Phylogenomic analysis shows underestimated species within Cupriavidus and the new species Cupriavidus phytohabitans sp. nov

During a survey of nodule-associated bacteria from legume plants and soil collected in southern Mexico, several strains were obtained in Mexico City using Phaseolus vulgaris as a trap plant, inoculated with rhizospheric soil from the legume Acacia sp. collected in the state of Veracruz, a bordering state to the Gulf of Mexico. The 16S rRNA gene sequence analysis identified the strains AcVe19-1a^T, AcVe19-6a, and AcVe19-6b as Cupriavidus (with 99.9% similarity to many type strains of Cupriavidus species and 99.9 to 100% similarity within the novel species). Comparative genomics by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) showed that strains AcVe19-1a^T and AcVe19-6a correspond to a new Cupriavidus genomic species (ANI values lower than 94% and dDDH values lower than 55% to any Cupriavidus strain, and the closest species Cupriavidus consociatus). The genome of the novel species harbors nitrogen-fixing and nodulation genes, enabling it to nodulate plants of P. vulgaris and Mimosa pudica, but it does so poorly with Acacia sp. However, nitrogen was not fixed in the nodule or the culture medium. According to the symbiovars guidelines, two symbiovars are proposed. The genome analysis, together with phenotypic, physiological, and chemotaxonomical analyses, corroborate that strains AcVe19-1a^T, AcVe19-6a, and AcVe19-6b correspond to a novel species, for which we propose the name Cupriavidus phytohabitans sp. nov. with the type strain AcVe19-1a^T = TSD-313^T = CDBB B-2084^T. In addition to the description of the novel species, a comparative genomic analysis of all Cupriavidus species in the NCBI database showed that many have been misclassified, and others correspond to new genomic species.