Water deficit affects inter‐kingdom microbial connections in plant rhizosphere

Summary The frequency and severity of drought are increasing due to anthropogenic climate change and are already limiting cropping system productivity in many regions around the world. Few microbial groups within plant microbiomes can potentially contribute towards the fitness and productivity of their hosts under abiotic stress events including water deficits. However, microbial communities are complex and integrative work considering the multiple co‐existing groups of organisms is needed to better understand how the entire microbiome responds to environmental stresses. We hypothesize that water deficit stress will differentially shape bacterial, fungal, and protistan microbiome composition and influence inter‐kingdom microbial interactions in the rhizospheres of corn and sugar beet. We used amplicon sequencing to profile bacterial, fungal, and protistan communities in corn and sugar beet rhizospheres grown under irrigated and water deficit conditions. The water deficit treatment had a stronger influence than host species on bacterial composition, whereas the opposite was true for protists. These results indicate that different microbial kingdoms have variable responses to environmental stress and host factors. Water deficit also influenced intra‐ and inter‐kingdom microbial associations, wherein the protist taxa formed a separate cluster under water deficit conditions. Our findings help elucidate the influence of environmental and host drivers of bacterial, fungal, and protistan community assembly and co‐occurrence in agricultural rhizosphere environments.