Community succession of the rhizosphere micro biome. Community succession

We developed an experimental selection system to investigate the role of plant genotype and soil in shaping the rhizosphere microbiomes of plants belonging to three distinct botanical families. Automated Ribosomal Intergenic Spacer Analysis (ARISA) finger-printing and 454 amplicon sequencing revealed that selection was highly plant-dependent in three model plants (Arabidopsis thaliana, Medicago truncatula and Brachypodium distachyon) and three crop plants (Brassica rapa, Pisum sativum and Triticum aestivum). From the same microbial inoculum, plants selected distinct microbiomes over successive generations, with the communities selected in sandy compared to rich soil significantly different. In poor, but not rich soil, the diversity of the rhizosphere microbiome collapsed in the third generation of plant growth, showing plants bias its composition but stability depends on soil structure and organic matter. Experimental selection favours rapidly growing R-strategists with cross-generational sweeps of bacterial opportunists and the fungal pathogen Olpidium brassicae on Brassica rapa. Notably, Arabidopsis mutants affected in innate immune recognition of antimicrobial production had significantly altered rhizosphere microbiomes. In particular, Actinobacteria were most sensitive to genetic perturbation of innate immunity. Our results suggest that wild-type plants actively recruit Actinobacteria to help the Arabidopsis immune system suppress competitors. Overall, root secretion, plant genotype and immunity interact with soil structure to select the rhizosphere microbiome.