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Ciliate assemblages play a significant role in the microbial food web. The effects of environmental temperature on assemblage composition may be influenced by abiotic factors such as seasonality and disturbance, but the effects of temperature on ciliate assemblages found on different substrata have not been explored. Sandy bottoms and submerged rocks harbour dissimilar ciliate assemblages, and it might be expected that their ciliate assemblages will respond differently to temperature., We studied how alpha diversity, beta diversity and total biomass of ciliate protist assemblages found on sandy bottoms and submerged rocks differed in 13 geothermally heated streams in Iceland whose mean temperatures range from 5 to 20 °C. We recorded number of operational taxonomic units ( OTUs) and measured the size of cells in ciliate assemblages from both substrata., Effects of temperature on natural ciliate assemblages were substratum dependent. On rock surfaces, both total ciliate biomass and alpha diversity declined with increasing temperature, and beta diversity increased with increasing temperature difference due to OTU nestedness (assemblages from warm streams being composed chiefly of subsets of the OTUs found in colder streams). In sandy substrata, however, ciliate assemblage composition was independent of temperature., Substratum-specific responses may be due to differences in mechanical disturbance, nutrient availability or exposure to invertebrate grazers. Rock-surface assemblages may be more exposed to the flow and retain less nutrient than those of sandy substratum; thus, they may be more strongly resource limited and more responsive to direct effects of temperature on metabolism. Alternatively, rock-surface assemblages may be more exposed to grazing by invertebrates, which intensifies with temperature., Our study highlights the need to account for environmental context such as substratum type to fully understand the effect of temperature on microbial assemblages in streams. Future increases in global temperatures may affect fresh waters differently depending on their prevalent substratum. Those dominated by hard substrata may have their ciliate assemblages, and thus, food-web structures and ecosystem functioning more strongly affected by warming relative to systems dominated by soft substrata. [ABSTRACT FROM AUTHOR]