Multilocus sequence analysis of the genus Bradyrhizobium

Rivas, R. and Martens, M. and de Lajudiec, P. and Willems, A. (2009) Multilocus sequence analysis of the genus Bradyrhizobium. Systematic and Applied Microbiology, 32 (2). pp. 101-110.

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The use of multilocus sequence analysis (MLSA) for the taxonomy of Bradyrhizobium was assessed. We compared partial sequences for atpD, recA, gyrB, rpoB and dnaK for a set of reference strains representing named species and genospecies, and a number of new isolates from Lupinus albus, Arachis hypogaea and Ornithopus compressus from Spain. The phylogenies of the individual genes were compared with previous DNA–DNA hybridization results. High hybridization values were well reflected, but intermediary hybridization values were less clearly apparent. However, the phylogeny of a concatenated dataset of the five genes did reflect all values and thus is more informative of overall genome similarity. Our results indicate that only for the genes gyrB, rpoB and dnaK there is a small gap between the interspecies sequence similarities and the intraspecies similarity, and therefore cut-off levels for species delineation cannot be set, although high sequence similarity (>99%) does permit identification. In a few instances, a reference strain did not group as expected for one of the five genes tested. This may be a result of horizontal gene transfer and recombination events occasionally involving housekeeping genes. This observation indicates it is best to consider more than one gene for taxonomic inferences. The majority of the new isolates from the three host species was identified as Bradyrhizobium canariense. Four strains from L. albus from León, Spain, formed a separate group close to Bradyrhizobium japonicum.

Item Type: Article
Additional Information: R.R. is grateful to the Ministry of Science and Education, Spain, for a post-doctoral fellowship. A.W. is grateful to the Fund for Scientific Research –Flanders for a research grant. We thank Encarna Vela´zquez for providing Spanish rhizobial isolates and Renata Coopman for excellent technical assistance.Supplementary data associated with this article can be found in the online version at doi:10.1016/j.syapm.2008. 12.005.
Uncontrolled Keywords: Bradyrhizobium, Phylogeny, Housekeeping genes, Multilocus sequence analysis, MLSA
Author Affiliation: Laboratory of Microbiology (WE10), Faculty of Sciences, Ghent University, Belgium Departamento de Microbiologı´a y Gene´tica, Universidad de Salamanca, Spain Laboratoire des Symbioses Tropicales et Me´diterrane´ennes, IRD-CIRAD-SupAgro-Universite´ Montpellier II, France
Subjects: Soil Science and Microbiology > Microbiology
Statistics and Experimentation
Crop Improvement
Divisions: Chickpea
Common Bean
Depositing User: Mr Arbind Seth
Date Deposited: 20 Feb 2013 11:41
Last Modified: 20 Feb 2013 11:41
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