Fig. 5

Compositional differences between domesticated and uncultivated soil communities correlate with differential plant growth in rice. a Heights of 21-day-old rice seedlings grown in calcined clay inoculated with live soil microbiota suspensions (solid circles) or mock suspensions (empty circles). Each color represents the history status and source of the soil used to generate the corresponding inoculum. Different letters specify significant differences between treatments (Tukey test, P < 0.05 after multiple-comparison adjustment). See also Additional file 1: Figure S9 for additional trait measurements. b Hierarchical clustering of endosphere communities based on Bray-Curtis dissimilarities between samples. The shape and color of each point represent inoculum type and soil source, respectively, and follow the same scheme as in panel a. The bar plot below each point displays the relative abundances of the most abundant phyla and Proteobacteria classes in each community. c Phylogenetic tree of endospheric OTUs significantly correlated with seedling height in plants grown in calcined clay inoculated with a live microbiota suspension (Wald test, P < 0.05 after multiple-comparison adjustment). The colored arcs indicate the phylum or Proteobacteria class of select branches and follow the same color scheme as in panel b