These are very large and mutated, presumably single celled organisms like the Bacterium that appeared in Parasite Eve. The Amoeba is very similar to the Flan commonly encountered in Final Fantasy. They cannot be damaged by most normal attacks save for grenades or Firefly rounds. Combustion and Necrosis can destroy then easily. Green Amoebas can be extremely hard to see because their dormant state is extremely small and it is easy for it to ambush Aya. Their attacks also inflict Silence which can be, very, very dangerous considering their immunity to physical attacks.
