Colony projects can be divided into two kinds: Ongoing conversion of a colony's Production output for either pollution, income, or export (industrial), or upgrading the planet's biome (terraforming).
Terraforming is the slow process of altering the environmental characteristics of a planet. This changes weather patterns, stabilizes extreme temperature fluctuations, and adjusts the abundance of surface water. Terraforming will only work on planets that have hospitable environments already. You can terraform a planet several times, but each application has an increased production cost.
Upgrades Desert planets to Grassland-class by dramatically altering moisture concentration in different areas of the planet via artificial underground aqueducts.
The Gaia Transformation introduces genetically engineered microorganisms into a world to create an environment perfectly suited to both plant and animal growth. The transformation can only be applied to Terran environments turning them into Gaia-class worlds.