Processes of assembly of endophytic prokaryotic and rhizosphere fungal communities in table grape are preponderantly deterministic

Understanding the assemblage of microbial communities is important for the health maintenance and post-harvest quality of fruit crops. However, systematic studies on the core microbiomes of table grapes and microbial community assembly of soil-plant continuum are still rare. To address this, samples were collected and analyzed from key microbiome compartments (bulk soil, rhizosphere of new roots and old roots, endosphere of new and old roots, and endosphere of leaves and fruits) of five table grape cultivars (Balado Black, Jingya, Fujimino, Victoria and Kyoho) at the swelling stage and harvest stage in the field plots. Prokaryotic and fungal communities were analyzed using 16S rRNA and ITS rRNA high-throughput sequencing, respectively. The compartment was the major factor attributable to the variations in both prokaryotic (52.5 %) and fungal communities (23.2 %), respectively. The richness and phylogenetic diversity of both prokaryotic and fungal communities decreased significantly along the compartment continuum from soil to fruit endosphere, but did not differ between the five cultivars across all samples. Occupancy-abundance distribution was used to define 97 core bacteria, 29 core fungi for rhizosphere soil and five core bacteria, 172 core fungi for endosphere. Functional annotations of the rhizosphere core bacteria were mostly associated with ureolysis and chemoheterotrophy, while endophytic core bacteria were mostly fermentative and symbiotic. Rhizosphere core fungi were saprophytic and the endophytic fungi were putatively pathogens. From rhizosphere soil to aboveground organs, the relative importance of deterministic processes for prokaryotic community assembly gradually increased but the contribution of stochastic processes increased for fungal community assembly. These findings highlight niche-specific microbial communities and shared core microbiomes in different grapevine cultivars. The deterministic processes contribute more to the assembly of prokaryotic communities in the aboveground than in the belowground while the assembly of fungal communities exhibits opposite trends. Management practices aiming at niche-specific microbiome should be developed for sustainable grape production. •The community of prokaryotes and fungi are niche-specific.•Core microbiomes exhibit functional differences between rhizosphere and endosphere.•Prokaryotic community assembly is mainly deterministic but fungal community exhibits opposite trends along the continuum.