So many rhizobial partners, so little nitrogen fixed: The intriguing symbiotic promiscuity of common bean (Phaseolus vulgaris L.)

Abstract

Symbiotic diazotrophic bacteria collectively called “rhizobia” can associate with legumes and form specialized structures in the roots, called nodules, where the biological nitrogen fixation (BNF) process takes place. Common bean (Phaseolus vulgaris L.) is a major protein source in the diet of the population of many countries such as Brazil and can benefit from the BNF process, but there is still little knowledge about the diversity and effectiveness of indigenous microsymbionts. In this study, the diversity and the nitrogen fixation ability of bacterial isolates trapped by common bean nodules in 14 municipalities of Mato Grosso do Sul state, Central-Western region, comprising three Brazilian biomes were investigated. The DNA profiles (BOX-PCR) of 82 isolates indicated outstanding diversity, with 12 main clusters and 36 isolates occupying single positions, joined at a final level of similarity of less than 20%. The 16S rRNA phylogeny of 56 isolates representing the DNA profiles indicated ten genera, with 38 isolates identified as “classical rhizobia” and Agrobacterium, and the remaining 18 belonging to six other genera. The 38 isolates had their glnII gene sequenced and were evaluated for the capacity of nodulation and BNF with common bean, and only 12 formed effective nitrogen-fixing nodules, five positioned in the R. etli and six in the R. tropici clades, and one of Agrobacterium. These results highlight the promiscuity of common bean in capturing a variety of microbial species in their nodules, whose function has not been well elucidated yet. Only one-fifth of the isolates were effective in fixing nitrogen, which might explain the frequently reported low rates of contribution of the BNF with this legume, an intriguing paradigm in the evolution of the symbiosis. Graphical abstract: [Figure not available: see fulltext.]