Sort and wash beans; place in a large Dutch oven. Cover with water to 2 inches above beans; bring to a boil. Cook 2 minutes. Remove from heat; cover and let stand 1 hour.
Drain beans; return to pan. Add 8 cups water and next 5 ingredients (water through pepper); bring to a boil. Cover, reduce heat, and simmer 1 1/2 hours. Add onion and next 5 ingredients (onion through garlic); simmer, uncovered, 50 minutes or until vegetables are tender. Stir in tomato paste; cook an additional 10 minutes. Ladle soup into bowls, and sprinkle with cheese.