Bacillus velezensis is not a later heterotypic synonym of Bacillus amyloliquefaciens; Bacillus methylotrophicus, Bacillus amyloliquefaciens subsp. plantarum and ‘Bacillus oryzicola’ are later heterotypic synonyms of Bacillus velezensis based on phylogenomics

Abstract

<i>Bacillus velezensis</i> was previously reported to be a later heterotypic synonym of <i>Bacillus amyloliquefaciens</i>, based primarily on DNA-DNA relatedness values. We have sequenced a draft genome of <i>B. velezensis</i> NRRL B-41580^T. Comparative genomics and DNA-DNA relatedness calculations show that it is not a synonym of <i>B. amyloliquefaciens.</i> It was instead synonymous with <i>Bacillus methylotrophicus.</i> '<i>Bacillus oryzicola</i>' is a recently described species that was isolated as an endophyte of rice (<i>Oryza sativa</i>). The strain was demonstrated to have plant-pathogen antagonist activity in greenhouse assays, and the 16S rRNA gene was reported to have 99.7 % sequence similarity with <i>Bacillus siamensis</i> and <i>B. methylotrophicus</i>, which are both known for their plant pathogen antagonism. To better understand the phylogenetics of these closely related strains, we sequenced the genome of '<i>B</i>. <i>oryzicola</i>' KACC 18228. Comparative genomic analysis showed only minor differences between this strain and the genomes of <i>B. velezensis</i> NRRL B-41580^T, <i>B. methylotrophicus</i> KACC 13015^T and <i>Bacillus amyloliquefaciens</i> subsp. <i>plantarum</i> FZB42^T. The pairwise <i>in silico</i> DNA-DNA hybridization values calculated in comparisons between the strains were all greater than 84 %, which is well above the standard species threshold of 70 %. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the strains share phenotype and genotype coherence. Therefore, we propose that <i>B. methylotrophicus</i> KACC 13015^T, <i>B. amyloliquefaciens</i> subsp. <i>plantarum</i> FZB42^T, and '<i>B. oryzicola'</i> KACC 18228 should be reclassified as later heterotypic synonyms of <i>B. velezensis</i> NRRL B-41580^T, since the valid publication date of <i>B. velezensis</i> precedes the other three strains.