Compositional changes of the bacterioplankton assemblages in four high altitude middle Atlas lakes were monitored over a complete seasonal cycle using combinations of culture-dependent and molecular approaches. Viable bacterial numbers varied between seasons, with the lowest numbers recorded in the winter and the highest in the summer in all four lakes. Also, bacterial occurrences were found to be strongly correlated with water temperature in all the four sites, i.e., Lake Aoua (0.88), Ifreh (0.59), Hechlef (0.77) and Affourgagh (0.79) during the study period. Standard microbiological characterization of bacteria isolates from the lakes revealed majority (68%) to be Gram positive. Seasonal variations in the microbial assemblages among the lakes were also validated by restriction fragment length polymorphism (RFLP). Shifts in microbial assemblages, especially of the fecal indicator bacteria appeared to also be influenced by differences in the morphometric and watershed characteristics among the lakes. This study further reveals the need to employ combinations of methodological approaches, including taxonomic, physiological and molecular methods to adequately delineate and fully understand the ecology of microbial assemblages in extreme environments.
 A. Alfreider, J. Pernthaler, R. Amann, B. Sattler, F.-O. Glockner, A. Willie and R. Psenner, “Community Analysis of the Bacterial Assemblages in the Winter Cover and Pelagic Layers of a High Mountain Lake by in Situ Hybridization,” Applied and Environmental Microbiology, Vol. 62, No. 6, 1996, pp. 2138-2144.
 M. Bahr, J. E. Hobbie and M. L. Sognin, “Bacterial Diversity in an Arctic Lake: A Freshwater SAR11 Cluster,” Aquatic Microbial Ecology, Vol. 11, No. 3, 1996, pp. 271-277. http://dx.doi.org/10.3354/ame011271
 A. K. Bej, R. J. Steffan, J. DiCesare, L. Haff and R. M. Atlas, “Detection of Coliform Bacteria in Water by Polymerase Chain Reaction and Gene Probes,” Applied and Environmental Microbiology, Vol. 56, No. 2, 1990, pp. 307-314.
 T. A. Cebula, W. L. Payne and P. Feng, “Simultaneous Identification of Strains of Escherichia coli Serotype O157:H7 and Their Shiga-Like Toxin Type by Mismatch Amplification Mutation Assay-Multiplex PCR,” Journal of Clinical Microbiology, Vol. 33, No. 1, 1995, pp. 248-250.
 B. B. Cho and F. Azam, “Major Role of Bacteria in Biogeochemical Fluxes in the Ocean’s Interior,” Nature, Vol. 332, 1988, pp. 441-443.
 M. T. Cottrell, L. A. Waidner, L. Yu and D. L. Kirchman, “Bacterial Diversity of Metagenomic and PCR Libraries from the Delaware River,” Environmental Microbiology, Vol. 7, No. 12, 2005, pp. 1883-1895.
 M. Felip, R. Sattler, R. Psenner and J. Cataln, “Highly Active Microbial Communities in the Ice and Snow Cover of High Mountain Lakes,” Applied and Environmental Microbiology, Vol. 61, 1995, pp. 2394-2401.
 X. Gao, O. A. Olapade, M. W. Kershner and L. G. Leff, “Algal-Bacterial Co-Variation in Freshwater Streams: A Cross-Stream Comparison,” Archiv für Hydrobiologie, Vol. 159, No. 2, 2004. pp. 253-261.
 F.-O. Glockner, E. Zaichikovg, N. Belkova, L. Denissova, J. Pernthaler, A. Pernthaler and R. Amann, “Comparative 16S rRNA Analysis of Lake Bacterioplankton Reveals Globally Distributed Phylogenetic Clusters Including an Abundant Group of Actinobacteria,” Applied and Environmental Microbiology, Vol. 66, No. 11, 2000, pp. 5053-5065.
 E. A. Gontang, W. Fenical and P. R. Jensen, “Phylogenetic Diversity of Gram-Positive Bacteria Cultured from Marine Sediments,” Applied and Environmental Microbiology, Vol. 73, No. 10, 2007, pp. 3272-3282.
 W. D. Hiorns, B. A. Methe, S. A. Nierzwicki-Bauer and J. P. Zehr, “Bacterial Diversity in Adirondack Mountain Lakes as Revealed by 16S rRNA Gene Sequences,” Applied and Environmental Microbiology, Vol. 63, 1997, pp. 2957-2960.
 M. Malki, I. Marín, A. Essahale, R. Amils and M. Moumni, “Physico-Chemical Parameters and Bacterial Diversity in the Moroccan’s Sebou River,” Journal of Food, Agriculture & Environment, Vol. 6, No. 1, 2008, pp. 172-176.
 N. C. Morgan, “An Ecological Survey of Standing Waters in North West Africa III: Site Descriptions for Morocco,” Biological Conservation, Vol. 24, No. 3, 1982, pp. 161-182. http://dx.doi.org/10.1016/0006-3207(82)90055-6
 O. A. Olapade, M. M. Depas, E. T. Jensen and S. L. Mc-Lellan, “Microbial Communities on Cladophora Mats along the Coastlines of Lake Michigan,” Applied and Environmental Microbiology, Vol. 72, No. 3, 2006, pp. 1932-1938. http://dx.doi.org/10.1128/AEM.72.3.1932-1938.2006
 O. A. Olapade and L. G. Leff, “Seasonal Response of Stream Biofilm Communities to Dissolved Organic Matter and Nutrient Enrichments,” Applied and Environmental Microbiology, Vol. 71, No. 5, 2005, pp. 2278-2287.
 O. A. Olapade, “Molecular Analyses of the Diversity in Marine Bacterioplankton Assemblages along the Coastline of the Northeastern Gulf of Mexico,” Canadian Journal of Microbiology, Vol. 56, No. 10, 2010, pp. 853-863.
 A. Oren, “Molecular Ecology of Extremely Halophilic Archaea and Bacteria,” FEMS Microbiology Ecology, Vol. 39, No. 1, 2003, pp. 1-7.
 J. Pernthaler, F.-O. Glockner, S. Unterholzner, A. Alfreider, R. Psenner and R. Amann, “Seasonal Community and Population Dynamics of Pelagic Bacteria and Archaea in a High Mountain Lake,” Applied and Environmental Microbiology, Vol. 64, 1998, pp. 4299-4306.
 M. Simon, B. C. Cho and F. Azam, “Significance of Bacterial Biomass in Lakes and the Ocean: Comparison to Phytoplankton Biomass and Biogeochemical Implications,” Marine Ecology Progress Series, Vol. 86, 1992, pp. 103-110. http://dx.doi.org/10.3354/meps086103
 R. L. Whitman, D. A. Shivey, H. Pawlik, M. B. Nevers and M. N. Byappanahalli, “Occurrence of Escherichia coli and Enterococci in Cladophora (Chryophyta) in Neashore Water and Beach Sand of Lake Michigan,” Applied and Environmental Microbiology, Vol. 69, No. 8, 2003, pp. 4714-4719.
 R. L. Whitman, S. E. Byers, D. A. Shivey, D. M. Ferguson and M. Byappanahalli, “Occurrence and Growth Characteristics of Escherichia coli and Enterococci within the Accumulated Fluid of the Northern Pitcher Plant (Sarracenia purpurea L.),” Canadian Journal of Microbiology, Vol. 51, No. 12, 2005, pp. 1027-1037.
 W. Zwister, N. Selje and M. Simon, “Seasonal Patterns of the Bacterioplankton Community Composition in a Large Mesotrophic Lake,” Aquatic Microbial Ecology, Vol. 31, No. 3, 2003, pp. 211-225.