Persian limes with brown bottoms have stylar end rot.
Also known as stylar end breakdown, stylar end rot generally affects Bearss, Tahitian, and other Persian limes species, though it has been seen in other lime and lemon varieties. Stylar end rot is a physiological disease, which means it is not caused by pests or pathogens. Instead, stylar end rot is caused by too much heat and drought. Even though limes, lemons, and other citrus have thick, waxy skins to protect themselves from the sun’s heat and drought conditions, sometimes that protection isn’t enough.
Symptoms of stylar end rot
The stylar end of a fruit is the part with the dried up flower petals, opposite the stem end. Stylar end rot starts out as a small, grayish sunken area, at the stylar end, that slowly becomes firm and leathery. Affected areas can spread to cover 1/4 to 1/2 of the fruit, which is often invaded by bacteria or fungi. The tissues inside break down and turn brown or pink. Diseased fruit can be added to the compost pile, but only if it is free of other fungi and bacteria. Otherwise, toss it in the trash. Stylar end rot found on guava has been found to be caused by a fungi, Phomopsis. Some fungal diseases exhibit similar symptoms:
I hope this information inspires you to grow more of your own food. You can ask your garden questions on my Home page.