This is because of the presence of bacteria and other micro organisms in soil. Usually the soil is well aeriated but when it becomes water logged, the organisms start to compete and start to eat other competitors. That’s why the roots start to rot.
Hope this helps.
Also, if the presence of water is too much, and very little is used, then it forms a hypertonic condition in the roots and this causes the cell walls of the cells in the roots to break and causing the lysosomes to release chemicals ( I don’t exactly remember which) which break down the rest of the cells in the roots. This could also be a reason. I just remembered this.
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