Exploiting mycorrhizal selection of beneficial rhizosphere bacteria from the soil microbiome.

Soil health is dependent on its diverse communities of microbes. Many of these microorganisms enhance plant growth and enrich the soil. However, the interactions between communities of beneficial microbes remain unclear. Arbuscular mycorrhizal fungi (AMF) are responsible for the most prolific beneficial plant-fungal interaction. However, their influence on the diverse range of plant growth promoting rhizobacteria (PGPR) that also associate with plant roots is yet to be fully elucidated. This research investigates the tripartite interactions between host plant-AMF-PGPR using next-generation sequencing and culture- dependent methodology to define the effect of AMF inoculation on the taxonomic and functional characteristics of the bacterial assemblage of the root microbiome of white clover (Trifolium repens). Soil from two land use types (grassland and bare fallow) amended with fertiliser and/or AMF inoculants are used to describe the effect of these management components on the function of beneficial microbes in cropping systems. The AMF Funneliformis geosporum affected the taxonomic composition of bacteria in the rhizosphere but not the rhizoplane. However, soil type and fertiliser were more influential determinants of bacterial taxa and function. Using split-root microcosm experiments with root exclusion meshes, the dispersal of bacteria was observed in the absence of AMF hyphae. The approaches were combined to show that root microbiome establishment is independent of AMF hyphal facilitation or selection of beneficial bacterial traits or taxa. In vitro predictive measures were used to design a putative Phosphorus solubilising consortium comprised of synergistic P-solubilising rhizobacteria and AMF. Plant health parameters were influenced by the addition of Ca₃PO₄ but were unaffected by any microbial combination. The performance of a putative bioinoculant is dependent on many external factors which can negatively impact the intended function. This work is an important indicator of the complexity of the soil microbiome and demonstrates the profound influence of agronomic inputs on microbial function.