During the D6 mission, some large glowing incubation sacs on the walls will drop slime and some rather unsavory balls that move toward you and explode, causing damage. These are the amoebas, and you'll likely kill 5 of them without even trying. If for some reason you run away and let your ally do all the fighting though, you could theoretically miss the achievement, so make sure you stick around and kill 5.
I've created a full Enlightened playthrough video showing almost every Moral Point in the game as well as pointing out items of interest, such as this achievement.
You can see the D6 mission starting at the
1:50:57 mark in the video. The portion with the amoebas is at
1:51:41.