ORIGINAL ARTICLE Diversity and phylogeny of soybean rhizobia in central India Parveen Ghazi Ansari & Desiraju Lakshmi Narsimha Rao & Kamal Krishna Pal Received: 27 August 2013 /Accepted: 25 December 2013 /Published online: 21 January 2014 # Springer-Verlag Berlin Heidelberg and the University of Milan 2014 Abstract Soybean is the most important crop legume with the highest share of biological nitrogen fixation among culti- vated legumes. During the early years following the introduc- tion 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 char- acterized 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 rela- tionships. We found that the rhizobia comprised both slow and fast growers, with the former having a higher Shannon–Wei- ner 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. Keywords Bradyrhizobium . Bioinoculants . Carbon utilization . Central India . Intrinsic antibiotic resistance . Microbial ecology Introduction Soybean is the most important legume crop since it fixes 16 Tg of atmospheric nitrogen each year, which represents nearly 77 % of the nitrogen biologically fixed by crop legumes (Herridge et al. 2008). Most of the soybean cultivation in India is concentrated in about 10.3 million ha in central and western India, an area of predominantly Vertisol soils. The large-scale cultivation of soybean in India began in the late 1960s with the use of inoculants prepared from Bradyrhizobium japonicum cultures imported from USA. Several acclimatized strains derived from the imported strains were subsequently used for the production of inoculants. The effects of inoculation during the early years of soybean culti- vation were very convincing (Dube 1975), but the response gradually declined over time (Rawat et al. 2008). Hungria and Vargas (2000) observed a similar declining trend of response to introduced rhizobial strains in Brazil and attributed this to the naturalization (evolution of native or indigenous strains) of the introduced strains—namely, the indigenously adapted rhizobia were more competitive in terms of nodulation occu- pancy than the introduced strains. Soybean has been reported to be nodulated worldwide by the slow-growing Bradyrhizobium japonicum strains. It has also been reported to be nodulated by the extra-slow-growing B. liaoningense and fast-growing Sinorhizobium fredii strains Electronic supplementary material The online version of this article (doi:10.1007/s13213-013-0799-2) contains supplementary material, which is available to authorized users. P. G. Ansari : D. L. N. Rao (*) Indian Institute of Soil Science, Nabi Bagh, Bhopal 462038, Madhya Pradesh, India e-mail: dlnrao@iiss.res.in K. K. Pal Directorate of Groundnut Research, Junagadh 362001, Gujarat, India Ann Microbiol (2014) 64:1553–1565 DOI 10.1007/s13213-013-0799-2