Rhizosphere microbiome response to host genetic variability: a trade-off between bacterial and fungal community assembly. Smart Farming

The plant species and cultivars strongly influence rhizosphere microbes. However, our knowledge on how the assembly of microbes is linked with the genetic distance of plant cultivars is still limited. Here, we took advantage of vegetative propagated Chrysanthemum (Dendranthema grandiflora) as a plant model to induce roots in five commercial cultivars Barolo, Chic, Chic 45, Chic Cream, and Haydar. We report a strong rhizosphere selection for bacterial community and less for fungal communities. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. The rhizosphere fungal selection was less clear and not significantly linked with plant genetic dissimilarities. Each chrysanthemum cultivar selected unique bacterial (B) and fungal (F) genera in the rhizosphere (Barolo = 6B and 0F; Chic = 6B and 0F; Chic 45 = 3B and 3F; Chic Cream = 2B and 5F; Haydar = 7B and 1F). We also observed a trade-off in the rhizosphere selection of bacteria and fungi, where the cultivar with the strongest selection of fungal communities was the weakest for the bacterial selection. We also found bacterial and fungal Family taxonomic groups consistently selected by all the cultivars (bacteria Chitinophagaceae, Beijerinckiaceae, and Acidobacteriaceae and fungi Pseudeurotiaceae and Chrysozymaceae). Altogether, our study showed that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by their genetic dissimilarity.