Freshwaters are among the most vulnerable ecosystems to climate warming, with projected temperature increases over the coming decades leading to significant losses of aquatic biodiversity. Experimental studies that directly warm entire natural ecosystems in the tropics are needed, for understanding the disturbances on aquatic communities. Therefore, we conducted an experiment to test the impacts of predicted future warming on density, alpha diversity, and beta diversity of freshwater aquatic communities, inhabiting natural microecosystems—Neotropical tank bromeliads. Aquatic communities within the tanks bromeliads were experimentally exposed to warming, with temperatures ranging from 23.58 to 31.72°C. Linear regression analysis was used to test the impacts of warming. Next, distance‐based redundancy analysis was performed to assess how warming might alter total beta diversity and its components. This experiment was conducted across a gradient of habitat size (bromeliad water volume) and availability of detrital basal resources. A combination of the highest detritus biomass and higher experimental temperatures resulted in the greatest density of flagellates. However, the density of flagellates declined in bromeliads with higher water volume and lower detritus biomass. Moreover, the combination of the highest water volume and high temperature reduced density of copepods. Finally, warming changed microfauna species composition, mostly through species substitution (β_repl component of total beta‐diversity). These findings indicate that warming strongly structures freshwater communities by reducing or increasing densities of different aquatic communities groups. It also enhances beta‐diversity, and many of these effects are modulated by habitat size or detrital resources.

Functional diversity approaches have been an efficient tool in gaining a better understanding of how environmental conditions selected species in a given environment and how they share resources, linking ecological processes to biodiversity patterns. Although most of the protist ciliates are not highly specialized, functional feeding groups with species which ingest similar food can be identified. Thus, this study aimed to compare the abundance of different Functional Feeding Groups (FFG) of ciliates in environments with different hydrodynamic conditions (lotic and lentic) in different hydrological periods (high and low water) in a neotropical flood plain. The samples for analysis of the community of ciliates were taken in March and September of 2010 and 2011, at the subsurface of 12 different hydrodynamic environments. The results of an RDA showed a spatial and temporal segregation of the sampling units, based on the abundance and occurrence of the FFG. In addition, a clear influence of food resources on the structuring of functional ciliate guilds was evidenced. Thus, there were both temporal (hydrological periods) and spatial (different hydrodynamic environments) differences in the distribution of the FFG, with a clear separation of the FFGs between the years studied. In summary, the results of the categorization of species of ciliates in FFG responded satisfactorily suggesting fluctuations in different food resources, which reinforces the idea that the grouping of species by functional characteristics can be a good indicator of the responses of organisms to environmental fluctuations.