When a bearded dragon's beard turns to a darker shade or black, it is typically as a sign of aggression. It is likely to be accompanied by a fluffing out of the beard in order to appear larger and more menacing.
Aggressive behaviors like this are not common among bearded dragons, but may be a warning of attack.
Other signs of aggression include hissing, biting and head bobbing. That said, head bobbing is also used as a means of communication between bearded dragons.
Handling a bearded dragon during times of aggression, ideally while wearing protective gloves, may help to strengthen a bond with it. In any case, not doing so is unlikely to lower its aggression.