Structure and functions of the bacterial root microbiota in wild and domesticated barley and signatures of positive selection in the rhizosphere metagenome

We have profiled the rhizosphere and the root bacterial communities retrieved from soil-grown, wild, landrace and modern accessions of barley using a 16S rRNA gene amplicon pyrosequencing approach. Phylogenetic assignment of the generated sequencing reads revealed that the microbial communities thriving at the barley root-soil interface appears to be gated, as indicated by a narrow phylogenetic composition, largely dominated by members of the families Flavobacteriaceae, Rhizobiaceae and Comamonadaceae Interestingly, constrained ordinations and linear model analysis revealed that host microhabitats (i.e. root and rhizosphere) are the major determinants of the barley microbiota, while the host genotype determines its ribotype profiles to a limited extent, suggesting that the structure of the barley microbiota is a conserved trait in the tested accessions. To gain insights on the molecular cues underlying microbial recruitment at the root-soil interface, we reconstructed 20Gbp of the barley rhizosphere metagenome. Interestingly, we observed that ~10% of the protein families encoded by the barley microbiome display a ratio between non-synonymous and synonymous substitutions (w) significantly higher than the mean of the sequenced metagenome. Intriguingly, these data might indicate an evolutionary pressure on proteins required for the microbial colonisation of the rhizosphere. Remarkably, proteins previously reported in host-microbe interactions studies (e.g. putative bacterial effectors) showed a w significantly different across genotypes, suggesting that host genetic traits contribute, at least in part, to bacterial functional diversification in the rhizosphere. Our work provides a foundation for future studies aiming at the characterisation of the genetic bases of plant-microbiota interactions and, in the long term, the introgression of the microbiota metabolic potential into plant breeding