Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent.
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.
Vinuesa
Pablo
P
Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México UNAM, Cuernavaca CP 62210, Morelos, México. vinuesa@ccg.unam.mx
Rojas-Jiménez
Keilor
K
Contreras-Moreira
Bruno
B
Mahna
Suresh K
SK
Prasad
Braj Nandan
BN
Moe
Hla
H
Selvaraju
Suresh Babu
SB
Thierfelder
Heidemarie
H
Werner
Dietrich
D
D001208:Asia; D001426:Bacterial Proteins / Q000235:genetics; D015373:Bacterial Typing Techniques; D020369:Bradyrhizobium / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D002980:Climate; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D005843:Geography; D008969:Molecular Sequence Data; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D011110:Polymorphism, Genetic; D017421:Sequence Analysis; D013025:Glycine max / Q000382:microbiology*
D001426:Bacterial Proteins; D004269:DNA, Bacterial
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