prometheus - Where did the worm that appeared in the black goo chamber come from?

"We've changed the atmosphere of the room" - Dr. Shaw

Presumably the door acted as an air lock. Maybe the room was sealed off to halt the biological processes of EVERYTHING in the room (which is why the head is perfectly preserved), and the worms where already in the soil. By breaking the seal for the room, the biological processes are able to continue - maybe there was some sort of cryogenic freezing happening because of the room being sealed.

Once the seal is broken, and the biological processes have started again, the "black goo" begins to ... "unthaw" (for want of a better word), the worms begin to crawl around in the room.

At least, that was my interpretation of it.