Microbial identification of the Nichupte-Bojorquez coastal lagoon in Cancun, Mexico Ma. Fabiola Leo ´n-Galva ´n Æ Noel Carbajal Æ Tancred Frickey Æ Leticia Santos Received: 18 August 2007 / Accepted: 19 February 2008 / Published online: 11 March 2008 Ó Springer Science+Business Media B.V. 2008 Abstract The microbial community of the Nich- upte-Bojorquez lagoon system located in Cancun, Mexico was evaluated using surface-water samples that were collected before and after the hurricane Wilma impacted the area on October 2005. The analysis was done using a culture-independent molecular approach involving Amplified Ribosomal DNA Restriction Analysis, and CLuster ANalysis of Sequences. A total of 61 16S ribosomal RNA genes were differentially selected and screened. The results show a bacterial profile dominated by Cytophaga- Flavobacteria/Flexibacter-Bacteroidetes group; the Bacteroidetes group in particular. The second most abundant group was assigned to the Proteobacteria group and a minor proportion of bacteria that belongs to the Cyanobacteria and Bacilli classes. Our study gives the first insight into the bacterial community adapted to this heavily polluted but occasional oligotrophic coastal lagoon; no substantial differ- ences were, however, found. Keywords 16S rDNA Á Hurricane Wilma Á Lagoon Abbreviations ARDRA Amplified Ribosomal DNA Restriction Analysis CLANS CLuster ANalysis of Sequences UPS Practical Units of Salinity Introduction The Nichupte-Bojorquez lagoon system is located at the northeastern part of the Peninsula of Yucata ´n, in the city of Cancun, State of Quintana Roo, Mexico. It embraces an area of about 48 km 2 , with depths varying between 0.3 and 4.5 m (Fig. 1a). The coastal lagoons, to some extent an oligotrophic system, consist of four interconnected shallow lagoons and two channel systems opened to the Caribbean Sea (Fig. 1b). Several studies on the region have reported physical and chemical characteristics like high concentration values Ma. F. Leo ´n-Galva ´n Á L. Santos (&) Division of Molecular Biology, Institute for Scientific and Technological Research of San Luis Potosi (IPICYT), Camino a la Presa San Jose ´ 2055, Col. Lomas 4a. Seccio ´n, C.P. 78216 San Luis Potosi, SLP, Mexico e-mail: lsantos@ipicyt.edu.mx N. Carbajal Division of Applied Geosciences, Institute for Scientific and Technological Research of San Luis Potosi (IPICYT), Camino a la Presa San Jose ´ 2055, Col. Lomas 4a. Seccio ´n, C.P. 78216 San Luis Potosi, SLP, Mexico T. Frickey Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra, ACT 2601, Australia L. Santos Haartman Institute, University of Helsinki, Haartmaninkatu 3, Helsinki 00250, Finland 123 Aquat Ecol (2009) 43:197–205 DOI 10.1007/s10452-008-9171-1