providing it with plenty of water and a dormant-style fertilizer. However, there are exceptions. Pruning seals may be recommended for very vulnerable species, like elm trees, in areas where dangerous diseases such as Dutch elm disease are prevalent. In these specific situations, the protection offered by a sealant can outweigh its downsides. For advice tailored to your situation, especially after cutting large branches, it is best to consult a local tree trimming professional.

The best way to protect tree roots is to avoid the roots entirely by excavating outside the root radius of the tree. For nearby projects, it’s a good idea to construct a temporary retaining wall. But that’s not always possible, depending on the project and the root system. In these cases, consider using alternative equipment like an auger to tunnel under the ground.

Remember, tree roots can damage nearby cement foundations as they grow. If a tree is close enough to interfere with large excavations, it may be better to remove the tree than risk future problems.