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Applied and Environmental Microbiology, November 2008, p. 6987-6996, Vol. 74, No. 22
0099-2240/08/$08.00+0     doi:10.1128/AEM.00875-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent {triangledown} ,{dagger}

Pablo Vinuesa,1* Keilor Rojas-Jiménez,2,3 Bruno Contreras-Moreira,4 Suresh K. Mahna,2,5 Braj Nandan Prasad,2,6 Hla Moe,2,7 Suresh Babu Selvaraju,2,8 Heidemarie Thierfelder,2 and Dietrich Werner2

Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México,1 FB Biologie, FG für Zellbiologie und Angewandte Botanik, Philipps Universität Marburg, Marburg, Germany,2 Instituto Nacional de Biodiversidad, Santo Domingo de Heredia, Costa Rica,3 Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain,4 Department of Botany, Maharshi Dayanand Saraswati University Ajmer, Ajmer, India,5 School of Biotechnology, Chemical and Biomedical Engineering, VIT University, Vellore, India,6 Department of Botany, University of Mandalay, Mandalay, Myanmar,7 Research Children's Mercy Hospitals and Clinics, Kansas City, Missouri8

Received 17 April 2008/ Accepted 7 September 2008

A highly supported maximum-likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix obtained from the concatenation of partial atpD, recA, glnII, and rpoB sequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified as B. japonicum type Ia (USDA110/USDA122-like), B. liaoningense, B. yuanmingense, or B. elkanii, whereas one represented a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the of B. japonicum I and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree.

* Corresponding author. Mailing address: Centro de Ciencias Genómicas, UNAM, Av. Universidad S/N, Col. Chamilpa, AP 565-A, Cuernavaca CP 62210, Morelos, México. Phone: 52 777 3175867. Fax: 52 777 3175581. E-mail: vinuesa{at}ccg.unam.mx

{triangledown} Published ahead of print on 12 September 2008.

{dagger} Supplemental material for this article may be found at http://aem.asm.org/.

Applied and Environmental Microbiology, November 2008, p. 6987-6996, Vol. 74, No. 22
0099-2240/08/$08.00+0     doi:10.1128/AEM.00875-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Contreras-Moreira, B., Sachman-Ruiz, B., Figueroa-Palacios, I., Vinuesa, P. (2009). primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies. Nucleic Acids Res 37: W95-W100 [Abstract] [Full Text]  


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