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Complexity of river ciliate communities at a National Park highlights the need for microbial conservationQuintela-Alonso, P.; Perez-Uz, B.; Sanchez-Jimenez, A.; Murciano, A.; Centeno, JD.; Garcia-Rodriguez, M.; Montero, E.; Munoz, B.; Olmedo, C.; Refoyo, P.; et al. (Wiley, 2017-12-07)Microorganisms play pivotal roles in aquatic ecosystems. Free‐living protists are the main components of the eukaryotic microbial communities at the base of freshwater ecosystems. Ciliate grazing channels a large proportion of organic matter into multicellular organisms. Surprisingly, ciliates and other microorganisms are neglected in global conservation schemes. Interstitial ciliates were sampled in three sites of varying human pressure on the River Manzanares (La Pedriza National Park, Spain). Abundances of trophic groups and species were adjusted to a generalized linear model (GLM Poisson regression). Ciliate communities were rich in species (74 morphotypes) and although traditional microscopy retrieved a high number of species that appeared only once or in low numbers, rarefaction analyses estimated much larger species richness. These results illustrate that rarefaction assays are a useful first step for exploring the extent of the ciliate cryptic diversity in freshwater ecosystems. Benthic ciliate communities changed significantly, both spatially and at a short temporal scale. The fluctuating nature of the community was manifested by the presence of many ephemeral species at the same river site, revealing a complex and transient community structure. No significant short‐term changes were observed in the physical–chemical properties. Therefore, even slight differences in the abiotic variables may cause rapid shifts of ciliate species. Overall, human pressure had an effect on the interstitial (or benthic) ciliates that resulted in a reduction of species richness and their abundance.