Combining ecophysiological and microbial ecological approaches to study the relationship between Medicago truncatula genotypes and their associated rhizosphere bacterial communities

To assess how plant genotype and rhizosphere bacterial communities may interact, the genetic structure and diversity of bacterial communities in the rhizosphere soil of different Medicago truncatula genotypes were studied in relation to the plant carbon and nitrogen nutrition at the whole plant level. The genetic structure and diversity of plant-associated rhizosphere bacterial communities was analysed by Automated Ribosomal Intergenic Spacer Analysis and 454-pyrosequencing. In parallel, the carbon and nitrogen nutrition of the plants was estimated by a phenotypic description at both structural level (growth) and functional level (using carbon and nitrogen isotope labeling and an ecophysiological framework). An early effect of the plant genotype was observed on the rhizosphere bacterial communities, while few significant differences were detected at the plant structural phenotypic level. However, at a functional level, the different Medicago truncatula genotypes could be distinguished by their different nutritional strategies. Moreover, a comparison analysis showed that ecophysiological profiles of the different Medicago truncatula genotypes were correlated to the genetic structure and the diversity of the rhizosphere bacterial communities. The exploration of the genetic structure and diversity of rhizosphere bacterial communities combined with an ecophysiological approach is an innovative way to progress in our knowledge of plant-microbe interactions in the rhizosphere.