In a large pot, cook the bacon over medium-low heat, stirring occasionally, until crisp, about 10 minutes. Using a slotted spoon, transfer the bacon to a paper-towel-lined plate. Discard all but about 3 tablespoons bacon grease.
Add the onion to the pot and cook over medium heat, stirring, until soft, about 8 minutes. Add the chopped apples, squash, sweet potatoes, celery root, turnips and thyme sprigs. Cover and cook, stirring occasionally, until crisp-tender, about 15 minutes. Stir in the chicken broth and 5 cups of water, cover, bring to a simmer and cook until the vegetables are softened, about 10 minutes. Discard the thyme sprigs; season with salt and pepper.
Using an immersion blender, puree the soup. Finely chop the remaining apple half. Top the soup with the apple, bacon and thyme leaves.