New insights into the origins and evolution of rhizobia that nodulate common bean (Phaseolus vulgaris) in Brazil

https://doi.org/10.1016/j.soilbio.2006.10.008Get rights and content

Abstract

It is generally accepted that there are two major centers of genetic diversification of common beans (Phaseolus vulgaris L.): the Mesoamerican (Mexico, Colombia, Ecuador and north of Peru, probably the primary center), and the Andean (southern Peru to north of Argentina) centers. Wild common bean is not found in Brazil, but it has been grown in the country throughout recorded history. Common bean establishes symbiotic associations with a wide range of rhizobial strains and Rhizobium etli is the dominant microsymbiont at both centers of genetic diversification. In contrast, R. tropici, originally recovered from common bean in Colombia, has been found to be the dominant species nodulating field-grown common-bean plants in Brazil. However, a recent study using soil dilutions as inocula has shown surprisingly high counts of R. etli in two Brazilian ecosystems. In the present study, RFLP-PCR analyses of nodABC and nifH genes of 43 of those Brazilian R. etli strains revealed unexpected homogeneity in their banding patterns. The Brazilian R. etli strains were closely similar in 16S rRNA sequences and in nodABC and nifH RFLP-PCR profiles to the Mexican strain CFN 42T, and were quite distinct from R. etli and R. leguminosarum strains of European origin, supporting the hypothesis that Brazilian common bean and their rhizobia are of Mesoamerican origin, and could have arrived in Brazil in pre-colonial times. R. tropici may have been introduced to Brazilian soils later, or it may be a symbiont of other indigenous legume species and, due to its tolerance to acidic soils and high temperature conditions became the predominant microsymbiont of common bean.

Introduction

Domestication or semi-domestication of several plant species probably begun in the Americas some 8000–10,000 years ago (Harlan, 1971; Gepts and Debouck, 1991), however, new patterns were established from 1492, with European colonization. The Portuguese officially arrived in Brazil in 1500, and abruptly reduced an indigenous population estimated at 1–10 million people; as traditions were passed down orally, knowledge of the past was compromised. Written history began, but was recorded from the European point-of-view; nowadays, there are evidences that the agricultural resources of the remaining indigenous population poorly reflect pre-colonial patterns (Prous, 1997; FUNAI, 2005).

There is general agreement that common bean (Phaseolus vulgaris L.) was domesticated separately in two major centers of genetic diversification: the Mesoamerican center or northern group—and maybe it could represent the primary center—with alleles originating from Mexico to the northern region of South America (Colombia, Ecuador and north of Peru) and the Andean center of South America or southern group, with alleles from southern Peru to the north of Argentina; a third minor domestication may have taken place in Colombia (Kaplan, 1965, Kaplan, 1980; Harlan, 1971; Debouck et al., 1983; Debouck, 1986; Gepts, 1990; Gepts and Debouck, 1991).

Common bean establishes symbiotic associations with a wide range of rhizobial bacteria forming specific structures—root nodules—in which N2 fixation takes place. Five rhizobial species nodulating this legume have been described: Rhizobium leguminosarum bv. phaseoli, R. etli bv. phaseoli, R. gallicum (bv. phaseoli and bv. gallicum), R. giardinii (bv. phaseoli and bv. giardinii) and R. tropici (Jordan, 1984; Martínez Romero et al., 1991; Segovia et al., 1993; Amarger et al., 1997). While common bean is highly promiscuous in its relationship with rhizobia (Michiels et al., 1998; Herrera-Cervera et al., 1999; Martinez-Romero, 2003), R. etli is the dominant microsymbiont in both the Mesoamerican and the Andean centers of origin (Segovia et al., 1993; Souza et al., 1994; Aguilar et al., 1998, Aguilar et al., 2004; Bernal and Graham, 2001; Martinez-Romero, 2003). This is not always the case in other areas where the crop is now grown (Amarger et al., 1994, Amarger et al., 1997; Herrera-Cervera et al., 1999; Bernal et al., 2004). 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 bv. phaseoli to R. gallicum bv. phaseoli and R. giardinii bv. phaseoli (Amarger et al., 1997). It should be noted, however, that common bean-nodulating R. gallicum, R. etli (Tlusty et al., 2005) and R. giardinii (Beyhaut et al., 2006) also occur as the natural microsymbionts of Dalea spp. and Desmanthus illinoensis, respectively, in the natural prairie regions of the Central USA. R. tropici is well adapted to acid soils and high temperatures and was originally recovered from common bean in Colombia (Graham et al., 1982; Martínez Romero et al., 1991); however, it has also been isolated in Europe (e.g., Amarger et al., 1994; Herrera-Cervera et al., 1999) and in Africa (e.g., Anyango et al., 1995).

