Merzouga sand dunes were among the Moroccan extreme environments. Actinobacteria from this under investigated desert habitat were isolated and their antimicrobial activity was evaluated. One hundred sixty three Actinobacteria isolates were isolated from sand collected from several dunes and screened for their antibacterial and antifungal activities. To test the antimicrobial effect of isolates, four microorganisms known as human potential pathogens were used. The electrophoretic profiles of the isolates obtained by repetitive element PCR fingerprinting (rep-PCR) were compared by clustering. Results showed that among the tested isolates, 59% were active against one or more of tested Gram positive, Gram negative and the yeast Candida albicans. The importance of culture media for the activity expression is revealed. A comparative analysis of antimicrobial activity divided isolates into fifteen groups. The comparison of the average diameters of inhibition zones of all isolates using Minitab V.17 allowed subdividing the previous 15 groups into 20 subgroups. Dendrogram derived from the BOXA1R-PCR fingerprints showed that 36 isolates were grouped in 16 clusters containing from two to four isolates while 127 isolates weren’t grouped. The tested antimicrobial activities showed a low biological diversity but the Rep-PCR revealed a high taxonomic diversity of isolates. The combination of antimicrobial activity and rep-PCR results revealed a relatively high diversity patterns of Merzouga sand dune Actinobacteria.

Keywords: Actinobacteria, Merzouga sand dunes, Antimicrobial Activities, Rep-PCR, Taxonomic diversity.