Deciphering core microbiomes and community assembly of table grapes

Abstract

Abstract Aims 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. Methods We collected samples from different compartments (bulk soil, rhizosphere soil of new roots and old roots, endosphere of new and old roots, and the endosphere of leaves and fruits) of five table grape varieties of Victoria, Balado Black, Fujimino, Jingya and Kyoho at the swelling stage and harvest stage. Microbial communities were analyzed using 16S rRNA and ITS rRNA high-throughput sequencing. Results The compartment was the major factor attributable to the variations in both bacterial and fungal communities. The alpha-diversity of both bacterial and fungal community decreased significantly along the compartment continuum from soil to fruit endosphere, but did not differ among the five varieties across all samples. We used the occupancy-abundance distribution to define core microbiomes for rhizosphere soil and endosphere. Functional annotations of the rhizospheric core bacteria were mainly associated with the redox process, while endophytic bacteria were mainly fermentative and symbiotic. Rhizospheric core fungi were saprophytic and the endophytic fungi were putatively pathogens. The null models indicated that the relative contribution of deterministic processes especially homogeneous selection gradually increased along the soil-plant continuum. Conclusion Our findings highlight niche-specific microbial communities are observed in different grape varieties. The deterministic processes contribute more to the assembly of microbial communities in the aboveground than in the belowground.