A co-inoculation of a Rhizobium leguminosarum symbiovar viciae core collection with a panel of Fabeae legumes revealed emerging properties of rhizobial populations.

Fabeae legumes form dinitrogen (N2)-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae (Rlv). Genetic determinants controlling the Ability to Form root Nodules (AFN) vary between individuals within natural populations and consequently, members often display a wide range of Competitiveness to Form root Nodules (CFN). Because the CFN and the Symbiotic N2 Fixation (SNF) capacity of Rlv are genetically independent, CFN may limit the effectiveness of symbiotic services. Although this concept is discussed since several decades, little is known about genetic determinants controlling CFN. New Generation of Sequencing (NGS) has allowed significant advances in genomics, metagenomics and metabarcoding, and bacteria can be now individually discriminate within complex mixtures. In this study, based on the genomic comparison of 121 Rlv genome sequences, a core collection of 32 Rlv representatives of geographic and genomic diversities was established, and a barcode was designed to discriminate each of the 32 bacteria in mixture. A panel of genetically diverse Pisum sativum, Vicia faba and Lens culinaris genotypes was co-inoculated with this core collection and the relative CFN was measured by metabarcoding. This co-inoculation strategy identified contrasted bacterial host-specificities and revealed emerging properties of rhizobial populations. A comparative genomic analysis identified genes associated with CFN in these Fabeae-Rlv symbioses.