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Abstract Aim: We investigated the spatial and temporal patterns of abundance and diversity of planktonic ciliate community, in the last undammed stretch of the Upper Paraná River, Brazil. Methods In order to reach this result, seven field campaigns were performed over two years. Plankton samples were collected from 10 transects through this stretch of the river (230 Km), near the banks and on the center, as well on seven of its tributaries. Results 118 ciliate species were identified, among which the peritrichs were the most abundant while the order Hymenostomatida was the most specious group. We recorded a remarkable increase in abundance and species richness along the river, especially in the rainy period. Moreover, in this period we found an increase in the beta-diversity along the river, which consists in a remarkable distinction among the low, middle and high stretch of the river. In this way, continuous changes in the community structure of planktonic ciliates were evidenced, highlighting the importance of the precipitation and tributaries in the maintenance of the highest regional diversity in the studied area. Conclusion Our results strongly suggest the requirement for conservation actions with the purpose to maintain those tributaries undammed, in order to avoid biotic homogenization processes and the consequent reduction of aquatic biodiversity in this important neotropical ecosystem.

Abstract: Aim: We aimed to assess the influence of bottom-up and top-down control mechanisms on the abundance and size structure of protist communities (heterotrophic flagellates and ciliates). We formulated the following hypothesis: bottom-up control mechanisms, related to the availability of resources in the environment, are responsible for structuring the abundance of these communities, whereas top-down control mechanisms, related to predation effects, determine the size pattern of these organisms. Methods Samples for planktonic organisms were taken in 20 shallow lakes belonging to the upper Paraná River floodplain. We evaluated linear regression models to select the best model which predicts the patterns observed according to Akaike Information Criterion. Results The best models selected to explain the abundance of heterotrophic flagellates included negative relations with picophytoplankton abundance and positive with rotifers abundance, while for their size structure, negative relationships were found with heterotrophic bacteria, ciliates and rotifers biovolumes. In relation to the ciliates, their abundances were positively related to the rotifers and picophytoplankton abundances and negatively with the heterotrophic bacteria abundance. On the other hand, for the size structure, the best models selected strong negative relations with the microcrustaceans biovolumes, in addition to relations with the different fractions of the phytoplankton. Conclusion For both flagellates and ciliates, their abundance is being mainly regulated by a bottom up control mechanism, whereas for the size structure the results showed that both food resources and predators were important, indicating that bottom-up and top-down mechanisms act simultaneously in determining the size of these microorganisms.