Reclassification of Pseudomonas boreopolis Gray and Thornton 1928 (Approved Lists 1980) as Xanthomonas boreopolis comb. nov. and Pseudomonas carboxydohydrogena (ex Sanjieva and Zavarzin 1971) Meyer et al. 1980 as Afipia carboxydohydrogena comb. nov. based on comparative genomic analysis.

Abstract

In the present study, we conducted the whole-genome sequence analysis of Pseudomonas boreopolis JCM 13306^T and Pseudomonas carboxydohydrogena DSM 1083^T from the genus Pseudomonas for assigning taxonomic placement. Sequence analysis of the 16S rRNA gene revealed that P. boreopolis JCM 13306^T had the highest sequence similarity to Xanthomonas species, with sequence similarities ranging from 97.24% to 97.92% nucleotide identity. Likewise, sequence analysis of the 16S rRNA gene exhibited P. carboxydohydrogena DSM 1083^T with 99.36%, 99.00% and 98.93% similarity to Afipia felis ATCC 53690^T, Afipia carboxidovorans ATCC 49405^T and Afipia clevelandensis ATCC 49720^T, respectively. P. boreopolis JCM 13306^T and P. carboxydohydrogena DSM 1083^T have indicated a distinct position in the phylogenetic (based on concatenated sequences of 81 core proteins and 16S rRNA gene) and phylogenomic trees from some type strains of the Pseudomonadaceae family; however, P. boreopolis JCM 13306^T and P. carboxydohydrogena DSM 1083^T were strongly clustered with species of the Xanthomonas (family Lysobacteraceae) and Afipia (family Nitrobacteraceae), respectively. Besides, the amino acid identity values between P. boreopolis JCM 13306^T and the members of the Pseudomonadaceae family were 53.95-57.98%, as well as between P. carboxydohydrogena DSM 1083^T and this family which were 50.43-51.41%. These values were below the cut-off level for genus demarcation (60-85%). The scores of digital DNA-DNA hybridization (70%), average nucleotide identity by blast (95-96%) and average nucleotide identity using MUMmer (96%) between P. boreopolis JCM 13306^T and P. carboxydohydrogena DSM 1083^T, with the members of the Pseudomonadaceae family, were below the threshold value for bacterial species delineation. Therefore, based on genomic and phylogenomic analysis, we propose reclassifying P. boreopolis JCM 13306^T and P. carboxydohydrogena DSM 1083^T as Xanthomonas boreopolis comb. nov. in the Lysobacteraceae family and Afipia carboxydohydrogena comb. nov. in the Nitrobacteraceae family, respectively.