A survey of the microbial community in the rhizosphere of two dominant shrubs of the Negev Desert highlands, Zygophyllum dumosum (Zygophyllaceae) and Atriplex halimus (Amaranthaceae), using cultivation-dependent and cultivation-independent methods

Premise of the study: Plant roots comprise more than 50% of the plant's biomass. Part of that biomass includes the root microbiome, the assemblage of bacteria and fungi living in the 1-3 mm region adjacent to the external surface of the root, the rhizosphere. We hypothesized that the microorganisms living in the rhizosphere and in bulk soils of the harsh environment of the Negev Desert of Israel had potential for use as plant-growth-promoting bacteria (PGPB) to improve plant productivity in nutrient- poor, arid soils that are likely to become more common as the climate changes. Methods: We used cultivation-dependent methods including trap experiments with legumes to fi nd nitrogen-fi xing rhizobia, specialized culture media to determine iron chelation via siderophores and phosphate-solubilizing and cellulase activities; cultivation-independent methods, namely 16S rDNA cloning and sequencing; and also community-level physiological profi ling to discover soil microbes associated with the Negev desert perennials Zygophyllum dumosum and Atriplex halimus during the years 2009-2010. Key results: We identifi ed a number of PGPB, both epiphytes and endophytes, which fi x nitrogen, chelate iron, solubilize phosphate, and secrete cellulase, as well as many other bacteria and some fungi, thereby providing a profi le of the microbiomes that support the growth of two desert perennials. Conclusion: We generated a snapshot of the microbial communities in the Negev Desert, giving us an insight in its natural state. This desert, like many arid environments, is vulnerable to exploitation for other purposes, including solar energy production and dry land farming.