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

Rhizosphere microbial community composition is strongly influenced by plant species and cultivar. However, our understanding of the impact of plant cultivar genetic variability on microbial assembly composition remains limited. Here, we took advantage of vegetatively propagated chrysanthemum (Chrysanthemum indicum L.) as a plant model and induced roots in five commercial cultivars: Barolo, Chic, Chic 45, Chic Cream and Haydar. We observed strong rhizosphere selection for the bacterial community but weaker selection for the fungal community. The genetic distance between cultivars explained 42.83% of the total dissimilarity between the bacteria selected by the different cultivars. By contrast, rhizosphere fungal selection was not significantly linked to plant genetic dissimilarity. Each chrysanthemum cultivar selected unique bacterial and fungal genera in the rhizosphere. We also observed a trade-off in the rhizosphere selection of bacteria and fungi in which the cultivar with the strongest selection of fungal communities showed the weakest bacterial selection. Finally, bacterial and fungal family taxonomic groups consistently selected by all cultivars were identified (bacteria Chitinophagaceae, Beijerinckiaceae and Acidobacteriaceae, and fungi Pseudeurotiaceae and Chrysozymaceae). Taken together, our findings suggest that chrysanthemum cultivars select distinct rhizosphere microbiomes and share a common core of microbes partially explained by the genetic dissimilarity between cultivars.

Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome.

Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.