The pruning joke in the movie Elemental is a reference to a scene where the characters Ember and Wade are caught by a security guard while sneaking around. When asked what they are doing, they claim they are just "pruning," which is a more socially acceptable activity that involves trimming a tree to help it grow. The joke is a play on words and is meant to be humorous. It is not a significant plot point in the movie and is just one of many jokes and puns throughout the film.