Heat the olive oil in a large sauce pot over medium heat and sauté the onions for at least 3 minutes before stirring. The onions should start to brown before you move them around with a spoon. Continue to cook the onions, stirring only occasionally in order for the natural sugar to brown. Cook for 20 minutes, until the onions are well browned. Add the mushroom, garlic, thyme and tomato paste. Continue to cook for 5 minutes, until the tomato paste turns golden brown. Add the wine, scraping the pan bottom to deglaze the pan. Cook down the wine as you simmer for another 2 minutes. Add the stock, tamari, dissolved miso and nutritional yeast. Continue to simmer, uncovered, for 10 minutes longer; season with pepper. Put a slice of bread in each bowl. Ladle soup over it then garnish with cheese. Serves 6 to 8.