Question
I have mature pecan trees that have a mushroom looking fungus at the
base part of the trunk. Will these hurt the tree and what do I do to keep
them from coming back after they are removed?
Thanks,
Cyndy

Answer
These are the fruiting bodies of fungi.  If they are connected to the trunk or roots then this a decay fungi. If they are not connected then these are just mushrooms growing in the duff of the soil.

Decay fungi enter the tree trunk through wounds and will over time eat away at the woody center part of the tree. They do not infect living cells so they are not really a health problem with the tree.
There is not really anything that can be done about the fungi growing in the trunk. It is not a problem unless you start to have the large limbs break and these are hollow. This would mean the decay has grown up into the trunk and maybe come a problem of breakage of large limbs and the trunk.  This will not be a real problem for many many years.

I would recommend that you fertilize the tree with 10-10-10 fertilizer at the rate of 1 lb of fertilizer per inch of trunk diameter scattered around the tree and watered in good. Apply just before a rain storm and you will not have to water.