just kill it lol --- http://i.somethingawful.com/inserts/articlepics/photoshop/10-17-08-gameskills/Designer0.jpg http://i.somethingawful.com/inserts/articlepics/photoshop/10-17-08-gameskills/Mediocre_Dane1.jpg
Amazon hasn't shipped my copy yet, but in other Castlevania games, there was a skeleton plucking a Mandragora out of the ground. You'd have to kill the Mandragora after it was plucked but before it screamed to get its soul/items. If you waited too long, it'd self-destruct. If you attack too early, you'd just kill the skeleton.
Don't know if they redid the Mandragora in OoE, though.
"Do you have any idea what irony is?" - Blackadder "Yeah, it's like goldy and bronzy, only it's made of iron." - Baldrick