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Bacterial biofilm communities formed on different membrane surfaces were investigated based on 16S rRNA gene sequence analysis. The biofilm communities were distinct from those of mixed-liquor and consisted mainly of Beta- and Gammaproteobacteria. Sequences of Xathomonas and Aquabacterium were mostly retrieved from the biofilm samples rather than from the mixed liquor. Furthermore, statistical analyses demonstrated the importance of a physico-chemical property of membrane, surface roughness, in structuring the bacterial biofilm communities.