Fig. 1

Assembly of pepper bacterial and fungal communities. a Diagram of a pepper plant, and the below- and aboveground compartments, including the soil, root, stem, and fruit. b Non-metric multi-dimensional scaling (NMDS) ordinations of Bray–Cutis dissimilarity matrices with permutational analysis of variance (PERMANOVA), showing significant association of the bacterial (left) and fungal (right) community composition with, in the order of importance, the compartment (R² = 0.47 for bacteria and R² = 0.53 for fungi), Fusarium wilt disease (FWD, R² = 0.06 and 0.03, respectively), and sampling site (R² = 0.01 and 0.02, respectively). c Contribution of FWD and sampling site to the variation of bacterial (left) and fungal (right) communities in a single compartment, based on PERMANOVA. FWD explains the higher variation of fungal community than that of the bacterial community in most compartments. d Beta-dispersion analysis (based on Bray–Cutis dissimilarity) indicating higher dissimilarity of the bacterial (left) and fungal (right) communities in diseased plants than in healthy plants .e–f Shannon diversity indices of bacterial and fungal communities in the 12 compartments of healthy (red) and diseased (blue) plants