Keep your bottles up meaning
Elias : We're picking up large sonar blasts in your area
           That amount of water pressure could have lethal effects.
           Keep your bottles up and your heads down, copy?

what is the meaning of bottles up??

I would imagine that this is talking about scuba divers, and thus the 'bottle' is the diving cylinder that stores the air for breathing.  Why one should keep 'bottles up and heads down' in this situation, though, I couldn't say.