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Patterns in rainfall and soil water availability are considered to be the main drivers governing arid and semiarid ecosystems. While the mechanisms by which water limits aboveground net primary production has been widely explored, few long-term studies have examined interactions between precipitation, soil resources, plant communities, and soil microbial communities; these may be critical to understanding soil biogeochemical cycles and above- and belowground interactions. We capitalized on a long-term biotic manipulation (exclusion of small mammal herbivores from replicate plots) and long-term variation in rainfall to assess how precipitation, small mammals, and shrub cover act directly and interactively to influence the spatial and temporal distribution of soil microorganisms, a key first step to understanding soil biogeochemical cycles. We measured the abundance of arbuscular mycorrhiza (AM), soil fungi, soil bacteria, and soil physicochemical characteristics over 10 consecutive years in a semiarid thorn scrub community in north central Chile; we sampled two microhabitats (under shrub cover, and in open spaces between shrubs colonized by ephemeral plants), and in plots with or without the presence of native small mammals, the main herbivores in this environment. Annual rainfall ranged widely (11 356 mm) in this period and was the primary factor affecting abundance of AM root colonization and soil microbes. While the percentage of root length with AM was higher in dry compared to wet years, free-living soil bacteria and fungi were more abundant during wet years. All microorganisms were more abundant in the resource islands beneath the shrubs compared to open microhabitat between shrubs, although the relation between soil biota and the concentration of some particular nutrients was negative. These patterns were modulated by the presence of small mammals, which enhanced root colonization by AM fungi, particularly for ephemeral plants, but which were negatively associated with soil fungi abundance. The abundance of soil bacteria showed a more complex response to the presence of small mammals and was dependent on microhabitat and year. The spatial and temporal heterogeneity of soil resources and the activity of small mammals are important modulators of subterranean biotic responses to rainfall, the primary factor affecting soil microbiota abundance in this semiarid ecosystem. (C) 2015 Elsevier Ltd. All rights reserved.