Search

Background Leguminous plants alter patterns of gene expression in response to symbiotic colonization and infection by their cognate rhizobial bacteria, but the extent of the transcriptomic response has rarely been examined below the species level. Here we describe the identification of 12 rhizobial biotypes of Ensifer meliloti, which form nitrogen-fixing nodules in the roots of alfalfa (Medicago sativa L.), followed by a comparative RNA-seq analysis of four alfalfa cultivars each inoculated with two E. meliloti strains varying in symbiotic performance and phylogenetic relatedness. Results Rhizobial biotypes were identified on the basis of their symbiotic performance, particularly shoot dry weight. Differentially expressed genes (DEGs) and metabolic pathways were determined by comparing the RNA-seq data with that of the uninoculated control plant. Significant differences were found between DEGs generated in each cultivar with the inoculation of two rhizobial strains in comparison (P M. sativa genome. The proportion of DEGs ranges from 0.5 to 12.2% for each alfalfa cultivar. Interestingly, genes with predicted roles in flavonoid biosynthesis and plant-pathogen interaction (NBS-LRR) were identified as the most significant DEGs. Other DEGs include Medsa002106 and genes encoding nodulins and NCR peptides whose expression is specifically induced during the development of nitrogen-fixing nodules. More importantly, strong significant positive correlations were observed between plant transcriptomes (DEGs and KEGG pathways) and phylogenetic distances between the two rhizobial inoculants. Conclusions Alfalfa expresses significantly distinct sets of genes in response to infection by different rhizobial strains at the below-species levels (i.e. biotype or strain). Candidate genes underlying the specific interactions include Medsa002106 and those encoding nodulins and NCR peptides and proteins in the NBS-LRR family.

Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%–98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%–100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa ‘Gannong No. 3’, ‘Gannong No. 9’, and ‘Qingshui’ was much less than that on M. sativa ‘Longzhong’ and ‘WL168HQ’. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.