Members of the Leguminosae form the largest plant family on Earth, with around 18,000 species. The success of legumes can largely be attributed to their ability to form a nitrogen-fixing symbiosis with specific bacteria known as rhizobia, manifested by the development of nodules on the plant roots in which the bacteria fix atmospheric nitrogen, a major contributor to the global nitrogen cycle. Rhizobia described so far belong exclusively to the alpha-subclass of Proteobacteria, where they are distributed in four distinct phylogenetic branches. Although nitrogen-fixing bacteria exist in other proteobacterial subclasses, for example Herbaspirillum and Azoarcus from the phylogenetically distant beta-subclass, none has been found to harbour the nod genes essential for establishing rhizobial symbiosis. Here we report the identification of proteobacteria from the beta-subclass that nodulate legumes. This finding shows that the ability to establish a symbiosis with legumes is more widespread in bacteria than anticipated to date.

Following the initial discovery of two legume-nodulating Burkholderia strains (L. Moulin, A. Munive, B. Dreyfus, and C. Boivin-Masson, Nature 411:948-950, 2001), we identified as nitrogen-fixing legume symbionts at least 50 different strains of Burkholderia caribensis and Ralstonia taiwanensis, all belonging to the ␤-subclass of proteobacteria, thus extending the phylogenetic diversity of the rhizobia. R. taiwanensis was found to represent 93% of the Mimosa isolates in Taiwan, indicating that ␤-proteobacteria can be the specific symbionts of a legume. The nod genes of rhizobial ␤-proteobacteria (␤-rhizobia) are very similar to those of rhizobia from the ␣-subclass (␣-rhizobia), strongly supporting the hypothesis of the unique origin of common nod genes. The ␤-rhizobial nod genes are located on a 0.5-Mb plasmid, together with the nifH gene, in R. taiwanensis and Burkholderia phymatum. Phylogenetic analysis of available nodA gene sequences clustered ␤-rhizobial sequences in two nodA lineages intertwined with ␣-rhizobial sequences. On the other hand, the ␤-rhizobia were grouped with free-living nitrogen-fixing ␤-proteobacteria on the basis of the nifH phylogenetic tree. These findings suggest that ␤-rhizobia evolved from diazotrophs through multiple lateral nod gene transfers.Members of the Leguminosae, comprising about 18,000 species, play an important ecological role, with representatives in nearly every type of plant on Earth. Most species are able to form nitrogen-fixing symbioses with specific bacteria known as rhizobia. The recent identification of two ␤-proteobacterial strains of the genus Burkholderia able to nodulate legumes (10) changed the long-held dogma that only bacteria of the ␣ subdivision are able to nodulate legumes (18, 23). These two strains were subsequently described as Burkholderia tuberum and Burkholderia phymatum (24). In addition, eight strains isolated from root nodules of Mimosa spp. were recently described as Ralstonia taiwanensis, also classified as ␤-proteobacteria (1), although their nodulation capacity was not confirmed. The terms ␣-and ␤-rhizobia were proposed to distinguish the rhizobial ␣-and ␤-proteobacteria, respectively (10). This unexpected discovery raised the question as to whether nodulation by ␤-proteobacteria is an extremely rare phenomenon or whether it had simply been overlooked until now. Moreover, the fact that the first two nodulating Burkholderia strains were isolated from Aspalathus and Machaerium spp., which are known to be associated with Bradyrhizobium (2, 12), may suggest that these ␤-proteobacteria are not the specific partners of the respective host legumes.In this article, we confirm the widespread phylogenetic diversity of nitrogen-fixing legume symbionts by identifying as ␤-rhizobia an additional 2 Burkholderia strains from the species Burkholderia caribensis and a collection of at least 44 R. taiwanensis strains. These data increase to four the number of different ␤-rhizobial species identified so far, originating from three different continents. Moreove...

Rhizobia described so far belong to three distinct phylogenetic branches within the ␣-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, "Methylobacterium nodulans," within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the ␣ subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that "M. nodulans" is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that "M. nodulans" NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer.Symbioses between leguminous plants and soil bacteria commonly referred to as rhizobia are of considerable environmental and agricultural importance since they are responsible for most of the atmospheric nitrogen fixed on land. Rhizobia are able to elicit on most of the 18,000 species of the Leguminosae family the formation of specialized organs, called nodules, in which they reduce atmospheric nitrogen to ammonia to the benefit of the plant. Nodule formation is controlled by extracellular bacterial signal molecules, called Nod factors, which are recognized by the host plant (21, 34). The rhizobial species described so far are very diverse and do not form an evolutionary homogenous clade. They belong to three distinct branches within the ␣-2 subclass of Proteobacteria and are phylogenetically intertwined with non-symbiotic bacteria (40) (Fig. 1). A first large branch groups the genera Rhizobium, Sinorhizobium, Mesorhizobium, and Allorhizobium with Agrobacterium, a pathogenic bacterium of plants. A second branch contains the genus Bradyrhizobium together with photosynthetic free-living Rhodopseudomonas, whereas the third branch includes the genus Azorhizobium as well as the chemiautotroph Xanthobacter. Each rhizobial species has a defined host range, varying from very narrow, as in the case of Azorhizobium caulinodans (6), to very broad, as in the case of Sinorhizobium sp. strain NGR234 (30). Symbionts of legumes exhibiting ecological and agronomic potential should be characterized prior to their use in sustainable agriculture and environment management.Crotalaria spp. are herbs and shrubs of the subfamily Papilionoideae; it is the largest plant genus in Africa. More than 500 species commonly occur in diverse climatological situations, from semidesert to rain forests and high mountains (1, 29). Some Crotalaria spp. are of great agronomic interest since they are used as green manure to improve soil fertility o...

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Environmental screening of bacteria for the presence of genes of interest is a challenging problem, due to the high variability of the nucleotide sequence of a given gene between species. Here, we tackle this general issue using a particularly well-suited model system that consists of the nodulation gene nodC, which is shared by phylogenetically distant rhizobia. 41mer and 50mer oligonucleotides featuring the nucleotide diversity of two highly conserved regions of the NodC protein were spotted on glass slides and cross hybridized with the radioactive-labeled target genomic DNA under low-stringency conditions. Statistical analysis of the hybridization patterns allowed the detection of known, as well as new, nodC sequences and classified the rhizobial strains accordingly. The microarray was successfully used to type the nodC gene directly from legume nodules, thus eliminating the need of cultivation of the endosymbiont. This approach could be extended to a panel of diagnostic genes and constitute a powerful tool for studying the distribution of genes of interest in the environment, as well as for bacteria identification.

Until recently, nitrogen fixing rhizobia that form symbiotic relationships were exclusively classified in the α-subclass of Proteobacteria. The identification of rhizobia within Proteobacteria from the β-subclass, including Burkholderia and Ralstonia, shows that the ability to establish a symbiosis with legumes is more widespread.

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