Open Access Highly Accessed Research article

Genomic basis of broad host range and environmental adaptability of Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 which are used in inoculants for common bean (Phaseolus vulgaris L.)

Ernesto Ormeño-Orrillo1*, Pâmela Menna2, Luiz Gonzaga P Almeida3, Francisco Javier Ollero4, Marisa Fabiana Nicolás3, Elisete Pains Rodrigues5, Andre Shigueyoshi Nakatani2, Jesiane Stefânia Silva Batista2, Ligia Maria Oliveira Chueire2, Rangel Celso Souza3, Ana Tereza Ribeiro Vasconcelos3, Manuel Megías4, Mariangela Hungria2 and Esperanza Martínez-Romero1

Author affiliations

1 Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico

2 Embrapa Soja, C. P. 231, Londrina, Paraná, 86001-970, Brazil

3 Laboratório Nacional de Computação Científica (LNCC), Avenida Getúlio Vargas 333, Petrópolis, Rio de Janeiro, Brazil

4 Universidad de Sevilla, Apdo Postal 874, Sevilla, 41080, Spain

5 Universidade Estadual de Londrina, Cx. Postal 60001, Londrina, Paraná, 86051-990, Brazil

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Citation and License

BMC Genomics 2012, 13:735  doi:10.1186/1471-2164-13-735

Published: 27 December 2012



Rhizobium tropici CIAT 899 and Rhizobium sp. PRF 81 are α-Proteobacteria that establish nitrogen-fixing symbioses with a range of legume hosts. These strains are broadly used in commercial inoculants for application to common bean (Phaseolus vulgaris) in South America and Africa. Both strains display intrinsic resistance to several abiotic stressful conditions such as low soil pH and high temperatures, which are common in tropical environments, and to several antimicrobials, including pesticides. The genetic determinants of these interesting characteristics remain largely unknown.


Genome sequencing revealed that CIAT 899 and PRF 81 share a highly-conserved symbiotic plasmid (pSym) that is present also in Rhizobium leucaenae CFN 299, a rhizobium displaying a similar host range. This pSym seems to have arisen by a co-integration event between two replicons. Remarkably, three distinct nodA genes were found in the pSym, a characteristic that may contribute to the broad host range of these rhizobia. Genes for biosynthesis and modulation of plant-hormone levels were also identified in the pSym. Analysis of genes involved in stress response showed that CIAT 899 and PRF 81 are well equipped to cope with low pH, high temperatures and also with oxidative and osmotic stresses. Interestingly, the genomes of CIAT 899 and PRF 81 had large numbers of genes encoding drug-efflux systems, which may explain their high resistance to antimicrobials. Genome analysis also revealed a wide array of traits that may allow these strains to be successful rhizosphere colonizers, including surface polysaccharides, uptake transporters and catabolic enzymes for nutrients, diverse iron-acquisition systems, cell wall-degrading enzymes, type I and IV pili, and novel T1SS and T5SS secreted adhesins.


Availability of the complete genome sequences of CIAT 899 and PRF 81 may be exploited in further efforts to understand the interaction of tropical rhizobia with common bean and other legume hosts.

Nodulation; Nitrogen fixation; Plant-microbe interactions; Antimicrobial resistance