My original background is biological water treatment technology; I have focused on aquatic microbial ecology since my PhD, studying the ciliate-induced processes behind the activated sludge treatment using continuous flow cultivation, eliminating xenobiotics, and the enhanced phosphorus accumulation process. In 90' I co-introduced a direct measurement of the ciliate feeding rate by using fluorescently labelled prey and started to study ciliates in water reservoirs (1994-2018, Slapy and Římov reservoir, Czech), and oligotrophic lakes (the EU Environment and Climate Programme MOLAR). During the 90' cholera pandemic in Mexico, I study the possible Vibrio cholerae elimination in brackish water and saline lakes, and experimentally modelling the processes. For the last decades, my granted research has dealt with the role of ciliates within the microbial loop in stratified athalassohaline lakes with an anoxic hypolimnion Alchichica, Mexico; ciliates since 2003). Picophytoplankton quantification and bacterioplankton direct hybridization in situ identification in ciliate vacuoles, and infrared fluorescence microscopy of anoxygenic photosynthetic bacteria were introduced. Long-term changes in the water bodies’ microbial loop are being evaluated from the point of view of climate changes in the above-mentioned water bodies.