Reputation is a system introduced in Alpha 3.12 that tracks a player's relationship with various NPCs/Organizations. Reputation is stored in Long Term Persistence, meaning that your progress will save between wipes/resets.
One can gain/lose reputation with all mission givers (except Ruto) via completing or failing contracts given to the player by them. Interactions with mission givers will vary depending on your current reputation with them, primarily in the form of different dialogue. Failing too many contracts will cause a mission giver to fire you, in which you will not be able to receive contracts from them for 24 hours.
Bounty and assassination missions utilize reputation with contracts being given by three organizations (Crusader Security, Hurston Security, and Northrock Service Group) all overseen by the Bounty Hunters Guild. As reputation with the Bounty Hunters Guild is increased, the player will be able to attempt a certification mission. Once completed, they will receive a new license and higher level bounties will be made available. Earning enough reputation with one of the three organizations listed will also result in a promotion within their ranks, earning you a pay increase depending on your current rank. More "perks" such as that are planned. Assassination missions follow the same structure as the aforementioned organizations, however are only provided by one Organization lead by a man named Vaughn.