Diversity and phylogeny of soybean rhizobia in central India

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Soybean is the most important crop legume with the highest share of biological nitrogen fixation among cultivated legumes. During the early years following the introduction of soybean cultivation in India, the effects of rhizobial inoculation were impressive, but they have declined over time due to naturalization of the introduced strains. We have characterized the diversity of soybean rhizobia, mainly those from central India, for phenotypic features, such as utilization of carbon sources and intrinsic resistance to antibiotics. The PCR-amplified 16S rRNA gene products of the strains were sequenced to study genetic diversity and phylogenetic relationships. We found that the rhizobia comprised both slow and fast growers, with the former having a higher Shannon–Weiner Diversity Index (H = 2.93 and 3.00 for carbon utilization and intrinsic antibiotic resistance, respectively) than the latter (H = 2.62 and 1.90, respectively). There were two 16S rRNA sequence types among the slow growers—Bradyrhizobium spp. (99.4–99.8 % sequence homology) and Rhizobium radiobacter (96.1–99.7 %). In contrast, the fast growing strains belonged exclusively to R. radiobacter (98.9–99.7 %). Bradyrhizobium japonicum strain USDA 110, which was originally introduced on a large scale in Indian soils more than four decades ago, shared 34–81 % phenotypic and 63–83 % genotypic similarity with the other Indian rhizobial isolates characterized. There was conservation of 16S rRNA gene sequences among rhizobia in various soybean-growing areas and the evolution of native rhizobial strains among slow and fast growers. These results on the biodiversity of soybean rhizobia are important for strain selection, which is crucial for the design of successful inoculation programs.