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Genetic diversity of indigenous soybean-nodulating Bradyrhizobium elkanii from southern Japan and Nueva Ecija, Philippines

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Abstract

Aims

Understanding the factors that influence the diversity of soybean-nodulating rhizobia is important before doing inoculation. Since studies about this topic in tropical regions are limited, this could lay the groundwork for related research particularly on Bradyrhizobium elkanii.

Methods

To determine the genetic diversity of B. elkanii in different regions, we conducted Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) and sequence analysis of 16S rRNA gene, internal transcribed spacer (ITS) region and rpoB gene. Also, sequence analysis of symbiotic nifD and nodD1 genes was conducted.

Results

Analysis of the rpoB gene revealed a higher genetic diversity than the ITS region, and possible endemic B. elkanii strains were observed. Meanwhile, no variation was detected among the strains in both nifD and nodD1 phylogenies. Through rpoB gene analysis, variations in the ITS-rpoB type of B. elkanii strains were distinguished and differentiated with that of the closest reference strains. We identified potential soybean inoculants which possess symbiotic efficiency regardless of the Rj genotypes used, suggesting broad host-range of the strains.

Conclusions

We show how the genetic diversity of soybean-nodulating B. elkanii strains in subtropical and tropical regions might be influenced by temperature and soil pH and, provided some insights between the symbiotic genes and Rj genotypes.

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Acknowledgements

This study was supported by JSPS KAKENHI (Grant-in-Aid for Scientific Research (B) no. 26310313) and the Japanese Government (MEXT) Scholarship program.

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Authors and Affiliations

  1. Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, 889-2192, Japan

    Maria Luisa Tabing Mason

  2. College of Agriculture, Science City of Muñoz, Central Luzon State University, 3120, Nueva Ecija, Philippines

    Maria Luisa Tabing Mason & Apolinario Laxamana Domingo

  3. Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan

    Shota Matsuura, Akihiro Yamamoto & Yuichi Saeki

  4. Faculty of Life and Environmental Science, Shimane University, 1060 Nishikawatsu, Matsue, Shimane, 690-8504, Japan

    Sokichi Shiro

  5. Faculty of Agriculture, Shizuoka University, 836 Otani, Suruga-ku, Shizuoka, Shizuoka, 422-8529, Japan

    Reiko Sameshima-Saito

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  1. Maria Luisa Tabing Mason
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  2. Shota Matsuura
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  3. Apolinario Laxamana Domingo
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  7. Yuichi Saeki
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Correspondence to Yuichi Saeki.

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Electronic supplementary material

Table S1

List of primers used in this study for the PCR amplification and sequence analysis of 16S rRNA, ITS, rpoB, nifD and nodD1. (PDF 73 kb)

Table S2

Shoot and nodule parameters of 19 representative B. elkanii isolates employing three Rj genotypes. Mean comparison was conducted in triplicates only between isolates within the same Rj genotype. (PDF 89 kb)

Table S3

List of accession numbers for selected Bradyrhizobium USDA reference strains and isolates from the sequence analysis of 16S rRNA gene, 16S–23S rRNA gene ITS region, rpoB housekeeping gene and symbiotic genes nifD and nodD1. (PDF 79 kb)

Figure S1

Indication of the usefulness of rpoB-RFLP analysis as shown by the similarity in the phylogeny and RFLP band patterns. (PDF 58 kb)

Figure S2

Phylogenetic tree based on sequence analysis of 16S rRNA gene. The tree was constructed using the Neighbor- Joining method with the Kimura 2-parameter (K2P) distance correlation model and 1000 bootstrap replications in MEGA v.7 software. (PDF 138 kb)

Figure S3

Phylogenetic tree based on sequence analysis of (A) nifD gene and (B) nodD1 gene. The tree was constructed using the Neighbor-Joining method with the Kimura 2-parameter (K2P) distance correlation model and 1000 bootstrap replications in MEGA v.7 software. The first letter of isolates’ name indicates the location as follows: H - Kumamoto; O - Okinawa; P - C. Luzon, Philippines. (PDF 235 kb)

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Mason, M.L.T., Matsuura, S., Domingo, A.L. et al. Genetic diversity of indigenous soybean-nodulating Bradyrhizobium elkanii from southern Japan and Nueva Ecija, Philippines. Plant Soil 417, 349–362 (2017). https://doi.org/10.1007/s11104-017-3263-4

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