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Plant-associated bacteria fulfill important functions for plant growth and health. However, our knowledge about the impact of bacterial treatments on the host's microbiome and physiology is limited. The present study was conducted to assess the impact of bacterial inoculants on the microbiome of chamomile plants  Chamomilla recutita  (L.) Rauschert grown in a field under organic management in Egypt. Chamomile seedlings were inoculated with three indigenous Gram-positive strains ( Streptomyces subrutilus  Wbn2-11,  Bacillus subtilis  Co1-6,  Paenibacillus polymyxa  Mc5Re-14) from Egypt and three European Gram-negative strains ( Pseudomonas fluorescens  L13-6-12,  Stenotrophomonas rhizophila  P69,  Serratia plymuthica  3Re4-18) already known for their beneficial plant-microbe interaction. Molecular fingerprints of 16S rRNA gene as well as real-time PCR analyses did not show statistically significant differences for all applied bacterial antagonists compared to the control. In contrast, a pyrosequencing analysis of the 16S rRNA gene libraries revealed significant differences in the community structure of bacteria between the treatments. These differences could be clearly shown by a shift within the community structure and corresponding beta-diversity indices. Moreover,  B. subtilis  Co1-6 and  P. polymyxa  Mc5Re-14 showed an enhancement of the bioactive secondary metabolite apigenin-7- O -glucoside. This indicates a possible new function of bacterial inoculants: to interact with the plant microbiome as well as to influence the plant metabolome.

Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants