It is definitely one of the fungal rots but there is no way I know of to ID the specific fungal cause agent without a lab. And in the long run it doesn't make much difference to the plant. All the fungi are present in all soil naturally, it is providing them the ideal conditions to grow that causes the damage. And that condition is your watering regimen - frequent shallow watering. The development of the interveinal chlorosis on the lower leaves and the adventitious roots on the stem is proof of excess surface level/shallow moisture.

Your plan of 4x a day for such a brief period of time is very unusual. Depending on the size of your emitters (the GPH) even in full sand and in a desert location it is excessive. Drip irrigation isn't frequency-oriented. It is time-oriented. Less frequent but for much longer periods of time so that you get deep water penetration is the key to success in using it. My personal system in my garden soil runs for 2 hours no more than 2x per week. In my containers it is currently set to run every other day for 45 mins as that is how long it takes for water to begin running out of the bottom of the containers.

Dave

Thank you Dave for the in depth answer. I will adjust the watering regiment accordingly and I will move some soil above the crow in hope of new roots growth in order to salvage the plants. I will try to break the hard pan using metal rods that I will disinfect after each holes. Do you have any other ideas to add to this strategy?

Heavy mulching of the plants with a good organic mulch like straw will help stablize the soil moisture levels, reduce the water needs and help break-up the hard pan soil.