Wild common beans are not found in Brazil (Debouck, 1986), but the legume has been cultivated in the country throughout recorded history. Nowadays, the legume is a major component of the Brazilian diet, and the country is the largest producer and consumer worldwide (CONAB, 2006). All described common bean rhizobial species except for R. gallicum have been already isolated from host plants in Brazil (Mercante et al., 1998; Straliotto et al., 1999; Andrade et al., 2002; Mostasso et al., 2002; Grange and Hungria, 2004), in addition to other rhizobial genera and species (Hungria et al., 1993; Straliotto et al., 1999; Grange and Hungria, 2004). However, R. tropici seems clearly dominant under field conditions, even when cultivars of the Mesoamerican group are used as trap hosts (Hungria et al., 1997, Hungria et al., 2000, Hungria et al., 2003; Mercante et al., 1998; Mostasso et al., 2002). Nevertheless, in a recent study, when soil dilutions were used as inocula under axenic conditions, Grange and Hungria (2004) identified R. etli as the predominant symbiont of common bean in two Brazilian ecosystems. Our objective in this work was to study nod and nif gene diversity among R. etli strains isolated in the latter study, to further illuminate possible migration routes of this legume and its rhizobia.

Section snippets

Strains

Common bean rhizobia used as reference strains, including type strains, are shown in Table 1. Forty-three R. etli strains from the study of Grange and Hungria (2004) were further considered in this study. The taxonomy of these strains was determined using RFLP-PCR and 16S ribosomal DNA gene-sequence analysis (Grange and Hungria, 2004), with information on these strains shown in Table 2. All strains isolated by Grange and Hungria (2004) were originally designated as “PRF” strains, but are shown

Results

Sizes obtained for the PCR products were: nodA, ∼660 bp; nodB, ∼600 bp; nodC, ∼930 bp; and nifH between 780 and 890 bp (data not shown).

The dendrogram obtained by RFLP-PCR of the nodA region with six restriction enzymes showed a high level of diversity, with three great groups distinguishable (data not shown). The first great group (GG I) clustered fifteen strains at a 37% level of similarity and included only reference strains belonging to species other than R. etli bv. phaseoli (designated

Discussion

Despite being the largest producer of common bean in the world, Brazil's yields per unit area are low (789 kg ha−1 average) (CONAB, 2006). Constraints include poor technology and cropping in acid soils that are low organic matter content and deficient in N. Increased availability of N through the root-nodule symbiosis with efficient rhizobial strains might increase yields at a low cost and with environmental benefits. However, poor nodulation and low N2 fixation rates and lack of responses to

Acknowledgments

The authors thank Dr. Fernando G. Barcellos, Ligia Maria O. Chueire, Glaciela Kaschuk, Pâmela Menna, Fabiana G. Pinto and Fábio L. Mostasso (Embrapa Soja) for help in several steps of this work, and to Dr. Ligia V. Terasawa, Dr. Berenice Steffens, Dr. Chirlei (UFPR) and Dr. Galdino de Andrade Filho (UEL) for helpful discussion. Authors thank especially to Dr. Fabio Freitas (Embrapa Cenargen), for introducing new concepts in our work. Research described herein was partially supported by MCT

References (67)

  • N.O. Pérez-Ramírez et al.

