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rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains

  • Applied Genetics and Molecular Biotechnology
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Abstract

In tropical soils, diversity and biotechnological potential of symbiotic diazotrophic bacteria are high. However, the phylogenetic relationships of prominent strains are still poorly understood. In addition, in countries such as Brazil, despite the broad use of rhizobial inoculants, molecular methods are rarely used in the analysis of strains or determination of inoculant performance. In this study, both rep-PCR (BOX) fingerprintings and the DNA sequences of the 16S rRNA gene were obtained for 54 rhizobial strains officially authorized for the production of commercial inoculants in Brazil. BOX-PCR has proven to be a reliable fingerprinting tool, reinforcing the suggestion of its applicability to track rhizobial strains in culture collections and for quality control of commercial inoculants. On the other hand, the method is not adequate for grouping or defining species or even genera. Nine strains differed in more than 1.03% (15) nucleotides of the 16S rRNA gene in relation to the closest type strain, strongly indicative of new species. Those strains were distributed across the genera Burkholderia, Rhizobium, and Bradyrhizobium.

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Acknowledgments

The work was partially supported by CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil), projects 552393/2005-3 and 577933/2008-6, PQ (300698/2007), and PNPD (558455/2008-5). The authors thank also Ligia Maria Oliveira Chueire (Embrapa Soja) for help in several steps of this work and Dr. Allan R.J. Eaglesham for helpful discussion. P. Menna acknowledges fellowships from CNPq (projects 505946/2004-1 and 558455/2008-5), and F.G. Barcellos acknowledges a pro-doc fellowship from CAPES.

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Authors and Affiliations

  1. Embrapa Soja, Cx. Postal 231, 86001-970, Londrina, Paraná, Brazil

    Daisy Rickli Binde, Pâmela Menna, Fernando Gomes Barcellos & Mariangela Hungria

  2. Universidade Estadual de Londrina, Londrina, Paraná, Brazil

    Daisy Rickli Binde, Fernando Gomes Barcellos & Mariangela Hungria

  3. Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq-MCT), Brasília, Federal District, Brazil

    Pâmela Menna & Mariangela Hungria

  4. FEPAGRO, Rua Gonçalves Dias 579, 90130-060, Porto Alegre, Rio Grande do Sul, Brazil

    Eliane Villamil Bangel

  5. Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), Brasília, Federal District, Brazil

    Fernando Gomes Barcellos

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  1. Daisy Rickli Binde
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  2. Pâmela Menna
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  3. Eliane Villamil Bangel
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  4. Fernando Gomes Barcellos
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  5. Mariangela Hungria
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Correspondence to Mariangela Hungria.

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Binde, D.R., Menna, P., Bangel, E.V. et al. rep-PCR fingerprinting and taxonomy based on the sequencing of the 16S rRNA gene of 54 elite commercial rhizobial strains. Appl Microbiol Biotechnol 83, 897–908 (2009). https://doi.org/10.1007/s00253-009-1927-6

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