Methylotrophic Methylobacterium Bacteria Nodulate and Fix Nitrogen in Symbiosis with Legumes

Abstract

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...

Methanol oxidation by temperate soils and environmental determinants of associated methylotrophs

“…Plant species composition can also be correlated with the overall community structure of soil bacteria (Berg and Smalla, 2009). Methylotroph plant interactions can be very specific (for example, root nodule formation) or can be less stringent when soil methylotrophs modulate growth of their host plants (for example, Sy et al, 2001;Fedorov et al, 2011). In the case of methane-oxidizing methylotrophs, the presence of trees correlates with certain methanotrophic genotypes (Kolb, 2009b;Degelmann et al, 2010).…”

Rhizosphere microbiome assemblage is affected by plant development

“…Interestingly, most of the transcripts that aligned to pathogens were significantly expressed early during development (8 genes) while transcripts that aligned to microbes involved in plant growth promotion or N fixation were more abundant late (23 genes; Table 4). For example, the transcripts involved in bacterial chemotaxis (two-component system, chemotaxis family, response regulator) were significantly more abundant at late time points and aligned to the nitrogen fixing PGPR Methylobacterium extorquens (Ivanova et al, 2001;Sy et al, 2001;Lidstrom and Chistoserdova, 2002). On the other hand, the transcript involved in amoebiasis (Ras-related protein Rab-7A) was significantly more abundant at early time points, and it aligned with the pathogen Moniliophthora perniciosa.…”

A large diversity of non-rhizobial endophytes found in legume root nodules in Flanders (Belgium)

“…While traditionally, rhizobia belonged to the genera, Azorhizobium, Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium (Sawada et al, 2003), in recent years nitrogen fixing root nodule bacteria have also been described in other Alphaproteobacterial genera, including Ochrobactrum (Trujillo et al, 2005), Methylobacterium (Sy et al, 2001), Microvirga (Ardley et al, 2012;Radl et al, 2014), Devosia (Rivas et al, 2003) and Phyllobacterium . Furthermore, so-called Betarhizobia have in the last ten years been described in the Betaproteobacterial genera Burkholderia and Cupriavidus (Chen et al, 2001;Moulin et al, 2001;De Meyer et al, 2013a;De Meyer et al, 2013b;De Meyer et al, 2014).…”