Blossom-end rot affects tomatoes, peppers, squash and watermelon. It’s caused by a lack of calcium in the soil, not by an organism. Calcium deficiency is often induced by big fluctuations in watering, like when you get long periods of wet weather followed by dry weather.
It starts with the appearance of a dark, watery spot at the blossom end of the fruit. Small fruits may just drop off the plants, but larger fruits will usually stay on. As the spot develops, it gets bigger, becomes sunken and turns black and leathery.
To prevent it, you should test your soil before the growing season begins. If it needs calcium and the pH is also low, add limestone. If the pH is not excessively acidic, add gypsum.
Avoid over-fertilizing. Use nitrate nitrogen as the fertilizer nitrogen source, not ammoniacal nitrogen as ammonia will make the problem worse. Some people recommend foliar applications of calcium, where you apply it directly to the leaves, but studies show it doesn’t help much because it isn’t absorbed readily and doesn’t move to the fruit where it’s needed.
Mulch to help maintain an even moisture level and give your plants regular watering. Try not to let your soil dry out as the best defense is a nice, consistent soil moisture level. Blossom-end rot is most likely to occur with the earliest fruits so it doesn’t mean your entire crop will have it.