Change in resonant frequency of quartz crystal with atmospheric pressure?
Remember that a crystal works on mechanical motion.  When something vibrates in air, some power is transferred to the air.  Loudspeakers rely on this, for example.

Anything vibrating in air will make sound, which means some power from the vibrating thing gets transferred to the air.  With air around the crystal, some the energy stored at resonance is lost to the air each cycle.  Effectively this lowers the Q of the crystal.  This effect must be quite small, but it doesn't seem like a stretch to be able to measure it at the PPB level.