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 Rhizobitan in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseadomonas. 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. (C) 2021 The Authors. Published by Elsevier B.V.

Automated summary

Plant microbiome assembly is driven by root exudates and influenced by factors such as soil type, plant developmental stage, and genotype. Over successive cultivation cycles, divergence in microbiome assembly between modern and wild tomato genotypes significantly amplifies, leading to distinct compositions in the rhizosphere microbiome. Specific amplicon sequence variants in the rhizosphere microbiome are associated with early and late successions, with differences observed in taxonomic enrichments between modern and wild tomato genotypes.