When a tomato turns black or brown on the bottom, it has blossom-end rot. This problem is caused by calcium deficiency in the tissue and can be brought on by any of the following conditions. Fluctuations in soil moisture from extremely wet to extremely dry Rapid growth early in the season followed by a sudden period of dryness that slows growth. Excessive rains that suffocate the root hairs of the plant. Excess soil salts. Cultivation too close to the base of the plants. The best way to prevent blossom-end rot is to plant tomatoes in well-drained soil. Mulch your plants to maintain even soil moisture, water during periods of drought, avoid cultivating near the shallow roots, and use moderate amounts of nitrogen fertilizer.