Plant-specific microbial diversity ensures functional redundancy for beneficial interactions at the soil-root interface

Plant-specific microbial diversity reflecting host-microbe coevolution was frequently shown at the structural level but less on the functional scale. We studied the microbiome of three compartments at the soil root interface (endorhiza, rhizosphere, bulk soil) of medicinal plants cultivated under organic management in Egypt. At the structural level, we found the typical rhizosphere effect and plant-species-specific enrichment of bacterial diversity. For all structural parameters, the annual plants Calendula officinals and Matricaria chamomilla (both Asteraceae) were more similar than the perennial Solanum distichum (Solanaceae). Altogether, plant species explained 50.5% of the variation in bacterial community structures in the rhizosphere. Interestingly, our results indicate a stronger effect of the plant species in terms of modulating bacterial community structures in the rhizosphere than in endosphere samples. The plant-driven rhizosphere effect could be linked to redundant plant beneficial functions in the microbiome, while enrichment of specific genes related to amino acid ion transport and metabolism, carbohydrate transport and metabolism, defense mechanisms, and secondary metabolites biosynthesis were more specific. Our results indicated that different plant hosts specifically modulated microbial function in the rhizosphere associated with bacterial survival strategies and niche adaptation under pressure of antimicrobial metabolites. This was further supported by an increase of in abundance 36 CAZymes gene families related to fructan degradation occurred in higher abundances in the rhizospheres of the Asteraceae plants, which are known to accumulate fructan as reserve carbohydrates. Constructed metagenome assemble sequences (MAGs) belonging to Gammaproteobacteria, Alphaproteobacteria, Gemmatimonadetes, Nitrososphaeria, and Anaerolineae showed that similar microbial functions can be maintained by different bacterial communities in rhizospheres.