    Seeds of Phaseolus vulgaris bean carry Rhizobium etli

    FEMS Microbiology Ecology

    (1998)
  • C. Acosta-Durán et al.

    Diversity of rhizobia from nodules of the leguminous tree Gliricidia sepium, a natural host of Rhizobium tropici

    Archives of Microbiology

    (2002)
  • O.M. Aguilar et al.

    Prevalence of the Rhizobium-etli like allele in genes coding for 16S rRNA among the indigenous rhizobial populations found associated with wild beans from the Southern Andes in Argentina

    Applied and Environmental Microbiology

    (1998)
  • O.M. Aguilar et al.

    Analysis of Rhizobium etli and its symbiosis with wild Phaseolus vulgaris supports coevolution in centers of host diversification

    Proceedings of the National Academy of Sciences of the United States of America

    (2004)
  • N. Amarger et al.

    Rhizobium tropici nodulates field-grown Phaseolus vulgaris in France

    Plant and Soil

    (1994)
  • N. Amarger et al.

    Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules

    International Journal of Systematic Bacteriology

    (1997)
  • D.S. Andrade et al.

    The diversity of Phaseolus-nodulating rhizobial populations is altered by liming of acid soils planted with Phaseolus vulgaris L. in Brazil

    Applied and Environmental Microbiology

    (2002)
  • B. Anyango et al.

    Diversity of rhizobia nodulating Phaseolus vulgaris L. in two Kenyan soils with contrasting pHs

    Applied and Environmental Microbiology

    (1995)
  • G.R. Bernal et al.

    Diversity in the rhizobia associated with Phaseolus vulgaris L. in Ecuador, and comparisons with Mexican bean rhizobia

    Canadian Journal of Microbiology

    (2001)
  • G.R. Bernal et al.

    Characteristics of rhizobia nodulating beans in the central region of Minnesota

    Canadian Journal of Microbiology

    (2004)
  • E. Beyhaut et al.

    Rhizobium giardinii is the microsymbiont of Illinois bundleflower (Demanthus illinoensis (Michx.) Macmillan) in Midwestern prairies

    Canadian Journal of Microbiology

    (2006)
  • CONAB (Companhia Nacional de Abastecimento), 2006. Feijão total (1o, 2a e 3a safra)—Brasil—Série histórica. Retrieved...
  • H. Dagutat et al.

    Taxonomy and distribution of rhizobia indigenous to South African soils

  • D.G. Debouck

    Primary diversification of Phaseolus in the Americas: three centers?

    Plant Genetic Resources Newsletter

    (1986)
  • D.G. Debouck et al.

    Genetic diversity and ecological distribution of Phaseolus vulgaris (Fabacea) in northwestern South America

    Economic Botany

    (1983)
  • B.M. Emygdio et al.

    Diversidade genética em cultivares locais e comerciais de feijão baseada em marcadores RAPD

    Pesquisa Agropecuária Brasileira

    (2003)
  • M.C. Franco et al.

    Nodulação em cultivares de feijão dos conjuntos gênicos andino e meso-americano

    Pesquisa Agropecuária Brasileira

    (2002)
  • F.O. Freitas

    Evidências genético-arqueológicas sobre a origem do feijão comum no Brasil

    Pesquisa Agropecuária Brasileira

    (2006)
  • FUNAI (Fundação Nacional do Índio), 2005. Povos indígenas. Retrieved in 14 September 2005, from...
  • P. Gepts

    Biochemical evidence bearing on the domestication of Phaseolus (Fabaceae) beans

    Economic Botany

    (1990)
  • P. Gepts et al.

    Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.)

  • P.H. Graham et al.

