Genetics and Genomics of the Rhizobium-Legume Symbiosis

Dear Colleagues,

Leguminosae (Fabaceae, the legume family) is comprised of ca. 19,300 species, within 750 genera, which occur as herbs, shrubs, vines, or trees, in mainly terrestrial habitats, and are components of most of the world’s vegetation types. Most legume species can fix atmospheric nitrogen (N₂) via symbiotic bacteria ( ‘rhizobia’) in root nodules and this can give them an advantage under low soil nitrogen (N) conditions if other factors are favorable for growth. Additionally, N₂ fixation by legumes can be a major input of N into natural and agricultural ecosystems.

Genetic data have greatly increased our understanding of the biology and evolution of legumes, rhizobia, and legume–rhizobium symbiosis. For example, in 2017, a new classification of the legumes was proposed with six sub-families, based on the plastid matK gene sequences from ca. 20% of all legume species across ca. 90% of all currently recognized genera. These sub-families are a re-circumscribed Caesalpinioideae, Cercidoideae, Detarioideae, Dialioideae, Duparquetioideae and Papilionoideae. Additionally, over the past twenty-five years, phylogenetic analyses of sequences of the 16S ribosomal RNA (rRNA) gene, a range of ‘housekeeping’ genes and symbiosis genes (in particular, ‘nif’ genes, which encode the subunits of nitrogenase, the rhizobial enzyme that fixes N_2, and ‘nod’ genes, which encode Nod factors that induce various symbiotic responses on legume roots) have shown that species from a range of genera in the Alphaproteobacteria (most commonly Bradyrhizobium, Ensifer Mesorhizobium and Rhizobium) and two genera in the Betaproteobacteria (Burkholderia (Paraburkholderia) and Cupriavidus)) can form N₂ fixing nodules on specific legumes. Full genome sequences are becoming increasingly used in descriptions of rhizobia and in studies on their biology.

The nodulation process for almost all legumes studied is initiated by the legume production of a mix of compounds, mainly flavonoids, which induce synthesis of NodD protein in rhizobia. Different legumes produce different types/mixes of compounds. The NodD protein activates the transcription of other genes involved in the nodulation process including those required to produce Nod factors, the signal molecules produced by the rhizobia and detected by the plant that induce nodule organogenesis. The nodABC genes encode for the proteins required to make the core Nod factor structure. Nod factors from different rhizobia have a similar structure of a chitin-like N-acetyl glucosamine oligosaccharide backbone with a fatty acyl chain at the non-reducing end, but differ in their length of N-acetyl glucosamine oligosaccharide backbone and length and saturation of the fatty acid chain. The Nod-factor core is modified by species specific proteins, which results in various substitutions, including acetylation, glycosylation, methylation, and sulphation. Perception of the Nod-factor signal in legumes is mediated by Nod factor receptors. Specific nod genes have been shown to be major determinants of legume host specificity although legume-rhizobium specificity can be due to factors throughout the development of the symbiosis. The nif and nod genes are often carried on plasmids or symbiotic islands and these genes can be transferred (lateral transfer) between different bacterial species within a genus and more rarely across genera. This is an important mechanism, allowing legumes to form symbioses with rhizobia adapted to particular soils. It also maintains specificity between legume species and rhizobia species with specific symbiosis genes.

We invite submission of original research or review articles in which genetic/genomic data have been used to gain greater understanding of the biology/evolution of legumes, rhizobia and/or the legume rhizobium symbiosis.

Dr. Mitchell Andrews
Dr. Euan K. James
Dr. Marcelo Fragomeni Simon
Guest Editors

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• Classification and taxonomy of legumes
• Classification and taxonomy of rhizobia
• Legume biology; Rhizobia biology
• Specificity of the legume-rhizobium symbiosis
• Horizontal gene transfer
• nod genes
• Bacterial symbionts
• Nitrogen fixation
• Evolutionary history of the legume-rhizobium symbiosis