What is causing this is decaying root matter in your soil/hydroponic medium produces Carbon Dioxide which suffocate your root mass. Roots need oxygen to live. You should not reuse your soil/hydroponic medium because of this. If you use silica stone, gravel or hydrated rock & you are planning on reusing you should remove ALL decaying root matter. This usually involves lots of bleach and scrubbing with small brushes or you could presoak with an enzyme product (enzyme products break down decaying root matter and make them beneficial to the plant).