Genomic basis of symbiovar mimosae in Rhizobium etli.

Marco A Rogel,Víctor González,Julio Martínez-Romero,Esperanza Martínez-Romero,Patricia Bustos,Rosa I Santamaría,Miguel Ángel Cevallos,Luis Lozano,David Romero,Ernesto Ormeño-Orrillo,Jaime Castro-Mondragón

doi:10.1186/1471-2164-15-575

Abstract

BackgroundSymbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees.ResultsWe report on the genome of R. etli symbiovar mimosae strain Mim1 and its comparison to that from R. etli symbiovar phaseoli strain CFN42. Differences were found in plasmids especially in the symbiosis plasmid, not only in nod gene sequences but in nod gene content. Differences in Nod factors deduced from the presence of nod genes, in secretion systems or ACC-deaminase could help explain the distinct host specificity. Genes involved in P. vulgaris exudate uptake were not found in symbiovar mimosae but hup genes (involved in hydrogen uptake) were found. Plasmid pRetCFN42a was partially contained in Mim1 and a plasmid (pRetMim1c) was found only in Mim1. Chromids were well conserved.ConclusionsThe genomic differences between the two symbiovars, mimosae and phaseoli may explain different host specificity. With the genomic analysis presented, the term symbiovar is validated. Furthermore, our data support that the generalist symbiovar mimosae may be older than the specialist symbiovar phaseoli.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-575) contains supplementary material, which is available to authorized users.

Highlights

Symbiosis genes involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium
Plant nodulation assays L. leucocephala seeds were treated with concentrated sulfuric acid for 15 min, rinsed with water and surface disinfected with sodium hypochlorite as described [26]; the same procedure was used to disinfect P. vulgaris seeds
Identity (ANI) and the percentage of conserved DNA between Mim1 and CFN42 were 98.6% and 82.4% respectively on a whole genome analysis, confirming that both strains belong to the same species

Summary

Introduction

Symbiosis genes (nod and nif) involved in nodulation and nitrogen fixation in legumes are plasmid-borne in Rhizobium. Rhizobial symbiotic variants (symbiovars) with distinct host specificity would depend on the type of symbiosis plasmid. In Rhizobium etli or in Rhizobium phaseoli, symbiovar phaseoli strains have the capacity to form nodules in Phaseolus vulgaris while symbiovar mimosae confers a broad host range including different mimosa trees. Genes for plant nodulation and nitrogen fixation are plasmid-borne in Rhizobium spp. There are over twenty different symbiovars reported in Rhizobium and in Bradyrhizobium and in other genera of nodule forming bacteria [2,3,4,5,6,7]. A theoretical model proposes that a single species may exhibit alternative symbiovars depending on the presence of symbiotic plasmids or symbiotic islands [2]. P. vulgaris is a recent species (probably two million years old [14]), while mimosas seem to be older

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