Competitiveness and Phylogenetic Relationship of Rhizobial Strains with Different Symbiotic Efficiency in Trifolium repens: Conversion of Parasitic into Non-Parasitic Rhizobia by Natural Symbiotic Gene Transfer

Simple Summary Partially efficient and inefficient rhizobia strains can decrease biological nitrogen fixation in legumes, especially when not inoculated. This work shows the high nodulation competitiveness in Trifolium repens of two strains with intermediate nitrogen fixation capacity. The genome sequence of one of them resulted in the first identification of Rhizobium redzepovicii as a T. repens symbiont. The analysis of symbiotic genes of different Rhizobium sp. capable of nodulating T. repens evidences the horizontal transfer of genes from efficient to inefficient strains, leading to a strain with intermediate efficiency. For the first time, sequencing, and analysis of the genome of the rhizobium used as clover inoculant in Uruguay confirmed that it is a strain belonging to R. leguminosarum phylogenetically close to bv. viciae. The search for hrrP-like genes in different Rhizobium species shows their presence in the chromosome and plasmids. This is interesting because hrrP encodes a metallopeptidase of the M16A family whose activity is involved in symbiotic efficiency. Our results highlight the need for farmers to make an effort in seed inoculation to improve clover yields and mitigate the effect of parasitic and low-efficiency strains present in soils. In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.