Sauté the yellow onion in a stockpot over medium heat for 8 minutes.

Add water 1 to 2 tablespoons at a time to keep the onion from sticking.

Add the garlic, cumin, and oregano, and cook for another minute. Add the chipotles, black beans, and vegetable stock, and bring to a boil over high heat.

Decrease the heat to medium and cook the soup, covered, for 20 minutes.

Season with salt and purée the soup in batches in a blender. Return the puréed soup to a pot and keep warm.

Serve garnished with the lime wedges, cilantro, and red onion.