Diversity of Rhizobia

Rhizobia is a gram-negative Proteobacteria with the capacity to fix atmospheric nitrogen when it is associated with the legume's roots. It is possible that the microorganisms associated with the common bean plant for its SNF may exhibit a similar arrangement of genetic diversity in Mesoamerican and Andean gene pools. While common bean is highly promiscuous in its relationship with rhizobia, R. etli bv. phaseoli has been found as the predominant nodule occupants in both the Mesoamerican and Andean centers of origin (Martinez-Romero 2003; Aguilar et al. 2004; Grange et al. 2007). This is not always the case in other areas where the crop is grown. Isolates belonging to R. etli bv. phaseoli, are predominant in soils of Mesoamerican countries (Eardly et al. 1995; Martinez-Romero and Caballero-Mellado 1996) and in Argentinean soils (Aguilar et al. 1998). A large genetic diversity has been documented for R. etli bv. phaseoli from the domestication centers and may be carried on bean-seed testa, possibly the means by which the species was distributed worldwide (Fig. 7.4). Differences in symbiotic effectiveness exist within R. etli bv. phaseoli isolates and these may be related to the large genetic differences observed in these bacteria and also the coadaptation of cultivar and bacteria. Occasionally, bacteria other than R. etli bv. phaseoli have been encountered in bean nodules in Mexico and they correspond to R. gallicum bv. phaseoli (Silva et al. 2003), whereas Andean cultivars form large number of nodules with R. tropici strains (Nodari et al. 1993). Thus, R. tropici is indigenous to South America and the reference strain was isolated in Colombia, likely a third center of the host common bean. R. tropici seems clearly dominant under field conditions, even when cultivars of Mesoamerican group are used as trap hosts (Mostasso et al. 2002; Hungria et al. 2003). Mesoamerican beans with high capacities to fix nitrogen nodulated poorly with R. tropici strains and in these beans R. tropici blocked R. etli bv. phaseoli nodulation when both strains were tested together (Martinez-Romero et al. 1998). Bean nodule isolates from Ecuador and Peru proved to be very diverse and could be divided into clusters distinct from the Mexican isolates. Ecuatorian and Mexican beans selected different R. etli bv. phaseoli strains both from Ecuatorian and Mexican soils (Bernal and Graham 2001) and efficiency in nodulation and nitrogen fixation was higher when both partners were from the same region. May it be that domestication and other human selections of beans indirectly affected host range?

A. caulinodans

A. caulinodans

Nodulation Noda

M. huakuii

Fig. 7.4 The tree is based on full-length sequences, and constructed by using the neighbor-joining method. Bootstrap values (% from 1,000 replications) are indicated. NodA sequences of published rhizobia are available in GenBank. A, Azorhizobium, B, Bradyrhizobium. M, Mesorhizobium. Me, Methylobacterium. R, Rhizobium. S, Sinorhizobium (Moullin et al. 2001)

R. leguminosarum bv. viciae

R. leguminosarum bv. trifolii

M. huakuii

Fig. 7.4 The tree is based on full-length sequences, and constructed by using the neighbor-joining method. Bootstrap values (% from 1,000 replications) are indicated. NodA sequences of published rhizobia are available in GenBank. A, Azorhizobium, B, Bradyrhizobium. M, Mesorhizobium. Me, Methylobacterium. R, Rhizobium. S, Sinorhizobium (Moullin et al. 2001)

What would be the consequence, in terms of N2 fixation, of inoculating a Mesoamerican cultivar with Mesoamerica versus Andean rhizobia strain?

In Europe, rhizobia strains have a narrow genetic diversity that was correlative to beans being an introduced crop (Laguerre et al. 1993). Segovia et al. (1993) proposed that when seeds containing R. etli bv. phaseoli were introduced into Europe, the symbiotic plasmid could have been transferred to R. leguminosarum. Later, the same process may have occurred from R. leguminosarum to R. gallicum and R. giardinii (Amarguer et al. 1997). It seems that in some sites of introduction bean is nodulated by other species in addition to diverse R. etli bv. phaseoli and the co-occurrence of several species is common. R. tropici is well adapted to acid soils and high temperatures and was also isolated in Europe and in Africa. It was demonstrated that pH can limit the presence of microorganism in soils and can be a barrier to diversity (Giongo et al. 2008). In Portugal, the molecular analysis of strains isolated from various soils revealed a novel species named R. lusitanum (Valverde et al. 2006). Remarkably, in a single soil in Spain five rhizobial species (R. etli bv. phaseoli, R. leguminosarum, R. gallicum, R. giardinii, and S. fredii) were found to nodulate P. vulgaris L. (Herrera-Cervera et al. 1999). The existence of one of the most genetically diverse collections of Rhizobium isolates recovered from root nodules of P. vulgaris L. from Spain was revealed (Martinez-Romero and Caballero-Mellado 1996). The most abundant species appeared to be R. etli bv. phaseoli presumably because they were brought into Spain from the Americas after introduction of beans about four centuries ago. It is also important to remember that, after 1492, a trade barrier was established in South America by the domains of Spain and Portugal, and isolation might have prevented the spread of other genotypes of R. etli. Thus, R. etli strains from Europe may have different origins. The results of Herrera-Cervera et al. (1999) indicate that extensive interspecific symbiotic gene exchange has taken place in this site and presumably, R. etli bv. phaseoli strains could have been the original gene donors. The other species, which have also been found at different locations in Europe, probably represent bacteria that preexisted in European soils when beans were first introduced and have received genetic material from the introduced R. etli bv. phaseoli. Thus, the Spanish soil studied represents a unique case where a donor and the putative DNA recipient coexist and probably compete for the same ecological niche. In a recent study, phenotypic features of 90 French rhizobia isolates from Phaseolus spp. nodules that were previously assigned to one of the three previously named species of rhizobia that nodulate beans (R. leguminosarum, R. tropici, and R. etli bv. phaseoli), were compared to the phenotypic features of reference rhizobial strains by numerical taxonomy. As a result of the present and previous studies, Amarguer et al. (1997) proposed that two new Rhizobium species should be created, R. gallicum and R. giardinii.

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