Cupriavidus phytorum sp. nov., isolated from Zea mays L. rhizosphere in Mexico and Mimosa diplotricha Sauvalle root nodule in Taiwan.

Abstract

Several Cupriavidus and Burkholderia strains from the north of Mexico were isolated during the description of Cupriavidus strains. Cupriavidus alkaliphilus, Cupriavidus plantarum and Cupriavidus agave were later described as novel species. Next, the Genomic Encyclopedia of Bacteria and Archaea project retrieved the genome sequences of several strains from the above species. Standard comparative genomic analysis showed that C. alkaliphilus MLR2-44 was taxonomically misclassified. This strain, isolated from the Zea mays rhizosphere, was analysed by average nucleotide identity (ANI), revealing that Cupriavidus nantongensis was the closest species (95.6%). However, the digital DNA-DNA hybridization (dDDH) resulted in values lower than 68% for any type strain of Cupriavidus species. Moreover, it was also found that Cupriavidus taiwanensis LMG 19430, isolated from Mimosa diplotricha root nodules, was closer to strain MLR2-44^T (99.9% ANI and 99.8% dDDH), instead of being associated with the type strain of C. taiwanensis LMG 19424^T (94.4% ANI and 54.6% dDDH), thus making strains MLR2-44^T and LMG 19430 a single genomic species. Accordingly, the polyphasic analysis showed that these strains represent a new species; therefore, we propose that strains MLR2-44^T (=CDBB B-2066^T=TSD-312^T) and LMG 19430 encompass a novel Cupriavidus species with the name of Cupriavidus phytorum sp. nov.