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For centuries, biodiversity has spellbound biologists focusing mainly on macroorganism’s diversity and almost neglecting the geographic mediated dynamics of microbial communities. We surveyed the diversity of soil bacteria and archaea along a steep precipitation gradient ranging from the Negev Desert in the south of Israel (<100mm annual rain) to the Mediterranean forests in the north (>900mm annual rain). Soil samples were retrieved from triplicate plots at five long-term ecological research stations, collected from two types of patches: plant interspaces and underneath the predominant perennial at each site. The molecular fingerprint of each soil sample was taken using terminal restriction length polymorphism of the 16S rRNA gene to evaluate the bacterial and archaeal community composition and diversity within and across sites. The difference in community compositions was not statistically significant within sites (P = 0.33 and 0.77 for bacteria and archaea, respectively), but it differed profoundly by ecosystem type. These differences could largely be explained by the precipitation gradient combined with the vegetation cover: the archaeal and bacterial operational taxonomic units were unique to each climatic region, that is, arid, semiarid and Mediterranean (P = 0.0001, for both domains), as well as patch type (P = 0.009 and 0.02 for bacteria and archaea, respectively). Our results suggest that unlike macroorganisms that are more diverse in the Mediterranean ecosystems compared with the desert sites, archaeal and bacterial diversities are not constrained by precipitation. However, the community composition is unique to the climate and vegetation cover that delineates each ecosystem. The ISME Journal (2010) 4, 553-563; doi:10.1038/ismej.2009.136; published online 24 December 2009