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The distribution of soil microbial species over environmental gradients underlies their response to changing environmental conditions. We used phylogenetic DNA microarrays to make high-resolution, replicated assessments of microbial community structure and its relationship to environmental parameters in soils from six distinct temperate and tropical ecosystems. We detected over 3000 different archaea and bacteria across all soils and used several multivariate techniques to examine patterns in community structure and their relationship to environmental variables. Soil moisture, pH, and the availability of nutrient cations and phosphorus explained 80% of the variability in bacteria and 96% of the variability in archaea community structure across all sites. Differences in community structure were largely driven by species of Euryarchaea, Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria whose richness and relative abundance varied significantly with gradients in moisture, pH and nutrients. While total bacteria species richness was not different between ecosystems, richness within the archaea and specific phyla of bacteria showed significant and contrasting responses to environmental factors. Our results show soil microbial community structure is tractable and predictable at scales large enough to enable regional estimates of microbial biogeography and its response to environmental change.