Bacterial community assembly based on pineapple-associated compartment rather than genotype

We present the first study to unravel bacterial community composition and assembly in a field-grown common garden of six contrasting pineapple cultivars in a subtropical region. Bacterial communities of plant-associated compartments (i.e., rhizosphere, root, stem, leaf and fruit) of each cultivar at the premature stage were compared. We found that alpha diversity differed between plant compartments and also genotypes, but the endophytic bacteria within compartments did not decrease sharply. The richness of bacterial communities followed a spatial differentiation with higher values in below(root and rhizosphere) than in above-ground compartments (leaf, stem and fruit), but that in the three aboveground compartments were similar. Methylobacterium, Bradyrhizobium and Bacillus are dominant genus across different pineapple cultivars and compartments, which could be associated with the improved nutrition uptake and stress resistance. Bacterial community assembly was driven by the pineapple-associated compartment, rather than genotype. There was also clear niche differentiation of bacterial community at the below- above-ground interface, and the similarity of endophytic bacteria between leaves, stems and fruits occurred. The community assembly in roots was primarily dominated by stochastic processes, as bacterial community in roots and rhizosphere separated each other. This study could be helpful for the effective microbiome management practices of pineapple plantation and fruit quality control.