Endophytic microorganisms colonise plant tissues without causing disease symptoms. Unravelling the dynamics that govern the assembly of bacterial endophytic communities is essential to understand the functioning of plants as living environments and is key to optimise the prospective application of these microorganisms as plant probiotics.

Endophytic microorganisms colonise plant tissues without causing disease symptoms. Unravelling the dynamics that govern the assembly of bacterial endophytic communities is essential to understand the functioning of plants as living environments and is key to optimise the prospective application of these microorganisms as plant probiotics. Here we used 454 pyrotag sequencing of a long 16S rDNA segment encompassing the V5-V9 hypervariable regions, to describe the variation of bacterial endophytic communities in the above- and below-ground organs in Vitis vinifera L. through the year and in different climatic conditions. To understand the effect of temperature alone, a separate experiment was set up where identical cuttings were grown in greenhouse at set temperatures. Our findings indicate that seasonality plays a central role in shaping endophytic communities. We also highlight how endophytic communities in plant roots and stems differ in taxonomic composition and in their dynamic response to changes in both season and temperature. Alpha-diversity in stem endophytic communities was highest in summer, while the peak diversity for root endophytes occurred in autumn. Noticeably, more taxa were affected by seasonal variations in the plant stems as compared to plant roots, which suggests that roots are a more stable and less easily perturbed environment. The analysis of correlation networks amongst relative abundances in plant stems showed that several taxa (including Mesorhizobium, Burkholderia, Ralstonia, Bradyrhizobium, Dyella and Propionibacterium) are ecologically linked both in field and greenhouse conditions.