Classification of Austrian Rhizobia and the Mexican Isolate FL27 Obtained from Phaseolus vulgaris L. as Rhizobium gallicum

Abstract

The phylogenetic positions of four rhizobial strains obtained from nodules of common bean plants (PhaseoZus vulgaris L.) grown in an Austrian soil and of the Mexican bean isolate FL27 are described. Analysis of the 16s rRNA genes revealed sequences almost identical to that of the Rhizobium gallicum type strain, R602sp, with a maximum of two nucleotide substitutions. Comparison of the 16s rRNA gene sequences with those from other bacteria indicated highest similarity to Rhizobium sp. strain OK-50, Rhizobium Zeguminosarum IAM 12609, and Rhizobium etli. DNA homology determined by DNA-DNA hybridization was high among the Austrian isolates and R602spT (45 to 90%) and ranged from 21 to 65% with FL27, but hybridization analysis revealed very low homology to the recognized common bean-nodulating species, R. Zeguminosarum bv. phaseoli, R. etli, and Rhizobium tropici. Ribosomal gene organization was studied by Southern hybridization with the 16s rRNA gene and temperature gradient gel electrophoresis, indicating identical organizations and the presence of three identical 16s rRNA copies in the genome of this species. The six strains investigated showed different plasmid profiles based on their geographical origins. We propose that the Austrian isolates and the Mexican strain FL27 are members of the species R. gallicum.Bacteria of the genus Rhizobium that are able to nodulate common bean plants (Phaseolus vulgaris L.) have been traditionally classified as Rhizobium leguminosarum bv. phaseoli (13) on the basis of the host plant they infect. Strains belonging to the other subdivisions of this species, R. leguminosarum bv. viciae and bv. trifolii, nodulate peas and clovers, respectively, and their symbiotic plasmids carry genes with different host specificities. Nevertheless, rhizobia from common bean plants have been found to be phylogenetically diverse based on different criteria, such as protein profiles (32), multilocus enzyme electrophoresis patterns (6, 28), results of DNA relatedness analysis (16,37,44), and differences in their 16s rRNA gene (rDNA) sequences (9,16,44). In addition to R. leguminosarum bv. phaseoli, two new species, Rhizobium etli (38) and Rhizobium tropici (20), have been described. Both R. leguminosarum bv. phaseoli and R. etli carry multiple copies of the nitrogenase reductase gene ( n i m on their symbiotic plasmids, but they have different 16s rRNA sequences (17,30,38). In contrast, R. tropici maintains only a single nifH gene copy on its symbiotic plasmid (20). R. etli and R. tropici show a broad host range, but they nodulate different hosts (9, 20). Several new species among bean-nodulating strains, including Rhizobium gallicum and Rhizobium giardinii, which comprise the French isolates (1, 16), as well as Rhizobium sp. (Phaseolus) RCR 3618D of unknown geographical origin, have been proposed (44). The partial 16s rDNA sequence of the R. gallicum type strain, R602sp, was found to be identical to that of strain FL27 (16), a Mexican isolate from the common bean which does not fixate N2 well (28). In ...

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts The GenBank accession numbers for the sequences reported in this paper are AF217261 through AF217272 for nodC and AF218126, AF275670 and AF275671 for nifH.

“…The hypothesis of interspecies gene transfer is supported by the high similarity of the Sym genes among the bv. phaseoli subgroups and the co-occurrence of all these species in Europe (Geniaux et al, 1993 ;Sessitsch et al, 1997 ;Herrera-Cervera et al, 1999). In the same way, the finding that the Sym genes of strains HT2a2 and HT4c1 and of R. tropici are similar although their 16S rDNA types are relatively distant, and the co-occurrence of these rhizobia in the southwest of France , argue for interspecies gene transfer.…”

“…R. tropici fell outside the bean symbiont cluster and the present data did not show evidence that R. tropici was more strongly associated with the bean symbionts than with other rhizobia. Each of the bvs phaseoli, gallicum and giardinii corresponded to distinct lineages or subclusters, which correlates with the differences observed in host plant range between these biovars Sessitsch et al, 1997). However, a close relationship was found between the nodC genes of R. gallicum bv.…”

“…So far, almost all isolates of R. gallicum have been obtained from Europe Sessitsch et al, 1997 ;Herrera-Cervera et al, 1999). Because of the Mesoamerican origin of bean and Phylogenetic analysis of nodC and nifH genes of R. gallicum strain FL27, Sessitsch et al (1997) suggested that R. gallicum might have been imported to Europe as a seed contaminant. However, taking into account the relative divergence among the Sym genes of the French and Mexican R. gallicum bv.…”

Rhizobium etli and Rhizobium gallicum Nodulate Common Bean ( Phaseolus vulgaris ) in a Traditionally Managed Milpa Plot in Mexico: Population Genetics and Biogeographic Implications

“…R. etli bv. phaseoli is found in regions where common bean has been introduced, such as Spain, France, Austria, Senegal, Gambia, and Tunisia (10,21,24,33,34,44). However, in these countries other Rhizobium species also nodulate this legume.…”

Identification of Lactobacillus UFV H2b20 (probiotic strain) using DNA-DNA hybridization

“…The correlation between DNA-DNA hybridization and homology to rDNA 16S is, in many cases, non-linear, i.e., distinct species may have high similarity in rDNA 16S sequences. Likewise, low DNA-DNA homology does not necessarily indicate low similarity of rDNA 16S among the strains, since this gene contains sequences that are preserved in the different bacteria groups (6,16,26).…”