Dear Mario,
When growing seedlings in large containers, it’s important not to over-water them. The problems you’re describing are all due to having too much water in your growing medium. Because the roots are so short, you can take care to only water the layers of mix in which they’re prevalent. Watering from below is a great way to get the roots to stretch and seek out water, resulting in more vigorous growth up top. You certainly shouldn’t be watering to runoff early in your plant’s life.
Also, as they grow bigger, never allow your plants to sit in stagnant runoff water. You may experience a little salt buildup, but once the taproot has reached the bottom of your container, you can water to runoff in order to leach some of those salts from your medium. Another way to avoid salt buildup early on is to feed your plants at one quarter or half strength of what’s recommended on the plant food bottle. Underfeeding is much easier to fix than overfeeding.
You can always start them in smaller containers and transplant them as they grow. Be sure they don’t become too root-bound prior to the transplant. Also, be gentle when removing the root ball and also when placing it into its new container and back-filling with extra soil. The roots will recover much more quickly if you apply yourself to making sure not to disturb them too much.
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