Healthy plants host a remarkable diversity of microorganisms known as plant microbiota, which provide host services such as pathogen protection and nutrient acquisition. Thus, plant microbiota emerges as a trait that extends the capacity of plants to adapt to their environment. So far, microbial community profiling has mostly allowed the description of the phylogenetic structure of plant microbiota, whereas functional insights were mostly obtained from experiments using model strains. Thus, the plant impact on the microbial functional genes pool in the rhizosphere remains largely unknown. The goals of the study were to (i) compare the functional genes pool of the rhizosphere microbiota of seven ecotypes of Medicago truncatulata, and (ii) identify the functional genes allowing the differentiation of the microbiota upon the plant ecotypes. Forty-two samples were analysed for their phylogenetic (454 pyrosequencing of 16S rRNA) and functional genes (2x125 bp shotgun sequencing, Illumina HiSeq) diversity. Fifty-five millions scaffolds were de novo assembled after removing reads mapped on M. truncatula genome. We used Prodigal as gene prediction from mRNA scaffolds and Kaiju for taxonomic classification of rRNA scaffolds. The three millions predicted mRNA (≥ 800 bp length) were filtered to remove scaffolds that carried transposable elements or came from organelles or Sinorhizobium sp. symbionts. A selected dataset of 6074 scaffolds ≥ 10 kb was used for statistical analyses. Results indicated that (i) the genetic structure of bacterial communities differed according to the plant ecotype, and (ii) the curation of the shotgun metagenomic dataset is necessary to have a better discrimination of the different rhizosphere microbiota. Furthermore, the membrane receptor TonB protein appeared to explain differences in the structure of the rhizosphere microbiota associated with the different ecotypes. Indeed, these proteins bind and transport ferric chelates made with siderophores, as well as various plant carbohydrates, and thus to mediate plant-microbe interactions.