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Soil microbes represent the unseen majority of life on Earth and are essential for the functioning of terrestrial ecosystems as they catalyze unique and indispensable transformations in the biogeochemical cycles of the biosphere (Whitman et al. 1998; van der Heijden et al. 2008). The significance of soil microbial diversity for the functioning of agricultural and natural ecosystems is still poorly understood and soil microbial communities can be considered as a black box (Kennedy and Smith 1995; Cortois and de Deyn 2012). Unraveling what soil microbes are doing in this black box has been identified as one of the major research areas in science.

An increasing number of studies demonstrate that agricultural practices, such as tree based intercropping (Lacombe et al. 2009; Bainard et al. 2012a, b), organic farming (Mäder et al. 2002; Bengtsson et al. 2005; Birkhofer et al. 2008; Verbruggen et al. 2010), reduced soil …