title: Taxonomy of rhizobia and agrobacteria from the Rhizobiaceae family in light of genomics.
abstract: Phylogenomic analyses showed two major superclades within the family Rhizobiaceae that corresponded to the Rhizobium/Agrobacterium and Shinella/Ensifer groups. Within the Rhizobium/Agrobacterium group, four highly supported clades were evident that could correspond to distinct genera. The Shinella/Ensifer group encompassed not only the genera Shinella and Ensifer but also a separate clade containing the type strain of Rhizobium giardinii. Ensifer adhaerens (Casida A(T)) was an outlier within its group, separated from the rest of the Ensifer strains. The phylogenomic analysis presented provided support for the revival of Allorhizobium as a bona fide genus within the Rhizobiaceae, the distinctiveness of Agrobacterium and the recently proposed Neorhizobium genus, and suggested that R. giardinii may be transferred to a novel genus. Genomics has provided data for defining bacterial-species limits from estimates of average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH). ANI reference values are becoming the gold standard in rhizobial taxonomy and are being used to recognize novel rhizobial lineages and species that seem to be biologically coherent, as shown in this study.
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Ernesto
authors: E
authors: Ormeño-Orrillo
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Luis E
authors: LE
authors: Servín-Garcidueñas
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Marco A
authors: MA
authors: Rogel
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Víctor
authors: V
authors: González
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Humberto
authors: H
authors: Peralta
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Jaime
authors: J
authors: Mora
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
authors: Julio
authors: J
authors: Martínez-Romero
authors: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico. Electronic address: emartine@ccg.unam.mx.
authors: Esperanza
authors: E
authors: Martínez-Romero
mesh_terms: D060054:Agrobacterium / Q000145:classification* / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D010802:Phylogeny; D012231:Rhizobium / Q000145:classification* / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial
keywords: Genome; Next generation sequencing; Phylogeny; Rhizobia; Root nodule bacteria; Systematics