Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification

Abstract

Species from the genus <i>Paenibacillus</i> are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify <i>Paenibacillus</i> strains. For this purpose, <i>Paenibacillus riograndensis</i> SBR5^T, <i>Paenibacillus sonchi</i> X19-5^T, and their close relatives were compared through phenotypic, genotypic, and genomic approaches. With respect to <i>P. sonchi</i> X19-5^T, <i>P. riograndensis</i> SBR5^T, <i>Paenibacillus</i> sp. CAR114, and <i>Paenibacillus</i> sp. CAS34 presented ANI (average nucleotide identity) values ranging from 95.61 to 96.32%, gANI (whole-genome average nucleotide identity) values ranging from 96.78 to 97.31%, and dDDH (digital DNA-DNA hybridization) values ranging from 68.2 to 73.2%. Phylogenetic analyses of 16S rRNA, <i>gyrB, recA, recN</i>, and <i>rpoB</i> genes and concatenated proteins supported the monophyletic origin of these <i>Paenibacillus</i> strains. Therefore, we propose to assign <i>Paenibacillus</i> sp. CAR114 and <i>Paenibacillus</i> sp. CAS34 to <i>P. sonchi</i> species, and reclassify <i>P. riograndensis</i> SBR5^T as a later heterotypic synonym of <i>P. sonchi</i> (type strain X19-5^T), with the creation of three novel genomovars, <i>P. sonchi</i> genomovar Sonchi (type strain X19-5^T), <i>P. sonchi</i> genomovar Riograndensis (type strain SBR5^T), <i>P. sonchi</i> genomovar Oryzarum (type strain CAS34^T = DSM 102041^T; = BR10511^T).