Conventional seed coating reduces prevalence of proteobacterial endophytes in Nicotiana tabacum

The seed microbiota of plants was recently identified as an important reservoir of beneficial microorganisms that can be vertically transferred across different generations. However, natural factors as well as agricultural practices that influence the community composition in seeds remain unknown. In the present study, Nicotiana tabacum was implemented as a model to study how seed coating, which is a highly prevalent agricultural practice, affects its bacterial endophytes. Comparative analysis of bacterial marker genes obtained from the endosphere of coated as well as uncoated seeds was conducted with the same plant cultivar and seed production batch. The community composition of coated and uncoated seeds showed highly significant (R = 0.97; p = 0.001) differences. Following data normalization, 57 out of 155 bacterial features (36.8 %) were found to be uniquely present in uncoated seeds. Another 23 features (14.8 %) showed a significantly lower abundance in coated seeds. Seed coating mostly affected bacteria from the phyla Proteobacteria and Bacteroidetes where the genera Pseudomonas, Rhizobium, Brevundimonas and Sphingobacterium accounted for the most frequent taxa that were either depleted or reduced in their relative abundance. On the contrary, 11 Gram-positive taxa were shown to be enriched following the procedure, indicating a higher resilience towards the employed coating material. Our results provide the first insights into community-level responses of seed-endophytic bacteria to seed coating. Moreover, they show that a substantial proportion of naturally occurring seed endophytes is affected by the employed procedure.