The intestinal liquid of A. emini was extracted using the vacuum aspiration technique, followed by measurement of ion concentrations and concomitantly recorded species abundance. Nitrate (NO3-) concentration decreased from the foregut to the hindgut. Nitrites (NO2-), ammoniums (NH4+) and orthophosphates (PO43-) reached their greatest levels in the midgut. Furthermore, correlation analyses between ion contents and ciliate abundance in different compartments were performed. In the foregut, a positive and significant correlation was found between the abundance of the Paracoelophrya ebebdensis and PO43-. In the midgut, a positive and significant correlation was observed between the number of the ciliates Dicoelophrya mediovacuolata; Coelophrya roquei; Coelophrya ovales; Ptychostomum commune and NO2-; Almophrya mediovacuolata and NH4+. In this same compartment, a positive and significant correlation was also observed between the abundance of Ptychostomum prolixus and NO2-. In the hindgut, a positive and significant correlation was found between the values of PO43- and Ptychostomum variabilis abundance. These results suggest that each portion of the digestive tract of A. emini can be considered as a set of natural micro-habitat in which a large number of ions generate ecological niches suitable for the Survival of a specific group of ciliate species.