Small black spots on tomatoes and tomato leaves often indicate bacterial spot.
Those black spots might not look significant, but this bacterial disease can also affect peppers, eggplant, groundcherries, and tomatillos. A close cousin to the bacterial spot of almonds and practically impossible to differentiate from bacterial speck without a microscope, bacterial spot (Xanthomonas campestris pv. vesicatoria) is perfectly capable of killing your tomato plants.
Bacterial spot symptoms
Symptoms of bacterial spot can appear at any time during a plant's development, from seedling to mature plant and on all aboveground plant parts. Bacteria enter through wounds and stomas. Infected younger plants can lose all their leaves. Older plants exhibit insignificant-looking water-soaked areas on mature leaves, usually near the bottom of the plant, making it easy to dismiss this disease. But that would be a mistake.
These lesions start yellow or light green, turning dark brown or black. Older spots may become raised areas that average 1/3" across. Larger damaged areas may occur at the margins (leaf edges).
Immature fruit can also be affected by bacterial spot. Bacteria enter through tiny hairs called trichomes. Infected areas have tiny, raised black dots that become sunken or dimpled and surrounded by a white halo, similar to bacterial canker. The halos eventually disappear as the spots get larger and become scabby. If these fruits mature before rotting on the vine, they are still edible. Just cut out the diseased areas and dispose of the infected parts in the trash. Do not add infected plant material to your compost pile.
Controlling bacterial spot
Because these bacteria overwinter in infected plant debris, you can protect next year's crops by clearing infected plant tissue out of your garden each fall. The disease can also appear on volunteer tomato plants, so watch rogue plants closely for signs of infection. Splashing rain, irrigation water, and contaminated tools can also spread the disease, so avoid overhead watering and sanitize your garden tools regularly.
Since these bacteria need humidity and water droplets to survive, pruning for good airflow can go a long way toward preventing this disease.
If you are like me and save seeds from each year's crops, be sure you don't use those from infected plants, as you will perpetuate the disease. As always, only buy certified disease-free plants and seeds and quarantine new plants. Fixed copper sprays may help reduce the chance of bacterial spot. There have been some cases of copper-resistant bacteria, so it's hard to say. Crop rotation can also help break this disease triangle.
Protect next year's crops by tossing plants infected with bacterial spot into the trash and providing good airflow around future plants.
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