Trends in Microbiology
Volume 17, Issue 10, October 2009, Pages 458-466
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Review
Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?

https://doi.org/10.1016/j.tim.2009.07.004Get rights and content

Rhizobia are phylogenetically disparate α- and β-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen (N2) in symbiosis with legumes. All rhizobia elicit the formation of root – or occasionally stem – nodules, plant organs dedicated to the fixation and assimilation of nitrogen. Bacterial colonization of these nodules culminates in a remarkable case of sustained intracellular infection in plants. Rhizobial phylogenetic diversity raised the question of whether these soil bacteria shared a common core of symbiotic genes. In this article, we review the cumulative evidence from recent genomic and genetic analyses pointing toward an unexpected variety of mechanisms that lead to symbiosis with legumes.

Section snippets

Variations on a theme

Symbioses are essential for eukaryotic life and a major source of evolutionary novelty 1, 2. One of the best studied symbioses involves plant legumes and bacteria collectively known as rhizobia. These partners cooperate in a nitrogen-fixing symbiosis of major ecological importance that occurs on all continents and accounts for a fourth of the nitrogen fixed annually on earth. This symbiosis involves most of the 18,000 legume species together with an expanding collection of α- and

Rhizobia are phylogenetically, metabolically and genetically diverse

Although diseases are usually provoked by specific taxonomical microbial groups, legume symbiosis relies on phylogenetically disparate bacteria spread over two subclasses of the proteobacteria 3, 4 (Box 1). In line with their phylogenetic diversity, rhizobia exhibit a large panel of metabolic properties [5]. To the best of our knowledge only one, Azorhizobium caulinodans, is a genuine diazotroph, able to grow ex planta at the expense of fixed nitrogen [6], at a relatively high oxygen

Nitrogen fixation: a common nif equipment with large variations in gene number and regulatory circuitries

All rhizobia rely on the most common form of nitrogenase, molybdenum-nitrogenase (EC 1.18.2.1), for nitrogen fixation. Alternative nitrogenases that use vanadium or iron instead of molybdenum or the atypical O2-requiring nitrogenase of Streptomyces thermoautotrophicus have not been found in rhizobia. Mo-nitrogenase endures two major drawbacks: a high-energy requirement with a minimal stoichiometry of 16 mol of ATP for each mole of N2 reduced, and an extreme sensitivity to oxygen, which is in

The Nod factor strategy is not universal

There was a long-held belief that nodulation of legumes involves an exchange of molecular signals where nodulation (nod) genes play an essential role (for reviews see Refs 17, 18, 19). Secondary plant metabolites—mainly (iso)flavonoids—induce the bacterial nod-dependent excretion of lipochitooligosaccharidic Nod factors (NFs) which in turn provoke nodule morphogenesis (Figure 3a). The same NF-dependent nodulation strategy (abbreviated below as NF strategy) was also shown to be used by the

Nodule infection

In general, rhizobia ultimately become intracellular symbionts of nodule cells. This is a remarkable feature given that endocellular colonization, including by pathogens, is rare in plant-associated bacteria. Infection designates the multistep process that drives external rhizospheric bacteria to their final endocellular niche. Yet all rhizobia do not infect in the same way. Some penetrate the epidermal and cortical layers of the emerging nodule by a very specific and sophisticated root hair

A scenario for the emergence of rhizobia

Although highly specialized, the rhizobium–legume interaction appears as very innovative. It involves many unrelated bacterial genera, presents diverse phenotypic characteristics from pair to pair of symbionts (Figure 1) and is supported by different genetic strategies. Such capacity of novelty—that is rare in other endosymbioses—presumably stems from the alternative saprophytic life of rhizobia that allows genetic material exchange with other soil bacteria 40, 41. Interestingly, in silico

Concluding remarks and future directions

Two features have animated the rhizobium–legume field in recent years: the genetics of model systems and the biodiversity of rhizobia. Combining these vertical and horizontal approaches led to the conclusion that symbiosis did not rely on a single rhizobium recipe but instead that rhizobia, regardless of their phylogeny, evolved several distinct strategies to enter in symbiosis with legumes. This suggests that rhizobial strategies have emerged largely independently from each other, even though

Acknowledgements

We are grateful to Dr. L. Rubio (IMDEA, Madrid) for his help in interpreting nif gene content, to Dr. J. Cullimore (LIPM, Toulouse) for careful reading of the manuscript and to members of the CMB/JB lab for stimulating discussions. Work in the authors’ laboratories is supported by grants from the SPE INRA department, INRA BioRessources, BRG and ANR-08-BLAN-0295-01 (C.M.B. and J.B.), IRD and ANR-06-BLAN-0095 (E.G.) and the University of Geneva as well as the Swiss National Science Foundation

Glossary

Cytokinins
adenine-derived signaling molecules involved in diverse plant developmental processes, including nodule development in legumes.
Determinate nodules
nodules with a transient meristem. Infected cells differentiate in a synchronous manner and a mature nodule contains a homogeneous population of bacterial nitrogen fixing cells.
Indeterminate nodules
nodules that have a persistent apical meristem and show a longitudinal gradient of differentiation.
Diazotrophy
capacity to fix and grow on N2 as

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