**Abstract**

Ciliates are important elements of the trophic networks of aquatic and terrestrial environments, they can be primary producers (myxotrophs), consumers of bacteria, algae, flagellates, even other ciliates and can serve as food for metazoans, for all the above they are the link between different levels of food webs. The structure of the ciliates varies according to the seasons of the year and depending on the trophic conditions of the aquatic systems. Ciliated communities have modifications and adaptations in response to environmental perturbations. The objective of this chapter is to describe the importance of different trophic groups of ciliates in different ecosystems, including anthropogenic perturbations and their impact on trophic webs.

**Keywords:** ciliates, trophic groups, food webs, perturbations
