Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts.
The nodC and nifH genes were characterized in a collection of 83 rhizobial strains which represented 23 recognized species distributed in the genera Rhizobium, Sinorhizobium, Mesorhizobium and Bradyrhizobium, as well as unclassified rhizobia from various host legumes. Conserved primers were designed from available nucleotide sequences and were able to amplify nodC and nifH fragments of about 930 bp and 780 bp, respectively, from most of the strains investigated. RFLP analysis of the PCR products resulted in a classification of these rhizobia which was in general well-correlated with their known host range and independent of their taxonomic status. The nodC and nifH fragments were sequenced for representative strains belonging to different genera and species, most of which originated from Phaselous vulgaris nodules. Phylogenetic trees were constructed and revealed close relationships among symbiotic genes of the Phaseolus symbionts, irrespective of their 16S-rDNA-based classification. The nodC and nifH phylogenies were generally similar, but cases of incongruence were detected, suggesting that genetic rearrangements have occurred in the course of evolution. The results support the view that lateral genetic transfer across rhizobial species and, in some instances, across Rhizobium and Sinorhizobium genera plays a role in diversification and in structuring the natural populations of rhizobia.
Laguerre
Gisèle
G
Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1.
Nour
Sarah M
SM
Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1.
Macheret
Valérie
V
Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1.
Sanjuan
Juan
J
Departamento de Microbiologı́a del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidı́n, CSIC, Profesor Albareda 1, E-18008 Granada, Spain2.
Drouin
Pascal
P
Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1.
Amarger
Noëlle
N
Laboratoire de Microbiologie des Sols, Centre de Microbiologie du Sol et de l'Environnement, INRA, 17 rue Sully, BP 86510,F-21065 Dijon Cedex, France1.
D001426:Bacterial Proteins; D020369:Bradyrhizobium / Q000145:classification* / Q000235:genetics; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D007887:Fabaceae / Q000382:microbiology*; D008969:Molecular Sequence Data; D017351:N-Acetylglucosaminyltransferases / Q000235:genetics*; D010088:Oxidoreductases / Q000235:genetics*; D010802:Phylogeny; D010946:Plants, Medicinal; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D012230:Rhizobiaceae / Q000145:classification* / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D020579:Sinorhizobium / Q000145:classification* / Q000235:genetics; D013559:Symbiosis
D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; C029130:nitrogenase reductase; D017351:N-Acetylglucosaminyltransferases; C060771:NodC protein, Rhizobiales