Prime Now in Austin recently started offering delivery from Sprouts in addition to Amazon's products. Owning Whole Foods outright will give them a *substantial* inventory to add to Prime Now for every major city in the US and a strong distribution network for things they're currently not very deep in.
While Whole Foods has been struggling with competition in the organic supermarket space recently, they retain a *lot* of prime retail space, from their HQ acting as a cultural hub in downtown Austin, to Columbus Circle, a billion spots in the Bay Area and SoCal, to Central London even. Amazon could leverage this in all sorts of potential ways.
Also note that automated "walk out the store with your purchases and get charged automatically" no-checkout retail tech they've been showing off recently.