    Acid pH tolerance in strains of Rhizobium and Bradyrhizobium, and initial studies on the basis for acid tolerance of Rhizobium tropici UMR1899

    Canadian Journal of Microbiology

    (1994)
  • G. Hardarson

    Methods for enhancing symbiotic nitrogen fixation

    Plant and Soil

    (1993)
  • Cited by (36)

    • Maize growth and yield promoting endophytes isolated into a legume root nodule by a cross-over approach

      2020, Rhizosphere
      Citation Excerpt :

      However, the highly competitive ability of the Bradyrhizobium isolates toward cowpea can be a key factor for the frequent isolation of this bacteria worldwide (Grönemeyer et al., 2014; Jaiswal and Dakora, 2019; Martins et al., 2003; Oliveira et al., 2020). Considering a bacterial community with a low abundance of Rhizobium and Bradyrhizobium, the existence of diluted populations of the more competitive bacteria allows the nodulation of the less competitive rhizobia, as was shown for other rhizobia in soils of Brazil (Grange et al., 2007). The field performance of Rhizobium sp.

    • Inoculation with native Bradyrhizobium strains formulated with biochar as carrier improves the performance of pigeonpea (Cajanus cajan L.)

      2020, European Journal of Agronomy
      Citation Excerpt :

      Thus, a successful inoculant strain needs to be a good N-fixer, similar to the strains used in this work, and it also needs an outstanding ability to form and colonize nodules. Although the nodule colonisation by the inoculated strain can be influenced by abiotic soil factors such as pH (Pérez-Fernández et al., 2015), usually the number of resident nodulating bacteria in the soil (Laguerre et al., 2003; Howieson and Ballard, 2004; Elias and Herridge, 2015) and their competitive ability (Ferreira and Hungria, 2002; Grange et al., 2007) are the most influencing factors. In this context, in our field trial we analysed the nodule occupancy by the inoculated strains, in soils with different counts of resident nodulating bacteria, and the obtained results confirmed that for pigeonpea, the number of resident nodulating bacteria had a statistically significant effect on the level of nodule occupancy by the inoculated strain.

    • Phaseolus vulgaris is nodulated by the symbiovar viciae of several genospecies of Rhizobium laguerreae complex in a Spanish region where Lens culinaris is the traditionally cultivated legume

      2019, Systematic and Applied Microbiology
      Citation Excerpt :

      Both legumes coevolved in their respective distribution centers with fast-growing rhizobial strains belonging to genus Rhizobium, which are able to nodulate and to fix atmospheric nitrogen in symbiosis with these legumes [42,43]. The symbiovar phaseoli is the main endosymbiont of P. vulgaris in its American distribution centers [3,4,8,12,15,40,44], whereas L. culinaris is nodulated by the symbiovar viciae in the Middle East distribution centers of this legume [30,31]. Both legumes, P. vulgaris and L. culinaris, currently worldwide cultivated, were introduced in other continents from their distribution centers at different times in history.

    • Novel Rhizobium lineages isolated from root nodules of the common bean (Phaseolus vulgaris L.) in Andean and Mesoamerican areas

      2013, Research in Microbiology
      Citation Excerpt :

      Diversity of the P. vulgaris nodule rhizobia has been extensively studied, showing that, at its sites of origin, there are preferred symbionts, but in introduced areas it is promiscuous and may function as a trap-host plant (Martínez et al., 1985; Michiels et al., 1998), forming nodules with diverse indigenous bacteria [reviewed in Martínez-Romero (2003)]. Additionally, in introduced areas, rhizobial species similar to those at the site of origin have also been found, probably introduced by carriage of rhizobia on seeds (Grange et al., 2007; Pérez-Ramírez et al., 1998). In Mexico, Rhizobium etli seems to be the main P. vulgaris symbiont, but this needs further analysis in view of a recent taxonomy revision that proposed reclassification of some R. etli strains as Rhizobium phaseoli, and revealed the existence of other common-bean-nodulating species-level lineages previously considered to be R. etli (López-Guerrero et al., 2012b).

    View all citing articles on Scopus
    View full text