Genetic diversity of indigenous soybean-nodulating Bradyrhizobium elkanii from southern Japan and Nueva Ecija, Philippines
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.
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.
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.
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.
KeywordsBradyrhizobium elkanii rpoB gene ITS region Philippines Symbiotic genes
- Barcellos FG, Menna P, Batista JS, Hungria M (2007) Evidence of horizontal transfer of symbiotic genes from a Bradyrhizobium japonicum inoculant strain to indigenous Diazotrophs Sinorhizobium (Ensifer) fredii and Bradyrhizobium elkanii in a Brazilian savannah soil. Appl Environ Micobiol 73:2635–2643CrossRefGoogle Scholar
- Bernstein L, MacKenzie AJ, Krantz BA (1955) Salt tolerance of field crops - soybeans. In: United States salinity laboratory report to collaborators. Riverside, CA, pp 35–36Google Scholar
- Manuel PC, Huelgas R, Espanto LH (1986) Adoption of soybean in Lupao, Nueva Ecija, Philippines. UN/ESCAP CGPRT Centre, regional coordination Centre for Research and Development of coarse grains, roots and tuber crops in the humid tropics of Asia and the Pacific. CGPRT no. 7: 62 ppGoogle Scholar
- Njira KOW, Nalivata PC, Kanyama-Phiri GY, Lowole MW (2013) An assessment for the need of soybean inoculation with Bradyrhizobium japonicum in some sites of Kasungu district, Central Malawi. Int J Curr Microbiol App Sci 2:60–72Google Scholar
- Ramirez-Bahena MH, Peix A, Rivas R, Camacho M, Rodriguez-Navarro DN, Mateos PF, Martinez-Molina E, Willems A, Velazquez E (2009) Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus. Int J Syst Evol Microbiol 59:1929–1934CrossRefPubMedGoogle Scholar
- Saeki Y, Shiro S (2014) Comparison of soybean-Nodulating Bradyrhizobia community structures along north latitude between Japan and USA, advances in biology and ecology of nitrogen fixation, prof. Takuji Ohyama (Ed.) InTech, pp. 195–224Google Scholar
- Sharma M, Srivastava K, Sharma S (2010) Biochemical characterization and metabolic diversity of soybean rhizobia isolated from Malwa region of Central India. Plant Soil Environ 56:375–383Google Scholar
- Vincent JM (1970) A manual for the practical study of the root-nodule bacteria. Blackwell Scientific, OxfordGoogle Scholar
- Vinuesa P, Rojas-Jiménez K, Contreras-Moreira B, Mahna SK, Prasad BN, Moe H et al (2008) Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that Nodulate soybeans on the Asiatic continent. Appl Environ Microbiol 74:6987–6996CrossRefPubMedPubMedCentralGoogle Scholar
- Wang J (2016) Analysis of the factors influencing Japan’s soybean import trade: based on gravity model. Am J Ind Bus Manag 6:109–116Google Scholar
- Young JM (2003) The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen et al. 1988, and Sinorhizobium morelense Wang et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination ‘Sinorhizobium adhaerens’ (Casida 1982) Willems et al. 2003 legitimate? Request for an opinion. Int J Syst Evol Microbiol 53:2107–2110CrossRefPubMedGoogle Scholar