Why are my green peppers have brown spots?
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If the spots are only on the peppers, and not the whole plant, then the peppers could just be getting sunburn. The peppers will still be fine and taste great, but they just aren't as pretty. It is hard to control once the plants are already producing fruit, but to help it for next year, give the plants plenty of Nitrogen fertilizer in the beginning so there is a lot of foliage to later shade the fruit.
Perhaps, too much water?
Get some fungicide and spray them. Remove the ones with brown spot.
Green Peppers can get the same diseases as tomatoes. Tomatoes get a disease known as Early Blight. It is characterized by numerous brown spots that start on the lower leaves and work up the plant. Early Blight can also produce brown spots on stems and fruit. It eventually will cause defoliation of the plant. Early Blight is very common during warm, and humid conditions. To prevent Early Blight, plant certified disease-free seeds or transplants, and plant disease-resistant pepper cultivars.
The fungus spends the winter in infected plant debris in or on the soil where it can survive at least one and perhaps several years. It can also be seed borne. New spores are produced the following season. The spores are transported by water, wind, insects, other animals including man, and machinery. Once the initial infections have occurred, they become the most important source of new spore production and are responsible for rapid disease spread.
To control: Remove and destroy crop residue at the end of the season. Practice good crop rotation (3 year rotation - don't plant tomatoes and peppers in the same spot each year). Be sure to control weeds. Provide good air circulation around your pepper plants. Orient rows in the direction of prevailing winds, avoid shaded areas, and avoid wind barriers. Irrigate early in the day to promote rapid drying of foliage. Avoid overhead watering if you can. Improve the fertility of the soil to encourage growth of vigorous plants. Hand picking diseased foliage, stems and fruit may slow the rate of disease spread but should not be relied on for control. Do not work in a wet garden. You may also need to use fungicides.
Two bacterial pathogens are important to mention: the Bacterial soft rot (Erwinia carotovora) which causes a soft slimy rot, and the bacterial spot (Xanthomonas versicatoria) which forms a raised rough pimply area on the fruit. On the leaves, the spot is first raised and wart like, and becomes necrotic spots with dark margins. The affected leaves turn yellow and drop. Most cultivars currently used for commercial production show resistance to BLS races 1, 2, and 3.
Sun scald is another physiological disorder that occurs commonly on sweet peppers when the fruit is exposed to hot sun. The flesh becomes light, dry and papery on areas that had direct sunlight on them.
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