When you say soil, is it out of your yard? Or are you using a peat based potting mix?
99% of the time when people say they are growing in soil, they are actually growing in soilless.
The difference is that soil roughly has 20% air, 30% water, 45% minerals and 5% organic matter, whereas soilless medium has far more organic medium and drastically less minerals.
If you use a properly aerated medium you will find it far harder to suffocate the roots. I used to run into this issue at first until I started adding extra aggregate and started using fabric pots.