Arbuscular mycorrhizal fungi co-colonizing on a single plant root system recruit distinct microbiomes

Background: Plant roots are usually colonized by various arbuscular mycorrhizal (AM) fungal species which vary in morphological, physiological and genetic traits and constitute the mycorrhizal nutrient uptake pathway (MP) in addition to roots. Simultaneously, the extraradical hyphae of each AM fungus is associated with a community of bacteria. However, whether the community structure and function of microbiome on the extraradical hyphae would differ between the AM fungal species are mostly unknown. Methods: In order to understand the community structure and the predicted functions of the microbiome associated with different AM fungal species, a split-root compartmented rhizobox culturing system, which allowed us to inoculate two AM fungal species separately in two root compartments was used. We inoculated two separate AM fungal species combinations, Funneliformis mosseae ( F.m ) and Gigaspora margarita ( G.m ), Rhizophagus intraradices ( R.i ) and G. margarita, on a single root system of cotton . The hyphal exudate fed active microbiome was measured by combining 13 C-DNA stable isotope probing with Miseq sequencing. Results: We found different AM fungal species, that were simultaneously colonizing on a single root system, hosted distinct active microbiomes from one another. Moreover, the predicted potential functions of the different microbiomes were distinct. Conclusion: We conclude that the arbuscular mycorrhizal fungi component of the system is responsible for the recruitment distinct microbiomes in the hyphosphere. The potential significance of the predicted functions of the microbiome ecosystem services is discussed.