In the 'bad' ending of Pikmin 1, Olimar is taken to the Onion and becomes a Pikmin like creature, but it's his head with a little black stem. Maybe Black Pikmin are like converted Hocotatians, plus in the 'Good' ending, you can see 4 Black Onions floating up to the atmosphere either to follow Olimar or hover above the planet for the night :O
just a thought since Spyro's got Black Pikmin in the story.