The effects of microbial amendment and water stress on apple rhizosphere and root microbiome

Establishment of apple trees following planting is crucial for apple production. Beneficial microbes such as arbuscular mycorrhizal fungi (AMF) and plant growth promoting rhizosphere bacteria (PGPR) can assist plants in tolerating abiotic and biotic stresses. We carried out a potted experiment to study the effect of water stress and beneficial microbe amendment (AMF and/or PGPR) at planting on apple tree growth, development of apple canker (Neonectria ditissima), and apple rhizosphere and root (rhizoplane + endosphere) microbiome. Water stress reduced tree grow; none of the treatments affected the incidence of apple canker development in the inoculated leaf scars. Rhizospheres and roots differed greatly in their microbial community structure as well as the relative bacteria:fungi biomass ratio. Fungal communities were more likely to be affected by water stress and microbial amendment than bacterial communities. Overall, the effect of water stress and AMF/PGPR amendment on the overall microbial community was limited but water stress and AMF inoculation affected relative abundance of many specific microbial taxa, particularly fungi in the rhizosphere. Water stress led to reduced relative abundance of nine AMF OTUs in the rhizosphere; AMF amendment led to increased relative abundance of a couple of AMF OTUs in the rhizosphere and roots.