Cyanobacteria are an abundant component of both free-living (phytoplankton) and</p><p>surface-attached (periphyton) freshwater communities. Despite this, it remains</p><p>unknown whether planktonic and periphytic cyanobacteria are structured by the same</p><p>ecological processes. Here, we explored the distribution of planktonic and periphytic</p><p>cyanobacteria diversity, based on 16S rRNA gene, in a subtropical lake system.</p><p>Variation partitioning analysis was employed to determine the influence of</p><p>environmental (water conditions) and biotic (abundance of heterotrophic bacteria)</p><p>variables on the cyanobacteria variation. We found that periphytic assemblages</p><p>showed a richness about three times higher than the planktonic ones, highlighting the</p><p>importance of the periphytic community to the overall diversity in subtropical lakes. The</p><p>picocyanobacteria Synechococcus was the dominant component of the plankton, a</p><p>taxon often underestimated using classical methods of quantification (e.g. optical</p><p>microscopy). Species replacement was the major component explaining the distribution</p><p>of diversity in both planktonic and periphytic assemblages. However, while planktonic</p><p>cyanobacteria was primarily influenced by water conditions, periphytic cyanobacteria</p><p>was influenced only by the abundance of heterotrophic bacteria. Together, our findings</p><p>showed that assemblages of planktonic and periphytic cyanobacteria are distinct,</p><p>suggesting a high habitat specialization, and the importance of environmental filtering</p><p>and biotic interactions in structuring planktonic and periphytic cyanobacteria</p><p>distribution, respectively.