PRIMARY RESEARCH PAPER Multifaceted approach for the analysis of the phototrophic microbial community in a freshwater recreational area of Xochimilco, Me ´xico Rosaluz Tavera • Beatriz Dı ´ez Received: 10 June 2009 / Revised: 19 September 2009 / Accepted: 5 October 2009 / Published online: 30 October 2009 Ó Springer Science+Business Media B.V. 2009 Abstract The freshwater microbial community in a recreational area of Xochimilco, Me ´xico was inves- tigated and compared based on spatial (three different sites) and temporal (dry and rainy seasons) environ- mental variables. Many of the 16S- and 18S rRNA gene sequences recovered by DGGE fingerprinting analysis were related to phototrophic microbial phyl- otypes of known identity. Our genetic and morpho- logical analysis indicated the ubiquitous presence of the microeukaryotic green algae Desmodesmus- Scenedesmus spp. and of the unicellular cyanobacteria Cyanobium spp. as the most representative popula- tions in the samples. While 18S rRNA-DGGE finger- printing analysis revealed a homogeneous community composition across sites and seasons, the 16S rRNA showed significant differences between localities and seasons. None of the cyanobacteria species with potential to produce toxins were identified across the investigated samples. Correlations between biotic and abiotic variables evidenced an important difference between the dry and the rainy season, with a greater consistency in data from the rainy season. According to Principal Component Analysis (PCA), a strong relation between inorganic nitrogen, species richness, and subaquatic irradiance determines environmental variability in Xochimilco. Complementary and rele- vant data in results obtained from microscopy, fingerprinting, and statistical analysis applied in ecology indicate that a multifaceted approach to the study of microbial communities is necessary to accomplish a comprehensive scientific framework and to generate proper management strategies. Keywords DGGE  Diversity  Phytoplankton  Picoplankton  PCA  Shallow lakes  Aquatic ecology Introduction Planktonic organisms are good indicators of water quality and aquatic ecosystem health (Stevenson & Smol, 2003). However, the most accurate taxonomic identification is required to assess diversity and ecological role of specific species in communities, and there are still many species that have not been Handling editor: J. Padisak R. Tavera (&) Department of Ecology and Natural Resources, Facultad de Ciencias, Universidad Nacional Auto ´noma de Me ´xico (UNAM), CU Coyoaca ´n, A.P. 70-747, 04510 Mexico, DF, Mexico e-mail: rts@hp.fciencias.unam.mx B. Dı ´ez Department of Botany, Stockholm University, 10691 Stockholm, Sweden B. Dı ´ez Department of Biologia Marina i Oceanografia, Institut de Cie ´ncies del Mar, CMIMA, CSIC, Passeig Marı ´tim de la Barceloneta, 37-49, 08003 Barcelona, Spain 123 Hydrobiologia (2009) 636:353–368 DOI 10.1007/s10750-009-9965-8