Applied Microbiology and Biotechnology

, Volume 83, Issue 5, pp 897–908 | Cite as

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

  • Daisy Rickli Binde
  • Pâmela Menna
  • Eliane Villamil Bangel
  • Fernando Gomes Barcellos
  • Mariangela HungriaEmail author
Applied Genetics and Molecular Biotechnology


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.


Bacterial fingerprinting Bacterial taxonomy Biological nitrogen fixation Culture collections Inoculants 16S rRNA 



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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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Daisy Rickli Binde
    • 1
    • 2
  • Pâmela Menna
    • 1
    • 3
  • Eliane Villamil Bangel
    • 4
  • Fernando Gomes Barcellos
    • 1
    • 2
    • 5
  • Mariangela Hungria
    • 1
    • 2
    • 3
    Email author
  1. 1.Embrapa SojaLondrinaBrazil
  2. 2.Universidade Estadual de LondrinaLondrinaBrazil
  3. 3.Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq-MCT)BrasíliaBrazil
  4. 4.FEPAGROPorto AlegreBrazil
  5. 5.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)BrasíliaBrazil

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