Preheat the dutch oven to 400 degrees. Finely dice the onion and mince the garlic. Saute onions in dutch oven with olive oil until softened (roughly 5 minutes) then add the garlic until fragrant (about 1-2 minutes).
While the onion and garlic are sauteing, thinly slice the rest of the vegetables using a mandolin. Slice them into the same shape.
Spread the softened onion and garlic in the bottom of the dish. Place the thinly sliced vegetables in the baking dish vertically, in an alternating pattern. Sprinkle generously with salt, pepper, thyme, and rosemary.
Cover the dish with foil and bake for 30 minutes.
Optional: Top with cheese and bake for another 15-20 minutes or until the cheese is golden brown.
Arrange Portobello caps on a work surface. Remove stems and gills and brush both sides with 2 teaspoons olive oil, salt and pepper.
Place on a parchment lined baking sheet and set aside.
Put the bread cubes in a large bowl and set aside.
Heat 2 tablespoons of oil in a large skillet over medium-high heat.
Add the onion, apple, carrot, celery, and pecans. Cook until the vegetables get soft, about 5 minutes. Add the broth, parsley, and sage and bring to a boil. Taste and adjust seasoning.
Pour the vegetable mixture over the stuffing cubes and toss until evenly moistened. Mix in the egg.
Fill the mushrooms with stuffing. Place pan in the oven for 30-40 minutes until the top of the stuffing is crusty and brown and mushrooms are soft.
Serve with fried sage leaves as garnish if desired.