Purchasing new colonies is the main means for increasing BPS and BPC.
All colonies and regular colony upgrades are used up when attacking a planet or entering a Black Hole.
Gene strand upgrades to colony production are only lost when entering a Black Hole, but BPC and BPS bonuses from the Dark Matter Institute and Premium purchases are permanent.
The effective production of colonies is also influenced by the equipped evolved bacteria, which can boost the total BPS, idle BPS, or reduce colony price.