Fig. 1

AM fungi-rich hyphal samples host a bacterial microbiome that is distinct from root and soil samples. A Schematic representation of 5-compartment microcosm in Experiment I. Compartment (COMP3) is filled with 30% of either organic (OS) or conventional (CS) soil, whereas COMP1, 2, 4, and 5 are filled with sterilized substrate. Roots are contained in COMP3 by filter mesh with 30-µm pores (white dashed lines), whereas extraradical AM hyphae are restricted from entering COMP1 by filter mesh with 1-µm pores (green dashed line). B PCoA of fungal communities using Bray–Curtis distances in root, soil and hyphal samples of plants growing in either CS (open symbols) or OS (closed symbols). C PCoA of bacterial communities in root, soil and hyphal samples of plants growing in either CS or OS. Colors in (B) and (C) indicate different sample types. Shapes depict the compartments of microcosm. D Relative abundance of fungal phyla in root and soil samples from COMP3 and hyphal samples from COMP5. Colors represent the distinct phyla as indicated in the legend. Phyla with relative abundance below 1% were aggregated and categorized as low abundant. E Relative abundance of Glomeromycota spp. in root, soil and hyphal samples in Experiment I. Colors represent the distinct AM fungal species as indicated in the legend