Unless you're playing in some hardcore difficulty settings, you have two main choices. Either you destroy every nest before they reach the pollution cloud (which requires artillery and an easy to expand robot or train network). Or you build walls with turrets. I usually go for full solar panel energy and laser turrets as I'm scared to death to "waste" resources. But to be honest, any type of turret can do for most of the game, you just have to decide what resources you want to spend on combat.