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Retrieved 16S rRNA and nifH sequences reveal co-dominance of Bradyrhizobium and Ensifer (Sinorhizobium) strains in field-collected root nodules of the promiscuous host Vigna radiata (L.) R. Wilczek

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Abstract

In the present study, the relative distribution of endophytic rhizobia in field-collected root nodules of the promiscuous host mung bean was investigated by sequencing of 16S ribosomal RNA (rRNA) and nifH genes, amplified directly from the nodule DNA. Co-dominance of the genera Bradyrhizobium and Ensifer was indicated by 32.05 and 35.84% of the total retrieved 16S rRNA sequences, respectively, and the sequences of genera Mesorhizobium and Rhizobium comprised only 0.06 and 2.06% of the recovered sequences, respectively. Sequences amplified from rhizosphere soil DNA indicated that only a minor fraction originated from Bradyrhizobium and Ensifer strains, comprising about 0.46 and 0.67% of the total retrieved sequences, respectively. 16S rRNA gene sequencing has also identified the presence of several non-rhizobial endophytes from phyla Proteobacteria, Actinobacteria, Bacteroides, and Firmicutes. The nifH sequences obtained from nodules also confirmed the co-dominance of Bradyrhizobium (39.21%) and Ensifer (59.23%) strains. The nifH sequences of the genus Rhizobium were absent, and those of genus Mesorhizobium comprised only a minor fraction of the sequences recovered from the nodules and rhizosphere soil samples. Two bacterial isolates, identified by 16S rRNA gene sequence analysis as Bradyrhizobium strain Vr51 and Ensifer strain Vr38, successfully nodulated the original host (mung bean) plants. Co-dominance of Bradyrhizobium and Ensifer strains in the nodules of mung bean indicates the potential role of the host plant in selecting specific endophytic rhizobial populations. Furthermore, successful nodulation of mung bean by the isolates showed that strains of both the genera Bradyrhizobium and Ensifer can be used for production of inoculum.

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Acknowledgements

The provision of consumables by Pakistan Science Foundation through project PSF/NSLP/P-NIBGE (315) and PhD fellowship to Sughra Hakim by the Higher Education Commission (HEC) for research work is thankfully acknowledged.

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Authors and Affiliations

  1. National Institute for Biotechnology and Genetic Engineering (NIBGE), P.O. Box 577, Faisalabad, Pakistan

    Sughra Hakim, Ahmad Zaheer, Asma Imran, Sumera Yasmin & M. Sajjad Mirza

  2. Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan

    Sughra Hakim, Ahmad Zaheer, Asma Imran, Sumera Yasmin & M. Sajjad Mirza

  3. Biology Department, Missouri State University, Springfield, MO, 65897, USA

    Babur S. Mirza

  4. Utah Water Research Laboratory, Utah State University, Logan, UT, USA

    Joan E. Mclean

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  1. Sughra Hakim
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Correspondence to M. Sajjad Mirza.

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Hakim, S., Mirza, B.S., Zaheer, A. et al. Retrieved 16S rRNA and nifH sequences reveal co-dominance of Bradyrhizobium and Ensifer (Sinorhizobium) strains in field-collected root nodules of the promiscuous host Vigna radiata (L.) R. Wilczek. Appl Microbiol Biotechnol 102, 485–497 (2018). https://doi.org/10.1007/s00253-017-8609-6

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