Identification and characterization of novel extremophiles from the desert sand,
and the “Sebkha” and “Chott” saline systems in the south of Tunisia

It has been recently discovered that desert sands are characterized by a microbial diversity much wider than previously recognized [Chanal et al., 2006]. By using culture-dependent and culture-independent approaches it has been shown that several new, previously unknown bacterial taxa inhabit desert sand. Among these, a new genus, named Ramlibacter (from Raml = sand in Arabic; [Heulin et al., 2003]), has been described. Several of the isolates from desert sand have been shown to be capable of resisting very stressful conditions including high doses of UV and gamma rays and desiccation, suggesting that these bacteria are well adapted to stressing conditions and that interesting biotechnological properties could be exploited from these organisms.
A group of organisms that can survive stressing conditions as those found in arid soils includes saprophytic actinomycetes of three genera, Blastococcus, Geodermatophilus, and Modestobacter, which are classified within the family Geodermatophilaceae. These actinomycetes are able to produce spores with chemotactic and aerotactic capabilities. These features increase their chance to survive in arid environments. Geodermatophilaceae of the genus Geodermatophilus have been isolated from soils in the Mojave [Garrity et al., 1996] Namib and Negev deserts [Eppard et al. 1996]; strains of genera Geodermatophilus, Blastococcus and Modestobacter have been isolated from arid environments like rocks and stone monuments in the Mediterranean basin [Urzì et al., 2001; Brusetti et al., 2008]. Strains of Modestobacter have been also found in dry-cold environments such as Antarctica soils [Mevs et al., 2000]. Since these bacteria displayed many physiologically interesting feature in terms of habitat, resistances and metabolism, a sequencing project of the two species Blastococcus saxobsidens and Modestobacter multiseptatus has been launched.

Phylogenetically close to Geodermatophilaceae, the Frankiaceae include actinomycetes capable of symbiotic nitrogen fixation with several species of trees [Gtari et al., 2002; Gtari et al., 2004]. These bacteria have been found in semiarid and arid soils, in association with actinorhizal plants or in soil without these plants. In a recent study a series of Frankia strains have been isolated from several semiarid soils in Tunisia [Gtari et al., 2004]. Strains that present a relatively high degree of molecular diversity have been isolated by plant (Elaeagnus) capture assay from soils where actinorhizal plants were present as well as from soils that never hosted these plants. Recently, it has been shown that a novel population of Frankia is associated to Casuarina present in the desert oasis in the area of Tozeur in the south of Tunisia, suggesting that endemism of nitrogen fixers adapted to arid soils have an important role in the nitrogen supply of the soil [Gtari et al., 2007].

Besides the above-mentioned bacterial groups a surface layer (from few mm to cm), defined as ‘biological soil crusts' (BSC), frequently characterizes semiarid and arid soils. BSC represent complex biological communities including bacteria, cyanobacteria, green algae, fungi, lichens and mosses that together form a structured matrix covering the underlying soil layers [Yeager et al., 2004]. In the BSC cyanobacteria play a very important role in the nutritional balance giving a substantial contribution to the nitrogen uptake by the way of atmospheric nitrogen fixation. BSC favour moisture retention determining a better water balance in the soil. How the BSC contribute to the water and nutrient balance in an arid soil depends on the development and maturation of the microbiological composition [Yeager et al., 2004]. We believe that a complex microbial network, in which different bacteria cooperate between each other and with other organisms to maintain favourable water balance and a dynamic nutrient recycle, inhabits desert soils. The study of these complex bacterial communities cannot be carried out in a comprehensive way by using the traditional microbiological approaches since most of these microorganisms are characterized by slow growth rate, are difficult to isolate and/or are intrinsically unculturable.

Molecular methods based on the analysis of molecular chronometers, like the 16S rRNA gene, will allow us to overcome the limits of bacterial culturability [Yeager et al., 2004]. The bacterial assemblage in desert soils has been studied in several desert regions on earth such as for example arid areas in the United States [Dunbar et al., 1999; Kuske et al., 2002; Yeager et al., 2004], but few investigations have been carried out in the desert soils of Sahara. The application of molecular techniques for microbial ecology studies will allow us to clarifying and dissect the bacterial network of the bacteria living in arid systems in the Saharan and sub-Saharan soils. Considering the complexity of such communities the employment of advanced techniques based on microarrays would enormously increase the amount and level of information that can be obtained with a single analysis. With DNA microarrays, the number of species that can be detected in a single analysis is virtually unlimited. A high density 16S rRNA microarray (PhyloChip) has been developed recently that has a resolution of 104 taxa and the ability to identify individual taxon varying over five orders of magnitude in abundance. The PhyloChip community analysis examines how microbial community composition changes in response to environmental changes [Brodie et al. 2006; Tsiamis et al., 2008].