Diverse and perennial cropping systems alter microbial community structure and increase the spatial variability of microbial diversity and functioning under a precipitation gradient

Agricultural systems are experiencing increased flooding and drought episodes due to climate change, negatively affecting wheat yields and belowground processes that support plant and soil health, especially in combination with intensive and monoculture agriculture. Higher crop diversity through intercropping and substituting annual wheat with a perennial alternative may mitigate the impacts of precipitation changes by leveraging plant-soil interactions to protect the belowground soil community from water-related disturbances. We hypothesized that both more diverse and perennial cropping systems would 1) increase the abundance, diversity, and activity of the soil bacterial and fungal community, as well as 2) their stability under variable precipitation. To test this, we collected soil from a crop diversity gradient (1 species - 4 intercropped species) that either included spring wheat ( Triticum aestivum L. ) or intermediate wheatgrass (IWG; Thinopyrum intermedium ) under ambient, elevated (+30%), or reduced (−30%) precipitation. We performed qPCR, 16S gene fragment and ITS2 region amplicon sequencing and quantified respiration to determine microbial abundance, diversity and activity. Our hypotheses were partially upheld, where both crop diversity and perenniality (IWG) increased arbuscular mycorrhizal fungal abundances and influenced fungal community structure, and IWG increased rhizosphere fungal α-diversity relative to wheat. However, these changes were often associated with increased variability of microbial community responses to precipitation, particularly in microbial α-diversity and CO 2 respiration. Further, recruitment dynamics from the bulk soil differed between annual wheat and IWG, with the latter reducing the evenness of the rhizosphere bacterial community. By clarifying how crop diversity and perenniality differ in shaping microbial communities, our results help refine strategies to maintain soil communities under variable precipitation. • Both crop diversity and perenniality affected AMF abundances and fungal communities • More AMF in IWG likely reflects rhizosphere selection • IWG selected for bacteria often considered beneficial for plants • IWG reduced the diversity of the rhizosphere bacterial community