Heat oil in a large Dutch oven over medium-high. Add bell peppers, garlic, and 1 ½ cups of the onion. Cook, stirring often, until onion is just tender, about 5 minutes.
Stir in tomatoes, chipotle chile, and adobo sauce; cook, stirring often, about 3 minutes.
Add black beans, 8 cups water, salt, oregano, and cumin. Bring to a boil. Reduce heat to medium-low, and simmer, stirring every 30 minutes, until beans are tender and creamy, 1 hour, 30 minutes to 2 hours. (Add water as needed during cooking to keep beans covered.)
Pour 3 cups of the bean mixture into a blender. Secure lid on blender; remove center piece to allow steam to escape. Place a towel over opening. Process until smooth, about 1 minute.
Pour pureed bean mixture into Dutch oven. Add more salt, if desired. Add more water, as needed, to reach desired consistency. Reserve 3 cups soup for Cheesy Black Bean Tostadas (recipe, page 93). Serve remaining soup with sour cream, cilantro, avocado, lime wedges, and remaining ½ cup onion.
