The referee is shouting 'Use It'. He is asking the team with possession of the ball to use the ball, and (in most cases) warning that if they do not, they will lose possession of it to the other team. Some referees even say 'Use it or lose it'.
Under the established laws of the game you most often hear this when the ball is in a maul that is no longer moving forward. Law 17.6 calls this an unsuccessful end of a maul - if the ball stops moving forward for 5 seconds, a scrum is called and the defending team get the put in. The referee is warning the attacking team that they are about to lose possession and they should do something with the ball - either continue moving the maul forwards, or pass the ball out of the maul.
Until recently you didn't often hear 'use it' in other situations. In a ruck there is not this 5 second law. If the attacking team keep the ball from emerging (i.e. keep it under the feet of people in the ruck), they can keep the ball in that position for many seconds while they organize their next attack, or just to slow the game down. The referee can deem too much time to have passed for the ball to emerge and call a scrum, but according to Law 16.7 the referee can allow a 'reasonable amount of time'. Also in a ruck if there is no obvious 'team moving forward' then the attacking team keeps the put-in so the 'lost it' part is not the case there. It probably does get called in deliberately slow rucks, but its usually advantageous to the attacking team to quickly recycle the ball and continue to attack, so having to warn the attacking team probably doesn't happen as often.
As pointed out by @Rawling, the Law Amendment Trials include proposed law changes that enforce specific behavior at the ruck - when the ball is available to a team to use, the referee will call 'Use It' after which they have 5 seconds to pick the ball up and use it. These are currently being trialled, but I'm not sure which competitions are using them - I've only recently watched the Six Nations, and I don't recall seeing this. Looking at the clip provided of the match - Hurricanes v Highlanders - it certainly appears that this game was using amended laws.
However even under existing non-amended laws where this call is not a formal part of the game, it is still a very common convention used by referees to prevent unnecessary stoppages for scrums - to encourage exciting continuous play in the game.