The competitiveness to form nodules shapes the capacities of Rhizobium leguminosarum sv viciae communities to promote symbiosis with specific hosts
Résumé
Cultivated fabeae legumes (pea, fababean, lentil) develop root nodules resulting from the symbiotic interaction with Rhizobium leguminosarum sv. viciae (Rlv). Individual Rlv bacteria are able to associate with various potential hosts, but in soil they are in mixture and they display a wide range of competitiveness to form nodules (CFN). Because in Rlv, CFN and capacity to fix nitrogen are genetically independent, CFN limits the effectiveness of inoculation strategies as efficient bacteria are often outcompeted by poorly efficient Rlv bacteria of the soil community. We developed a strategy to identify bacterial genes controlling CFN. A worldwide collection of 240 Rlv isolates was obtained by combining bacteria described in GenBank with new isolates obtained worldwide by pea, fababean and lentil root nodule trapping. 100 genomes (22 already in GenBank) were sequenced. The extended Rlv complex species includes probably 16 genospecies and two main groups of symbiosis plasmids that can be horizontally transferred. We identified phylogenetic clades of Rlv displaying contrasted levels of CFN upon pea and fababean. A molecular barcode was designed on nodD gene to discriminate and quantify intraspecific variability of Rlv in root systems allowing estimate CFN in symbiotic pea, fababean or lentil associations with multiple Rlv potential partners. Several plasmid regions genetically associated with pea/fababean CFN phenotypes were identified. Candidate genes include specific nod genes as well as other genes with unknown function in symbiosis.