Fill a large heavy bottomed pot with 12 cups water. To that add 4 turnips rough chopped and onion skins (the papery white part). Boil and bring to a simmer for about 50 minutes or until the veggies are soft. Strain and reserve stock. Throw away the turnips and onion skins.
In a large soup pot, soften the butter. Add the sliced onions and thyme bundle and cook over medium heat, until slightly browned, about 10 minutes. Add 1 tsp of salt.
Then add the reserved vegetable stock, mirin and soy sauce. If you want the soup to have more broth, add water. Cook about 5 more minutes and remove thyme bundle.
Serve by placing one piece of bread topped with a sprinkling of Gruyere in a soup bowl, then add the soup overtop and the cheese will melt. Garnish with a few thyme leaves and fresh cracked pepper.