Heat the olive oil in a large pot over medium heat. Add the onion and cook until it softens.
Stir in the garlic and chipotle peppers. Cook for one minute until fragrant.
Add the sweet potatoes and rutabaga to the pot. Stir to coat them with the oil and spices.
Pour in the vegetable broth. Add the salt and black pepper. Bring the mixture to a boil.
Reduce the heat to low and simmer for 20 minutes until the vegetables are tender.
Remove the pot from the heat. Use an immersion blender to puree the soup until smooth. If you use a regular blender, work in batches.
Taste and adjust salt if needed. Ladle into bowls and top with cilantro. Serve with lime wedges on the side.