Make soup: Cut fennel stalks flush with bulb, discarding them, and trim off any tough outer layers from bulb. Chop fennel into 1/2-inch pieces.
Cook pancetta in oil in a 7- to 9-quart heavy pot over moderate heat, stirring occasionally, until just beginning to brown, 5 to 7 minutes. Stir in fennel, onion, turnip, carrots, and cabbage and cook, stirring occasionally, until cabbage is wilted, 5 to 7 minutes. Add cheese rind, squash, potato, thyme sprigs, bay leaf, salt, and water and bring to a boil.
Reduce heat and simmer, uncovered, 10 minutes. Add lima beans, green beans, and cannellini and simmer until vegetables are tender, about 5 minutes. Discard cheese rind, thyme sprigs, and bay leaf. Stir in spinach and season with salt and pepper.
Make pistou while soup is simmering: Mince and mash garlic to a paste with salt (or pound with a mortar and pestle). Blend with basil in a food processor until basil is finely chopped. Add oil and cheese and puree.
Top servings with a spoonful of pistou, then stir.
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